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Conserved domains on  [gi|551894157|ref|NP_001272754|]
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U1 small nuclear ribonucleoprotein A [Mus musculus]

Protein Classification

U1 small nuclear ribonucleoprotein A( domain architecture ID 10189731)

U1 small nuclear ribonucleoprotein A is a component of the spliceosomal U1 snRNP, which is essential for recognition of the pre-mRNA 5' splice-site and the subsequent assembly of the spliceosome

CATH:  3.30.70.330
Gene Ontology:  GO:0000398|GO:0006397|GO:0003676
SCOP:  3000110

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM1_U1A cd12477
RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); ...
13-101 9.70e-57

RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import.


:

Pssm-ID: 409906 [Multi-domain]  Cd Length: 89  Bit Score: 177.10  E-value: 9.70e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  13 RANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12477    1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80

                 ....*....
gi 551894157  93 AKTDSDIIA 101
Cdd:cd12477   81 AKTDSDIIA 89
RRM2_U1A cd12480
RNA recognition motif 2 (RRM2) found in vertebrate U1 small nuclear ribonucleoprotein A (U1 ...
202-287 4.59e-53

RNA recognition motif 2 (RRM2) found in vertebrate U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A); This subgroup corresponds to the RRM2 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also binds to a flavivirus NS5 protein and plays an important role in virus replication. It contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and it may be free for binding other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import.


:

Pssm-ID: 409908 [Multi-domain]  Cd Length: 86  Bit Score: 167.99  E-value: 4.59e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 202 PAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMK 281
Cdd:cd12480    1 PPQPVSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAREALQGFKITQSNAMK 80

                 ....*.
gi 551894157 282 ISFAKK 287
Cdd:cd12480   81 ISFAKK 86
 
Name Accession Description Interval E-value
RRM1_U1A cd12477
RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); ...
13-101 9.70e-57

RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import.


Pssm-ID: 409906 [Multi-domain]  Cd Length: 89  Bit Score: 177.10  E-value: 9.70e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  13 RANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12477    1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80

                 ....*....
gi 551894157  93 AKTDSDIIA 101
Cdd:cd12477   81 AKTDSDIIA 89
RRM2_U1A cd12480
RNA recognition motif 2 (RRM2) found in vertebrate U1 small nuclear ribonucleoprotein A (U1 ...
202-287 4.59e-53

RNA recognition motif 2 (RRM2) found in vertebrate U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A); This subgroup corresponds to the RRM2 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also binds to a flavivirus NS5 protein and plays an important role in virus replication. It contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and it may be free for binding other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import.


Pssm-ID: 409908 [Multi-domain]  Cd Length: 86  Bit Score: 167.99  E-value: 4.59e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 202 PAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMK 281
Cdd:cd12480    1 PPQPVSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAREALQGFKITQSNAMK 80

                 ....*.
gi 551894157 282 ISFAKK 287
Cdd:cd12480   81 ISFAKK 86
RRM smart00360
RNA recognition motif;
17-90 5.89e-16

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 71.09  E-value: 5.89e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157    17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:smart00360   1 TLFVGNLPPDTTEEELRE----LFSKFGKVESVRLVRdkeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
215-277 9.09e-15

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 67.64  E-value: 9.09e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD----IAFVEFDNEVQAGAARDALQGFKITQN 277
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGrskgFAFVEFEDEEDAEKAIEALNGKELGGR 67
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
18-89 8.20e-12

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 59.55  E-value: 8.20e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157   18 IYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRIM--KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMR 89
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKD----LFSKFGPIKSIRLVRDEtgRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
215-274 9.46e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 56.83  E-value: 9.46e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157   215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGAARDALQGFKI 274
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETgkskgFAFVEFESEEDAEKALEALNGKEL 66
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
18-227 6.69e-08

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 53.27  E-value: 6.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   18 IYINNLNEKIKKDELKKslyaIFSQFGQILD--ILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAKT 95
Cdd:TIGR01628 288 LYVKNLDDTVTDEKLRE----LFSECGEITSakVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR 363
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   96 DSDIIAKMKGTYVE-RDRKREKRKPKSQETPAAKKAVQGGAAAPVVGAVQPV-PGMPPMPqAPRIMHHMPGQPPYMPPPG 173
Cdd:TIGR01628 364 KEQRRAHLQDQFMQlQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGwPRMSMMP-TPMGPGGPLRPNGLAPMNA 442
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  174 MIPPPGLAPGQIPPGAMPPQQLMPG-QMPPAQPLSENPPNHILFLTNLPEETNEL 227
Cdd:TIGR01628 443 VRAPSRNAQNAAQKPPMQPVMYPPNyQSLPLSQDLPQPQSTASQGGQNKKLAQVL 497
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
17-94 7.05e-08

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 48.94  E-value: 7.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLNEKIKKDELKkslyAIFSQFGQILDIlvsRIM------KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:COG0724    3 KIYVGNLPYSVTEEDLR----ELFSEYGEVTSV---KLItdretgRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKV 75

                 ....
gi 551894157  91 QYAK 94
Cdd:COG0724   76 NEAR 79
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
189-286 3.50e-04

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 41.91  E-value: 3.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  189 AMPPQQLMPGQMPP---------AQPLSENPPN-----HILFLTNLPEETNELMLSMLFNQF-PGfkEVRLVPGRHDIAF 253
Cdd:TIGR01648 196 AMARRKLMPGRIQLwghviavdwAEPEEEVDEDvmakvKILYVRNLMTTTTEEIIEKSFSEFkPG--KVERVKKIRDYAF 273
                          90       100       110
                  ....*....|....*....|....*....|...
gi 551894157  254 VEFDNEVQAGAARDALQGfKITQNNAMKISFAK 286
Cdd:TIGR01648 274 VHFEDREDAVKAMDELNG-KELEGSEIEVTLAK 305
 
Name Accession Description Interval E-value
RRM1_U1A cd12477
RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); ...
13-101 9.70e-57

RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import.


Pssm-ID: 409906 [Multi-domain]  Cd Length: 89  Bit Score: 177.10  E-value: 9.70e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  13 RANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12477    1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80

                 ....*....
gi 551894157  93 AKTDSDIIA 101
Cdd:cd12477   81 AKTDSDIIA 89
RRM2_U1A cd12480
RNA recognition motif 2 (RRM2) found in vertebrate U1 small nuclear ribonucleoprotein A (U1 ...
202-287 4.59e-53

RNA recognition motif 2 (RRM2) found in vertebrate U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A); This subgroup corresponds to the RRM2 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also binds to a flavivirus NS5 protein and plays an important role in virus replication. It contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and it may be free for binding other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import.


Pssm-ID: 409908 [Multi-domain]  Cd Length: 86  Bit Score: 167.99  E-value: 4.59e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 202 PAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMK 281
Cdd:cd12480    1 PPQPVSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAREALQGFKITQSNAMK 80

                 ....*.
gi 551894157 282 ISFAKK 287
Cdd:cd12480   81 ISFAKK 86
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
17-94 7.09e-52

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 164.24  E-value: 7.09e-52
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 551894157  17 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12246    1 TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKSLKMRGQAFVVFKDVESATNALRALQGFPFYGKPMRIQYAK 78
RRM1_U2B cd12478
RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins; ...
15-105 8.64e-52

RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins; This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus.


Pssm-ID: 409907 [Multi-domain]  Cd Length: 91  Bit Score: 164.72  E-value: 8.64e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  15 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12478    1 NHTIYINNINDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNALRQLQGFPFYGKPMRIQYAK 80
                         90
                 ....*....|.
gi 551894157  95 TDSDIIAKMKG 105
Cdd:cd12478   81 TDSDIVSKMRG 91
RRM2_U2B cd12481
RNA recognition motif 2 (RRM2) found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B") ...
208-287 4.84e-49

RNA recognition motif 2 (RRM2) found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B"); This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B"), a unique protein that comprises the U2 snRNP. It was initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus.


Pssm-ID: 240925 [Multi-domain]  Cd Length: 80  Bit Score: 157.48  E-value: 4.84e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 208 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 287
Cdd:cd12481    1 DNPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENEAQAGAARDALQGFKITPSHAMKITYAKK 80
RRM1_SNF cd12476
RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF ...
11-94 1.16e-48

RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF and similar proteins; This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently.


Pssm-ID: 409905 [Multi-domain]  Cd Length: 85  Bit Score: 156.62  E-value: 1.16e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  11 ETRANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd12476    2 DIRPNQTIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKDISSATNALRSMQGFPFYDKPMRI 81

                 ....
gi 551894157  91 QYAK 94
Cdd:cd12476   82 AYSK 85
RRM2_SNF cd12479
RNA recognition motif 2 (RRM2) found in Drosophila melanogaster sex determination protein SNF ...
208-287 7.98e-45

RNA recognition motif 2 (RRM2) found in Drosophila melanogaster sex determination protein SNF and similar proteins; This subgroup corresponds to the RRM2 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently.


Pssm-ID: 240923 [Multi-domain]  Cd Length: 80  Bit Score: 146.39  E-value: 7.98e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 208 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 287
Cdd:cd12479    1 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENEVQSAAAKEALQGFKITPTHAMKITFAKK 80
RRM2_U1A_like cd12247
RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily ...
211-283 2.29e-38

RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding.


Pssm-ID: 409693 [Multi-domain]  Cd Length: 72  Bit Score: 129.60  E-value: 2.29e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157 211 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPgRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS 283
Cdd:cd12247    1 PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVP-RRGIAFVEFETEEQATVALQALQGFKITPGHAMKIS 72
RRM_AtNSRA_like cd21618
RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein ...
211-286 4.11e-16

RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein A (AtNSRA) and similar protein; AtNSRA is an alternative splicing (AS) regulator that binds to specific mRNAs and modulates auxin effects on the transcriptome. It can be displaced from its targets upon binding to AS competitor long non-coding RNA (ASCO-RNA). Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410197 [Multi-domain]  Cd Length: 87  Bit Score: 71.91  E-value: 4.11e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 211 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP------GRHDIAFVEFDNEVQAGAARDALQGFKITQNN----AM 280
Cdd:cd21618    2 ASSTLYVEGLPLDATEREVAHIFRPFPGFKSVRLVPkegkrgRKLVLCFVDFADAQQAAAALETLQGYRLDEDDsdskGL 81

                 ....*.
gi 551894157 281 KISFAK 286
Cdd:cd21618   82 RISFAR 87
RRM smart00360
RNA recognition motif;
17-90 5.89e-16

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 71.09  E-value: 5.89e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157    17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:smart00360   1 TLFVGNLPPDTTEEELRE----LFSKFGKVESVRLVRdkeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
18-91 1.87e-15

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 69.62  E-value: 1.87e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQILDILV--SRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd00590    1 LFVGNLPPDTTEEDLRE----LFSKFGEVVSVRIvrDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
215-277 9.09e-15

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 67.64  E-value: 9.09e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD----IAFVEFDNEVQAGAARDALQGFKITQN 277
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGrskgFAFVEFEDEEDAEKAIEALNGKELGGR 67
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
15-93 6.29e-14

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 65.71  E-value: 6.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  15 NHTIYINNLNEKIKKDELKkSLYAIFSQFGQI-LDILVSRIMK---MRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd12239    1 SNRLYVKNLSKRVSEKDLK-YIFGRFVDSSSEeKNMFDIRLMTegrMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVV 79

                 ...
gi 551894157  91 QYA 93
Cdd:cd12239   80 QFA 82
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
18-89 8.20e-12

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 59.55  E-value: 8.20e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157   18 IYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRIM--KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMR 89
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKD----LFSKFGPIKSIRLVRDEtgRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
215-286 8.90e-12

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 59.56  E-value: 8.90e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLV-PGRHDIAFVEFDNEVQAGAARDALQGFKITQNN--AMKISFAK 286
Cdd:cd12245    5 LFVANLGPNVSEQELRQLFSRQPGFRRLRMHnKGGGPVCFVEFEDVPFATQALNHLQGAILSSSDrgGIRIEYAK 79
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
215-283 2.57e-11

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 58.45  E-value: 2.57e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD----IAFVEFDNEVQAGAARDALQGFKItQNNAMKIS 283
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGkskgFAFVEFESPEDAEKALEALNGTEL-GGRPLKVS 72
RRM smart00360
RNA recognition motif;
215-274 9.46e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 56.83  E-value: 9.46e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157   215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGAARDALQGFKI 274
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETgkskgFAFVEFESEEDAEKALEALNGKEL 66
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
17-89 2.40e-10

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 55.37  E-value: 2.40e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157  17 TIYINNLNEKIKKDELKKSlyaiFSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMR 89
Cdd:cd12354    2 TVYVGNITKGLTEALLQQT----FSPFGQILEV---RVFPDKGYAFIRFDSHEAATHAIVSVNGTIINGQAVK 67
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
15-92 4.78e-10

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 54.94  E-value: 4.78e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 551894157  15 NHTIYINNLNEKIKKDELkkslYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12241    2 NRILYVRNLPYKISSEEL----YDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIFDAKNACDHLSGFNVCNRYLVVLY 75
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
213-274 1.56e-08

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 50.79  E-value: 1.56e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157 213 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH----DIAFVEFDNEVQAGAARDALQGFKI 274
Cdd:cd12392    3 NKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNgkpkGLAYVEYENEADASQAVLKTDGTEI 68
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
18-227 6.69e-08

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 53.27  E-value: 6.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   18 IYINNLNEKIKKDELKKslyaIFSQFGQILD--ILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAKT 95
Cdd:TIGR01628 288 LYVKNLDDTVTDEKLRE----LFSECGEITSakVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR 363
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   96 DSDIIAKMKGTYVE-RDRKREKRKPKSQETPAAKKAVQGGAAAPVVGAVQPV-PGMPPMPqAPRIMHHMPGQPPYMPPPG 173
Cdd:TIGR01628 364 KEQRRAHLQDQFMQlQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGwPRMSMMP-TPMGPGGPLRPNGLAPMNA 442
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  174 MIPPPGLAPGQIPPGAMPPQQLMPG-QMPPAQPLSENPPNHILFLTNLPEETNEL 227
Cdd:TIGR01628 443 VRAPSRNAQNAAQKPPMQPVMYPPNyQSLPLSQDLPQPQSTASQGGQNKKLAQVL 497
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
18-94 6.95e-08

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 48.98  E-value: 6.95e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQILDIlvsRIM------KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12397    1 LFVGNLSFETTEEDLRK----HFAPAGKIRKV---RMAtfedsgKCKGFAFVDFKEIESATNAVKGPINHSLNGRDLRVE 73

                 ...
gi 551894157  92 YAK 94
Cdd:cd12397   74 YGE 76
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
17-94 7.05e-08

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 48.94  E-value: 7.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLNEKIKKDELKkslyAIFSQFGQILDIlvsRIM------KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:COG0724    3 KIYVGNLPYSVTEEDLR----ELFSEYGEVTSV---KLItdretgRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKV 75

                 ....
gi 551894157  91 QYAK 94
Cdd:COG0724   76 NEAR 79
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
14-94 7.83e-08

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 48.93  E-value: 7.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  14 ANHTIYINNLNEKIKKDELKKslyaIFSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12262    2 ASRNVYVGNLDDSLTEEEIRG----ILEKYGEIESI---KILKEKNCAFVNYLNIANAIKAVQELPIKNPKFKKVRINYG 74

                 .
gi 551894157  94 K 94
Cdd:cd12262   75 K 75
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
18-87 8.96e-08

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 48.41  E-value: 8.96e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  18 IYINNLNEKIKKDELKkslyAIFSQFGQILDILVSRIMKMR------GQAFVIFKEVTSATNALrSMQGFPFYDKP 87
Cdd:cd12298    3 IRVRNLDFELDEEALR----GIFEKFGEIESINIPKKQKNRkgrhnnGFAFVTFEDADSAESAL-QLNGTLLDNRK 73
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
20-93 1.07e-07

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 48.32  E-value: 1.07e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  20 INNLNEKIKKDELKKslyaIFSQFGQILDILV--SRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12414    4 VRNLPFKCTEDDLKK----LFSKFGKVLEVTIpkKPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
17-91 1.22e-07

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 48.02  E-value: 1.22e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDIlvSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12276    3 TLLVFNLDAPVSNDELKS----LFSKFGEIKEI--RPTPDKPSQKFVEFYDVRDAEAALDGLNGRELLGGKLKVA 71
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
20-94 1.40e-07

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 48.34  E-value: 1.40e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  20 INNLNEKIKKDelkkSLYAIFSQFGQILDILVsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDK--PMRIQYAK 94
Cdd:cd12422    6 VTNLLYPVTVD----VLHQVFSPYGAVEKIVI-FEKGTGVQALVQFDSVESAEAAKKALNGRNIYDGccTLDIQFSR 77
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
16-93 1.81e-07

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 47.66  E-value: 1.81e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 551894157  16 HTIYINNLNEKIKKDELkkslYAIFSQFGQILDILVSriMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12524    2 RTLFVRNINSSVEDEEL----RALFEQFGEIRTLYTA--CKHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHFS 73
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
215-272 2.08e-07

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 47.39  E-value: 2.08e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRhDIAFVEFDNEVQAGAARDALQGF 272
Cdd:cd12340    2 LFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDS-NFAFVEFEELEDAIRAKDSVHGR 58
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
18-94 2.35e-07

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 47.24  E-value: 2.35e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  18 IYINNLNEKIKKDELKKSlyaiFSQFGQildilVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12251    4 LYVRNLMLSTTEEKLREL----FSEYGK-----VERVKKIKDYAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLAK 71
RRM2_RIM4_like cd12454
RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; ...
17-92 3.17e-07

RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409888 [Multi-domain]  Cd Length: 80  Bit Score: 47.08  E-value: 3.17e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  17 TIYINNLNEKIkkdeLKKSLYAIFSQFGQILDI-LVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12454    5 SIFVGQLDPKT----TDSELFRRFSKYGKIVDCkLIKRPEPVNAFAFLRFESEEAAEAAVEEENHSEFLNKQIRVQK 77
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
18-93 3.80e-07

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 46.83  E-value: 3.80e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 551894157  18 IYINNLNEKIkkDElkKSLYAIFSQFGQILDILVSRIM---KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12347    1 LYVGGLAEEV--DE--KVLHAAFIPFGDIVDIQIPLDYeteKHRGFAFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA 75
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
17-94 4.10e-07

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 46.85  E-value: 4.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLNEKIKKDELKKsLYAIFSQFgqildilvsRIMKMRGQ-----AFVIFKEVTSATNALRSMQGF--PFYDK-PM 88
Cdd:cd12245    4 TLFVANLGPNVSEQELRQ-LFSRQPGF---------RRLRMHNKgggpvCFVEFEDVPFATQALNHLQGAilSSSDRgGI 73

                 ....*.
gi 551894157  89 RIQYAK 94
Cdd:cd12245   74 RIEYAK 79
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
18-90 9.70e-07

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 45.69  E-value: 9.70e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  18 IYINNLNEKIKKDELKkslyAIFSQFGQILDILVSRIMKM---RGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd12284    1 LYVGSLHFNITEDMLR----GIFEPFGKIEFVQLQKDPETgrsKGYGFIQFRDAEDAKKALEQLNGFELAGRPMKV 72
RRM2_U1A_like cd12247
RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily ...
15-81 1.51e-06

RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding.


Pssm-ID: 409693 [Multi-domain]  Cd Length: 72  Bit Score: 44.86  E-value: 1.51e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  15 NHTIYINNLNEKIKKDELKkslyAIFSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGF 81
Cdd:cd12247    2 NKILFLQNLPEETTKEMLE----MLFNQFPGFKEV---RLVPRRGIAFVEFETEEQATVALQALQGF 61
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
1-93 1.52e-06

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 49.15  E-value: 1.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157    1 MATIATMPVPETRANHTIYINNLNEKIKKDELKKslyaIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRS 77
Cdd:TIGR01622 200 AATETSGHHPNSIPFHRLYVGNLHFNITEQDLRQ----IFEPFGEIEFVQLQKdpeTGRSKGYGFIQFRDAEQAKEALEK 275
                          90
                  ....*....|....*.
gi 551894157   78 MQGFPFYDKPMRIQYA 93
Cdd:TIGR01622 276 MNGFELAGRPIKVGLG 291
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
14-80 2.06e-06

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 44.71  E-value: 2.06e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  14 ANHTIYINNLNEKIKKDELKKSlyaiFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQG 80
Cdd:cd12350    1 ATRTLFIGNLEKTTTYGDLRNI----FERFGEIIDIDIKKQNGNPQYAFLQYCDIASVVKAIKKMDG 63
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
18-94 2.22e-06

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 45.09  E-value: 2.22e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  18 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12453    5 LFVASLSSARSDEELCAAVTNHFSKWGELLNVKVLKDWSNRPYAFVQYTNTEDAKNALVNGHNTLLDGRHLRVEKAK 81
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
214-286 3.40e-06

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 44.16  E-value: 3.40e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157 214 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVpgrHDIAFVEFDNEVQAGAARDALQGFKITQNNaMKISFAK 286
Cdd:cd12251    3 VLYVRNLMLSTTEEKLRELFSEYGKVERVKKI---KDYAFVHFEERDDAVKAMEEMNGKELEGSE-IEVSLAK 71
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
15-90 3.70e-06

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 43.85  E-value: 3.70e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  15 NHTIYINNLNEKIKKDELKKslyaIFSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd12346    1 NTTVFVGGLDPNVTEEDLRV----LFGPFGEIVYV---KIPPGKGCGFVQFVNRASAEAAIQKLQGTPIGGSRIRL 69
RRM1_I_PABPs cd12378
RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily ...
36-96 3.86e-06

RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409812 [Multi-domain]  Cd Length: 80  Bit Score: 44.16  E-value: 3.86e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157  36 LYAIFSQFGQILDILVSRIMKMR---GQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAKTD 96
Cdd:cd12378   16 LYEKFSPAGPVLSIRVCRDAVTRrslGYAYVNFQQPADAERALDTLNFDVIKGKPIRIMWSQRD 79
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
17-84 3.95e-06

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 43.76  E-value: 3.95e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDI-LVSRIM-KMRGQAFVIFKEVTSATNALR----SMQGFPFY 84
Cdd:cd12391    1 TVFVSNLDYSVPEDKIRE----IFSGCGEITDVrLVKNYKgKSKGYCYVEFKDEESAQKALKldrqPVEGRPMF 70
RRM2_SF3B4 cd12335
RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
14-93 4.19e-06

RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409772 [Multi-domain]  Cd Length: 83  Bit Score: 43.88  E-value: 4.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  14 ANhtIYINNLNEKIkkDElkKSLYAIFSQFGQILDilVSRIMK------MRGQAFVIFKEVTSATNALRSMQGFPFYDKP 87
Cdd:cd12335    2 AN--LFIGNLDPEV--DE--KLLYDTFSAFGVILQ--TPKIMRdpdtgnSKGFGFVSFDSFEASDAAIEAMNGQYLCNRP 73

                 ....*.
gi 551894157  88 MRIQYA 93
Cdd:cd12335   74 ITVSYA 79
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
18-94 4.88e-06

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 43.93  E-value: 4.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIkkDElkKSLYAIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12382    4 LFIGGLNTET--NE--KALEAVFGKYGRIVEVLLMKdreTNKSRGFAFVTFESPADAKDAARDMNGKELDGKAIKVEQAT 79
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
17-96 6.46e-06

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 43.52  E-value: 6.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLNEKIKKDELKkslyAIFSQFGQILDILVS---RIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12312    2 SLFVRNVADDTRPDDLR----REFGRYGPIVDVYIPldfYTRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQFA 77

                 ...
gi 551894157  94 KTD 96
Cdd:cd12312   78 QGD 80
RRM1_Spen cd12308
RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily ...
17-92 7.29e-06

RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily corresponds to the RRM1 domain in the Spen (split end) family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also known as one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong- to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409749 [Multi-domain]  Cd Length: 78  Bit Score: 43.38  E-value: 7.29e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  17 TIYINNLNEKIKKDELKKSLYAIFSQFGQIlDILVSRIMKMRgQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12308    3 TLCVSNLPAKLSDEEIEDVLYHEFKKFGDV-SVRLQHDGDER-VAYVNFRHPEDAREAKHAKLRLVLFDRPLNVEP 76
RRM_DNAJC17 cd12429
RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17; The CD ...
26-93 7.75e-06

RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17; The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding.


Pssm-ID: 409863 [Multi-domain]  Cd Length: 74  Bit Score: 43.03  E-value: 7.75e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 551894157  26 KIKKDEL---KKSLYAIFSQFGQILDILVSRimKMRGQAFVIFKEVTSATNALRSMQGFPfyDKPMRIQYA 93
Cdd:cd12429    8 KSKKGNGgysEEELRKIFSKYGPVSDVVISS--KKKGSAIVEFATVVAADAAVENEVGLP--DNPLLVSWL 74
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
15-91 8.50e-06

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 43.06  E-value: 8.50e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 551894157  15 NHTIYINNLNEKIKkDELkksLYAIFSQFGQILDILV--SRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12336    1 DRTLFVGNLDPRVT-EEI---LYELFLQAGPLEGVKIpkDPNGKPKNFAFVTFKHEVSVPYAIQLLNGIRLFGREIRIK 75
RRM1_SF3B4 cd12334
RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
18-90 9.15e-06

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409771 [Multi-domain]  Cd Length: 74  Bit Score: 42.98  E-value: 9.15e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  18 IYINNLNEKIKkDELkksLYAIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd12334    1 VYVGNLDEKVT-EEL---LWELFIQAGPVVNVHMPKdrvTQQHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRV 72
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
18-95 1.27e-05

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 42.67  E-value: 1.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQILDIlvsRIMKMRGQ---------AFVIFKEVTSATNALRSMQGFPFYDKPM 88
Cdd:cd12223    4 LYVGNLPPSVTEEVLLR----EFGRFGPLASV---KIMWPRTEeerrrnrncGFVAFMSRADAERAMRELNGKDVMGYEL 76

                 ....*..
gi 551894157  89 RIQYAKT 95
Cdd:cd12223   77 KLGWGKA 83
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
17-83 1.27e-05

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 42.50  E-value: 1.27e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLNEKIKKDElkksLYAIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQGFPF 83
Cdd:cd12408    1 TIRVTNLSEDATEED----LRELFRPFGPISRVYLAKdkeTGQSKGFAFVTFETREDAERAIEKLNGFGY 66
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
33-92 1.30e-05

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 42.39  E-value: 1.30e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  33 KKSLYAIFSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12340   13 ESAIREIFSPYGPVKEV---KMLSDSNFAFVEFEELEDAIRAKDSVHGRVLNNEPLYVTY 69
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
16-80 1.31e-05

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 42.60  E-value: 1.31e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 551894157  16 HTIYINNLNEKIKKDELKKslyaIFSQFGQILDILVSR------IMKMRGQAFVIFKEVTSATNALRSMQG 80
Cdd:cd12318    1 TTLFVKNLNFKTTEEALKK----HFEKCGPIRSVTIAKkkdpkgPLLSMGYGFVEFKSPEAAQKALKQLQG 67
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
20-91 1.65e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 42.26  E-value: 1.65e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  20 INNLNEKIKKDELKKslyaIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12311    3 VDNLTYRTTPDDLRR----VFEKYGEVGDVYIPRdryTRESRGFAFVRFYDKRDAEDAIDAMDGAELDGRELRVQ 73
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
14-94 1.75e-05

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 42.00  E-value: 1.75e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  14 ANHTIYINNLNEKIKKDELkkslYAIFSQFGQILDILVSRimKMRGQ----AFVIFKEVTSATNALRSMQGFPFYDKPMR 89
Cdd:cd12309    1 ATRTLFVGNLEITITEEEL----RRAFERYGVVEDVDIKR--PPRGQgnayAFVKFLNLDMAHRAKVAMSGQYIGRNQIK 74

                 ....*
gi 551894157  90 IQYAK 94
Cdd:cd12309   75 IGYGK 79
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
18-94 1.91e-05

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 41.90  E-value: 1.91e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  18 IYINNLNEKIKKDELKKSlyaiFSQFGQIldilvSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12495    4 LFVRNLANTVTEEILEKA----FSQFGKL-----ERVKKLKDYAFIHFDERDGAVKAMDEMNGKDLEGENIEIVFAK 71
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
36-93 2.22e-05

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 41.73  E-value: 2.22e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157  36 LYAIFSQFGQILDIlvsRIM------KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12398   17 LKEIFSEVGPVVSF---RLVtdretgKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDFA 77
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
18-80 2.23e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 41.85  E-value: 2.23e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRimKMRGQAFVIFKEVTSATNALRSMQG 80
Cdd:cd12373    2 VYVGNLGPRVTKRELED----AFEKYGPLRNVWVAR--NPPGFAFVEFEDPRDAEDAVRALDG 58
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
215-271 2.41e-05

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 41.47  E-value: 2.41e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQG 271
Cdd:cd12276    4 LLVFNLDAPVSNDELKSLFSKFGEIKEIRPTPDKPSQKFVEFYDVRDAEAALDGLNG 60
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
18-94 2.48e-05

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 41.90  E-value: 2.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQI--LDILVSRIMKMRGQ----AFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12355    2 LWIGNLDPRLTEYHLLK----LLSKYGKIkkFDFLFHKTGPLKGQprgyCFVTFETKEEAEKAIECLNGKLALGKKLVVR 77

                 ...
gi 551894157  92 YAK 94
Cdd:cd12355   78 WAH 80
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
215-285 2.82e-05

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 41.62  E-value: 2.82e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLV--PGRHD-IAFVEFDNEVQAGAARDALQGFKItQNNAMKISFA 285
Cdd:cd12352    1 LYVGNLDRQVTEDLILQLFSQIGPCKSCKMIteHGGNDpYCFVEFYEHNHAAAALQAMNGRKI-LGKEVKVNWA 73
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
36-91 3.00e-05

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 41.45  E-value: 3.00e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 551894157  36 LYAIFSQFGqilDILVSRIM------KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12362   15 LYQLFAPFG---NVVSAKVFvdkntgRSKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLKVQ 73
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
18-88 3.01e-05

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 41.39  E-value: 3.01e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQILDILVSR--IMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPM 88
Cdd:cd12380    4 VYVKNFGEDVDDDELKE----LFEKYGKITSAKVMKddSGKSKGFGFVNFENHEAAQKAVEELNGKELNGKKL 72
RRM_RBPMS_like cd12420
RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like ...
215-273 3.56e-05

RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like proteins; This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4.


Pssm-ID: 409854 [Multi-domain]  Cd Length: 76  Bit Score: 41.16  E-value: 3.56e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVP---GRHDIAFVEFDNEVQAGAARDALQGFK 273
Cdd:cd12420    3 LFVSGLPLDVKERELYNLFRPLPGYEASQLKFtgkNTQPVGFVTFESRAAAEAAKDALQGMR 64
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
18-94 3.84e-05

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 41.17  E-value: 3.84e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  18 IYINNLNEKIKKDELKKSlyaiFSQFGQIldilvSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12494    4 LFVRNLATTVTEEILEKT----FSQFGKL-----ERVKKLKDYAFVHFEDRDAAVKAMDEMNGKEVEGEEIEIVLAK 71
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
17-80 4.93e-05

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 40.73  E-value: 4.93e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQG 80
Cdd:cd12393    3 TVYVSNLPFSLTNNDLHQ----IFSKYGKVVKVTILKdkeTRKSKGVAFVLFLDRESAHNAVRAMNN 65
RRM_hnRNPC_like cd12341
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...
18-90 5.85e-05

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.


Pssm-ID: 409778 [Multi-domain]  Cd Length: 68  Bit Score: 40.31  E-value: 5.85e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157  18 IYINNLN-EKIKKDELkkslYAIFSQFGQILDILVsrimkMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd12341    3 IFVGNLPtDQMTKEDL----EEIFSKYGKILGISL-----HKGYGFVQFDNEEDARAAVAGENGRTIKGQRLDI 67
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
18-80 6.36e-05

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 40.23  E-value: 6.36e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQI--LDILVSRIMKM-RGQAFVIFKEVTSATNALRSMQG 80
Cdd:cd12365    1 LHVGKLTRNVTKDHLKE----IFSVYGTVknVDLPIDREPNLpRGYAYVEFESPEDAEKAIKHMDG 62
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
18-80 6.48e-05

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 40.45  E-value: 6.48e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  18 IYINNLNEKIKKDELKKSlyaiFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQG 80
Cdd:cd12353    2 IFVGDLSPEIETEDLKEA----FAPFGEISDARVVKdtqTGKSKGYGFVSFVKKEDAENAIQGMNG 63
RRM3_PTBP1_like cd12423
RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
18-94 6.61e-05

RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409857 [Multi-domain]  Cd Length: 74  Bit Score: 40.29  E-value: 6.61e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 551894157  18 IYINNLNE-KIKKDelkkslyAIFSQFGQILDILVSRIM-KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12423    2 LLVSNLNEeMVTPD-------ALFTLFGVYGDVLRVKILfNKKDTALIQMADPQQAQTALQHLNGIKLFGKPIRVTLSK 73
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
16-90 6.71e-05

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 40.67  E-value: 6.71e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  16 HTIYINNLNEKIKKDELKKslyaIFSQFGQILD--ILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd12412    3 NRIFVGGIDWDTTEEELRE----FFSKFGKVKDvkIIKDRAGVSKGYGFVTFETQEDAEKIQKWGANLVFKGKKLNV 75
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
17-90 6.78e-05

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 40.59  E-value: 6.78e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRI-----MKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd21619    3 TIYVGNIDMTINEDALEK----IFSRYGQVESVRRPPIhtdkaDRTTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
18-93 7.07e-05

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 40.33  E-value: 7.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKKDELKKSlyaiFSQFGqilDILVSRIM-----KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12381    4 LYVKNLDDTIDDEKLREE----FSPFG---TITSAKVMtdeggRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVAL 76

                 .
gi 551894157  93 A 93
Cdd:cd12381   77 A 77
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
18-117 7.31e-05

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 44.03  E-value: 7.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   18 IYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRIM--KMRGQAFVIFKEVTSATNALRSMQGfpfydkpmriqyakT 95
Cdd:TIGR01628 181 LYVKNLDPSVNEDKLRE----LFAKFGEITSAAVMKDGsgRSRGFAFVNFEKHEDAAKAVEEMNG--------------K 242
                          90       100
                  ....*....|....*....|..
gi 551894157   96 DSDIIAKMKGTYVERDRKREKR 117
Cdd:TIGR01628 243 KIGLAKEGKKLYVGRAQKRAER 264
RRM4_PTBP1_like cd12425
RNA recognition motif 4 (RRM4) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
215-286 8.34e-05

RNA recognition motif 4 (RRM4) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM4 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409859 [Multi-domain]  Cd Length: 76  Bit Score: 40.33  E-value: 8.34e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGF-KEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 286
Cdd:cd12425    2 LHLSNIPPSVTEEDLKDLFTSTGGTvKAFKFFQKDRKMALIQMGSVEEAIEALIALHNYQLSENSHLRVSFSK 74
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
18-93 9.08e-05

RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410031 [Multi-domain]  Cd Length: 80  Bit Score: 40.17  E-value: 9.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKkDElkkSLYAIFSQFGQILDilvSRIM------KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12619    4 IFVGDLSPEVT-DA---ALFNAFSDFPSCSD---ARVMwdqktgRSRGYGFVSFRSQQDAQNAINSMNGKWLGSRPIRCN 76

                 ..
gi 551894157  92 YA 93
Cdd:cd12619   77 WA 78
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
17-93 9.56e-05

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 40.11  E-value: 9.56e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  17 TIYINNLNEKIKKDELKkslyAIFSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12227    4 TLWVGHLSKKVTQEELK----NLFEEYGEIQSI---DMIPPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWA 73
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
8-94 9.67e-05

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409972 [Multi-domain]  Cd Length: 85  Bit Score: 40.28  E-value: 9.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   8 PVPETRANHTIYINNLNEKIKKDELKKSlyaiFSQFGQILDILVSRimKMRGQ----AFVIFKEVTSATNALRSMQGFPF 83
Cdd:cd12556    1 PEDDQRATRNLFIGNLDHNVSEVELRRA----FEKYGIIEEVVIKR--PARGQggayAFLKFQNLDMAHRAKVAMSGRVI 74
                         90
                 ....*....|.
gi 551894157  84 YDKPMRIQYAK 94
Cdd:cd12556   75 GRNPIKIGYGK 85
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
18-76 1.26e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 39.60  E-value: 1.26e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRIM--KMRGQAFVIFKEVTSATNALR 76
Cdd:cd12564    3 LIVKNLPSSITEDRLRK----LFSAFGTITDVQLKYTKdgKFRRFGFVGFKSEEEAQKALK 59
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
11-94 1.40e-04

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409971 [Multi-domain]  Cd Length: 87  Bit Score: 39.84  E-value: 1.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  11 ETRANHTIYINNLNEKIKKDELKKSlyaiFSQFGQILDILVSRimKMRGQ----AFVIFKEVTSATNALRSMQGFPFYDK 86
Cdd:cd12555    3 DQRANRTLFLGNLDITVTENDLRRA----FDRFGVITEVDIKR--PGRGQtstyGFLKFENLDMAHRAKLAMSGKVIGRN 76

                 ....*...
gi 551894157  87 PMRIQYAK 94
Cdd:cd12555   77 PIKIGYGK 84
RRM2_I_PABPs cd12379
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This ...
18-86 1.48e-04

RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409813 [Multi-domain]  Cd Length: 77  Bit Score: 39.48  E-value: 1.48e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157  18 IYINNLNEKIKKdelkKSLYAIFSQFGqilDILVSRIM-----KMRGQAFVIFKEVTSATNALRSMQGFPFYDK 86
Cdd:cd12379    5 IFIKNLDKSIDN----KALYDTFSAFG---NILSCKVAtdengGSKGYGFVHFETEEAAERAIEKVNGMLLNGK 71
RRM_CNOT4 cd12438
RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) ...
18-95 1.60e-04

RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T


Pssm-ID: 409872 [Multi-domain]  Cd Length: 98  Bit Score: 39.82  E-value: 1.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKI-KKDELKKSLYaiFSQFGQILDILVSRIMKMRGQ------AFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd12438    8 VYVVGLPPRLaDEEVLKRPEY--FGQYGKIKKIVINRSTSYAGSqgpsasAYVTYSRKEDALRAIQAVDGFVLDGRTLKA 85

                 ....*
gi 551894157  91 QYAKT 95
Cdd:cd12438   86 SFGTT 90
RRM2_hnRNPM cd12659
RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
17-91 1.63e-04

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410060 [Multi-domain]  Cd Length: 76  Bit Score: 39.26  E-value: 1.63e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQIL--DILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12659    2 TVFVANLDYKVGWKKLKE----VFSMAGVVVraDILEDKDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHVK 74
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
10-86 1.66e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 42.87  E-value: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   10 PETRANHT--IYINNLNEKIKKdelkKSLYAIFSQFGQILDILVSRIM--KMRGQAFVIFKEVTSATNALRSMQGFPFYD 85
Cdd:TIGR01628  81 PSLRRSGVgnIFVKNLDKSVDN----KALFDTFSKFGNILSCKVATDEngKSRGYGFVHFEKEESAKAAIQKVNGMLLND 156

                  .
gi 551894157   86 K 86
Cdd:TIGR01628 157 K 157
RRM2_NCL cd12404
RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to ...
215-274 1.71e-04

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.


Pssm-ID: 409838 [Multi-domain]  Cd Length: 77  Bit Score: 39.34  E-value: 1.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157 215 LFLTNLPEETNElmlSMLFNQFPGFKEVRLVPGRHD----IAFVEFDNEVQAGAARDALQGFKI 274
Cdd:cd12404    6 LFVKNLPYSTTQ---DELKEVFEDAVDIRIPMGRDGrskgIAYIEFKSEAEAEKALEEKQGTEV 66
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
14-94 1.76e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 39.34  E-value: 1.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  14 ANHTIYINNLNEKIKKDELKKSLyaifSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYdKPMRIQYA 93
Cdd:cd12523    2 ASRNVYLGNLPESITEEELREDL----EKFGPIDQI---KIVKEKNIAFVHFLSIANAIKVVTTLPLNPKW-AKRRIYYG 73

                 .
gi 551894157  94 K 94
Cdd:cd12523   74 K 74
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
215-277 1.84e-04

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 39.31  E-value: 1.84e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGAARDALQGFKITQN 277
Cdd:cd12448    1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTDRETgqpkgFGYVDFSTIDSAEAAIDALGGEYIDGR 68
RRM_SRSF10 cd12559
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and ...
15-105 1.88e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409975 [Multi-domain]  Cd Length: 95  Bit Score: 39.66  E-value: 1.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  15 NHTIYINNLNEKIKKDELKKSlyaiFSQFGQILDILVS---RIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12559    5 NTSLFVRNVADDTRSEDLRRE----FGRYGPIVDVYVPldfYTRRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQ 80
                         90
                 ....*....|....
gi 551894157  92 YAKTDSDIIAKMKG 105
Cdd:cd12559   81 FAQGDRKTPNQMKA 94
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
17-93 2.01e-04

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 39.07  E-value: 2.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDILVsrIM-----KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd21608    1 KLYVGNLSWDTTEDDLRD----LFSEFGEVESAKV--ITdretgRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVVN 74

                 ..
gi 551894157  92 YA 93
Cdd:cd21608   75 EA 76
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
218-272 2.01e-04

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 39.03  E-value: 2.01e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 218 TNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGAARDALQGF 272
Cdd:cd12408    5 TNLSEDATEEDLRELFRPFGPISRVYLAKDKETgqskgFAFVTFETREDAERAIEKLNGF 64
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
17-94 2.08e-04

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 39.21  E-value: 2.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQIldilvsRIMKMRGQ-------AFVIFKEVTSATNALRsMQGFPFYDKPMR 89
Cdd:cd12260    6 TVYVGNLDPSTTADQLLE----FFSQAGEV------KYVRMAGDetqptryAFVEFAEQTSVINALK-LNGKMFGGRPLK 74

                 ....*
gi 551894157  90 IQYAK 94
Cdd:cd12260   75 VNHSN 79
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
27-284 2.89e-04

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 41.85  E-value: 2.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   27 IKKDELKKSLYAIFSQFGQILD--ILVSRIMKM-RGQAFVIFKEVTSATNALRSMQGF--PFYDKPMRIQYAKTDSDIIA 101
Cdd:TIGR01661  97 LPKTMTQHELESIFSPFGQIITsrILSDNVTGLsKGVGFIRFDKRDEADRAIKTLNGTtpSGCTEPITVKFANNPSSSNS 176
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  102 K-MKGTYVERDRKREKRKPKSQETPAAkkavQGGAAAPVVGAVQPVPGMPPMPQAPRIMHHMpgqppympppgmipppgL 180
Cdd:TIGR01661 177 KgLLSQLEAVQNPQTTRVPLSTILTAA----GIGPMHHAAARFRPSAGDFTAVLAHQQQQHA-----------------V 235
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  181 APGQIPPGAMPPQ-QLMPGQMPPAQPLSENP-PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAF 253
Cdd:TIGR01661 236 AQQHAAQRASPPAtDGQTAGLAAGAQISASDgAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTnqckgYGF 315
                         250       260       270
                  ....*....|....*....|....*....|.
gi 551894157  254 VEFDNEVQAGAARDALQGFKITqNNAMKISF 284
Cdd:TIGR01661 316 VSMTNYDEAAMAILSLNGYTLG-NRVLQVSF 345
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
215-271 2.90e-04

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 38.75  E-value: 2.90e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRL---VPGRH-DIAFVEFDNEVQAGAARDALQG 271
Cdd:cd12320    3 LIVKNVPFEATRKEIRELFSPFGQLKSVRLpkkFDGSHrGFAFVEFVTKQEAQNAMEALKS 63
RRM_ScJSN1_like cd21616
RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar ...
35-94 3.05e-04

RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar proteins; JSN1, also called Pumilio homology domain family member 1 (PUF1), is a member of the PUF family of proteins. It facilitates association of Arp2/3 complex to yeast mitochondria. It may play a role in mitosis, perhaps by affecting the stability of microtubules. Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410195 [Multi-domain]  Cd Length: 118  Bit Score: 39.74  E-value: 3.05e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 551894157  35 SLYAIFSQFGqilDILVSRIMKMRGQAFVIFKEVTSATNALRSMQG--FPFYDKPMRIQYAK 94
Cdd:cd21616   57 SLASLCSKFG---DIISSRTLRGLNMALIEFESVDSAILALESLQGkeISIIGVPSDITFAK 115
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
189-286 3.50e-04

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 41.91  E-value: 3.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  189 AMPPQQLMPGQMPP---------AQPLSENPPN-----HILFLTNLPEETNELMLSMLFNQF-PGfkEVRLVPGRHDIAF 253
Cdd:TIGR01648 196 AMARRKLMPGRIQLwghviavdwAEPEEEVDEDvmakvKILYVRNLMTTTTEEIIEKSFSEFkPG--KVERVKKIRDYAF 273
                          90       100       110
                  ....*....|....*....|....*....|...
gi 551894157  254 VEFDNEVQAGAARDALQGfKITQNNAMKISFAK 286
Cdd:TIGR01648 274 VHFEDREDAVKAMDELNG-KELEGSEIEVTLAK 305
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
18-92 4.03e-04

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 38.12  E-value: 4.03e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  18 IYINNLNEKIKKDELKKSlyaiFSQFGQILDILVSRimkMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12351   10 VWLDGLSENVTEQYLTRH----FCRYGPVVKVVIDR---QKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
211-274 4.25e-04

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 38.40  E-value: 4.25e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157 211 PNHILFLTNLPEETNELMLSMLFNQFPG--FKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQG----FKI 274
Cdd:cd12313    1 PTNVLILRGLDVLTTEEDILSALQAHADlpIKDVRLIRDKltgtsRGFAFVEFSSLEDATQVMDALQNllppFKI 75
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
16-86 4.27e-04

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 38.47  E-value: 4.27e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157  16 HTIYINNLNEKIKKDELKKslyaIFSQFGQILDI-LVS-RIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDK 86
Cdd:cd12392    3 NKLFVKGLPFSCTKEELEE----LFKQHGTVKDVrLVTyRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDH 71
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
17-94 5.16e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 37.96  E-value: 5.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLNEKIKKDELKkslyAIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12413    1 TLFVRNLPYDTTDEQLE----ELFSDVGPVKRCFVVKdkgKDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELA 76

                 .
gi 551894157  94 K 94
Cdd:cd12413   77 K 77
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
18-90 5.70e-04

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 37.77  E-value: 5.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  18 IYINNLNEKIKKDelkkSLYAIFSQFGQILDILV---SRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRI 90
Cdd:cd12448    1 LFVGNLPFSATQD----ALYEAFSQHGSIVSVRLptdRETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPIRL 72
RRM2_PTBP1_like cd12693
RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
36-97 5.88e-04

RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410093 [Multi-domain]  Cd Length: 96  Bit Score: 38.48  E-value: 5.88e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157  36 LYAIFSQFGQILDIlVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDK--PMRIQYAKTDS 97
Cdd:cd12693   20 LHQIFSKFGTVLKI-ITFTKNNQFQALIQFADAVSAQAAKLSLDGQNIYNGccTLRIDFSKLTS 82
RRM4_MRN1 cd12522
RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This ...
14-94 6.45e-04

RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409942 [Multi-domain]  Cd Length: 81  Bit Score: 37.89  E-value: 6.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  14 ANHTIYINNLNEKIKKDELKksLYAIFSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKpMRIQYA 93
Cdd:cd12522    2 ASRNVYIGNIDDVRVLTEER--LRHDFSQYGEIEQV---NFLREKNCAFVNFTNIANAIKAIDKIKSKPYYKD-LKINFG 75

                 .
gi 551894157  94 K 94
Cdd:cd12522   76 K 76
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
17-91 7.17e-04

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 37.42  E-value: 7.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12599    1 RVYVGNLPMDIREREVED----LFSKYGPVVSIDLKIPPRPPAYAFVEFEDARDAEDAIRGRDGYDFDGHRLRVE 71
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
36-80 9.40e-04

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 37.17  E-value: 9.40e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 551894157  36 LYAIFSQFGQILDILVSRimkmrGQ--AFVIFKEVTSATNALRSMQG 80
Cdd:cd12431   20 LLEVFEKYGTVEDIVMLP-----GKpySFVSFKSVEEAAKAYNALNG 61
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
18-78 9.99e-04

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 37.23  E-value: 9.99e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRIMKMRGQ---AFVIFKEVTSATNALRSM 78
Cdd:cd12417    2 LWISGLSDTTKAADLKK----IFSKYGKVVSAKVVTSARTPGSrcyGYVTMASVEEADLCIKSL 61
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
17-91 1.06e-03

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 37.21  E-value: 1.06e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDILV--SRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12680    2 KLLVSNLDFGVSDADIKE----LFAEFGTLKKAAVhyDRSGRSLGTAEVVFERRADALKAMKQYNGVPLDGRPMKIQ 74
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
17-87 1.09e-03

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 38.06  E-value: 1.09e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  17 TIYINNLNEKIKKDELKKSlyaiFSQFGQILDILVSRIM---KMRGQAFVIFKEVTSATNALR---SMQGFPFYDKP 87
Cdd:cd21615   20 TLFVGRLDYSLTELELQKK----FSKFGEIEKIRIVRDKetgKSRGYAFIVFKSESDAKNAFKegnGLRGLKINDRT 92
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
13-94 1.27e-03

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.


Pssm-ID: 409746 [Multi-domain]  Cd Length: 75  Bit Score: 36.92  E-value: 1.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  13 RANHTIYINNlnEKIKKDELKKSlyaiFSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12305    2 RKGNTVYVSG--YGITEDVLKKA----FSPFGNIINI---SMEIEKNCAFVTFEKMESADQAIAELNGTTVEGVQLKVSI 72

                 ..
gi 551894157  93 AK 94
Cdd:cd12305   73 AR 74
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
18-91 1.31e-03

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 36.44  E-value: 1.31e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  18 IYINNLNEKIKKDELKkslyAIFSQFGQIL--DIlvsrimkMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12343    2 IFVGNLPDAATSEELR----ALFEKYGKVTecDI-------VKNYAFVHMEKEEDAEDAIKALNGYEFMGSRINVE 66
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
17-92 1.34e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 36.57  E-value: 1.34e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12338    1 RIYVGNLPGDIRERDIED----LFYKYGPILAIDLKNRRRGPPFAFVEFEDPRDAEDAIRGRDGYDFDGYRLRVEF 72
RRM2_TIAR cd12617
RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup ...
18-93 1.50e-03

RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410029 [Multi-domain]  Cd Length: 80  Bit Score: 36.89  E-value: 1.50e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 551894157  18 IYINNLNEKIKKDELKkslyAIFSQFGQILDILVSRIM---KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12617    4 VFVGDLSPEITTEDIK----SAFAPFGKISDARVVKDMatgKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWA 78
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
26-94 1.51e-03

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 410045 [Multi-domain]  Cd Length: 81  Bit Score: 36.59  E-value: 1.51e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  26 KIKKDELKKSLYAIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQG---FPFYDKPMRIQYAK 94
Cdd:cd12637    6 SLPKTATEQEVRDLFEAYGEVEEVYLMKdpvTQQGTGCAFVKFAYKEEALAAIRSLNGtvtFDGCSRPVEVRFAE 80
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
18-76 1.53e-03

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 36.77  E-value: 1.53e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRIM--KMRGQAFVIFKEVTSATNALR 76
Cdd:cd12565    3 IIVKNLPKYVTEKRLKE----HFSKKGEITDVKVMRTKdgKSRRFGFIGFKSEEEAQKAVK 59
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
33-94 1.66e-03

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 36.69  E-value: 1.66e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  33 KKSLYAIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12449   14 EQSLEEVFSKYGQISEVVVVKdreTQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGRQIRVDQAG 78
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
16-77 1.68e-03

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 36.81  E-value: 1.68e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  16 HTIYINNLNEKIKKDELKkslyAIFSQFGQI--LDILVSRIMKM-RGQAFVIFKEVTSATNALRS 77
Cdd:cd12415    1 KTVFIRNLSFDTTEEDLK----EFFSKFGEVkyARIVLDKDTGHsKGTAFVQFKTKESADKCIEA 61
RRM4_Prp24 cd12299
RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
217-271 1.77e-03

RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409740 [Multi-domain]  Cd Length: 71  Bit Score: 36.46  E-value: 1.77e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157 217 LTNLPEETNELMLSMLFNQF-PGFKEVRLVPgRHDIAFVEFDNEVQAGAARDALQG 271
Cdd:cd12299    5 LFNLSDTVNEEQIRAFFEKIgPDIRKILLVP-DHEGALVEFEDESDAGKASLSLDG 59
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
219-274 1.78e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 36.38  E-value: 1.78e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 219 NLPEETNELMLSMLFNQFPGFKEVRLVPGRHD----IAFVEFDNEVQAGAARDALQGFKI 274
Cdd:cd12414    6 NLPFKCTEDDLKKLFSKFGKVLEVTIPKKPDGklrgFAFVQFTNVADAAKAIKGMNGKKI 65
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
17-94 1.93e-03

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 36.28  E-value: 1.93e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 551894157  17 TIYINNLNEKIKKDELkkslYAIFSQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12622    2 TVYVGNLPPEVTQADL----IPLFQNFGVIEEV---RVQRDKGFGFVKYDTHEEAALAIQQLNGQPFLGRPIKCSWGK 72
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
17-98 2.03e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 39.40  E-value: 2.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   17 TIYINNLNEKIKKdelkKSLYAIFSQFGQILDILVSRIMKMR---GQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:TIGR01628   2 SLYVGDLDPDVTE----AKLYDLFKPFGPVLSVRVCRDSVTRrslGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWS 77

                  ....*
gi 551894157   94 KTDSD 98
Cdd:TIGR01628  78 QRDPS 82
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
17-94 2.24e-03

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409968 [Multi-domain]  Cd Length: 77  Bit Score: 36.38  E-value: 2.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLNEKIKKDELKKSlyaiFSQFGQILDILVSRIMKM---RGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12552    1 IIYVSHLPHGFHEKELKKY----FAQFGDLKNVRLARSKKTgnsKHYGFLEFVNPEDAMIAQKSMNNYLLMGKLLQVRVL 76

                 .
gi 551894157  94 K 94
Cdd:cd12552   77 P 77
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
15-78 2.38e-03

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 36.24  E-value: 2.38e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  15 NHTIYINNLNEKIKKDELKKslyaIFSQFGQILDIlvsRIMKMRGQ------AFVIFKEVTSATNALRSM 78
Cdd:cd12229    3 NHQLFVGNLPHDITEDELKE----FFSRFGNVLEL---RINSKGGGgrlpnfGFVVFDDPEAVQKILANK 65
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
215-285 2.44e-03

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 36.23  E-value: 2.44e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGAARDALQGFKItQNNAMKISFA 285
Cdd:cd12375    2 LIVNYLPQSMTQEELRSLFGAIGPIESCKLVRDKITgqslgYGFVNYRDPNDARKAINTLNGLDL-ENKRLKVSYA 76
RRM2_Bruno_like cd12636
RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar ...
18-93 2.56e-03

RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 410044 [Multi-domain]  Cd Length: 81  Bit Score: 36.01  E-value: 2.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKKDELKkslyAIFSQFGQILDILVSRIM--KMRGQAFVIFKEVTSATNALRSM---QGFPFYDKPMRIQY 92
Cdd:cd12636    4 LFVGMLSKKCNESDVR----IMFSPYGSIEECTVLRDQngKSRGCAFVTFTSRQCAVNAIKAMhhsQTMEGCSSPLVVKF 79

                 .
gi 551894157  93 A 93
Cdd:cd12636   80 A 80
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
215-284 2.60e-03

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 35.73  E-value: 2.60e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRhDIAFVEFDNEVQAGAARDALQGfKITQNNAMKISF 284
Cdd:cd12332    4 LFVGNLPNDITEEEFKELFQKYGEVSEVFLNKGK-GFGFIRLDTRANAEAAKAELDG-TPRKGRQLRVRF 71
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
214-286 2.60e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 35.77  E-value: 2.60e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157 214 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVpgrHDIAFVEFDNEVQAGAARDALQGfKITQNNAMKISFAK 286
Cdd:cd12494    3 VLFVRNLATTVTEEILEKTFSQFGKLERVKKL---KDYAFVHFEDRDAAVKAMDEMNG-KEVEGEEIEIVLAK 71
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
18-93 2.64e-03

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 35.84  E-value: 2.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKKDELKkslyAIFSQFGQILDIlvsRIMKMRGQ----AFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12352    1 LYVGNLDRQVTEDLIL----QLFSQIGPCKSC---KMITEHGGndpyCFVEFYEHNHAAAALQAMNGRKILGKEVKVNWA 73
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
17-74 2.67e-03

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 35.72  E-value: 2.67e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 551894157  17 TIYINNLNEKIKKDELKKSLYaifsQFGQILDIlvsRIMKMRGQAFVIFKEVTSATNA 74
Cdd:cd12224    3 TLYVGGLGDKITEKDLRDHFY----QFGEIRSI---TVVARQQCAFVQFTTRQAAERA 53
RRM2_MEI2_like cd12529
RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...
17-78 2.70e-03

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409948 [Multi-domain]  Cd Length: 71  Bit Score: 35.95  E-value: 2.70e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDIlvSRIMKMRGQAFVIFKEVTSATNALRSM 78
Cdd:cd12529    3 TLVVFNLDPSISNDDLHQ----IFGAYGEIKEI--RETPNKRHHKFIEFYDVRSAEAALKAL 58
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
33-93 3.06e-03

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 35.67  E-value: 3.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  33 KKSLYAIFSQFGQILDIlvsRIMK-----MRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12320   14 RKEIRELFSPFGQLKSV---RLPKkfdgsHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLEYA 76
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
40-77 3.21e-03

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 35.62  E-value: 3.21e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 551894157  40 FSQFGQILDILVSrimKMRGQAFVIFKEVTSATNALRS 77
Cdd:cd12257   23 FSKFGTIVNIQVN---YNPESALVQFSTSEEANKAYRS 57
RRM2_TIA1 cd12618
RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
18-92 3.30e-03

RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410030 [Multi-domain]  Cd Length: 78  Bit Score: 35.75  E-value: 3.30e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 551894157  18 IYINNLNEKIKKDELKkslyAIFSQFGQILDILVSRIM---KMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12618    5 VFVGDLSPEITTEDIK----AAFAPFGRISDARVVKDMatgKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW 78
RRM_RBPMS cd12682
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing ...
215-273 3.39e-03

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing (RBP-MS); This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development.


Pssm-ID: 410083 [Multi-domain]  Cd Length: 76  Bit Score: 35.79  E-value: 3.39e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFDNEVQAGAARDALQGFK 273
Cdd:cd12682    4 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIkLTSKQPVGFVSFDSRSEAEAAKNALNGIR 63
RRM2_MYEF2 cd12660
RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This ...
17-91 3.56e-03

RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410061 [Multi-domain]  Cd Length: 76  Bit Score: 35.76  E-value: 3.56e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQI--LDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12660    2 TIFVANLDFKVGWKKLKE----VFSMAGTVkrADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRPMHVK 74
RRM1_hnRNPA_like cd12578
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
18-74 3.62e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409992 [Multi-domain]  Cd Length: 78  Bit Score: 35.49  E-value: 3.62e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKKDELKKSlyaiFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNA 74
Cdd:cd12578    2 LFIGGLSYETTDDSLRNH----FEQWGEITDVVVMKdpaTKRSRGFGFVTYSSASEVDAA 57
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
216-287 3.70e-03

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 35.50  E-value: 3.70e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 551894157 216 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRhDIAFVEFDNEVQAGAARDALQGFKItQNNAMKISFAKK 287
Cdd:cd12622    4 YVGNLPPEVTQADLIPLFQNFGVIEEVRVQRDK-GFGFVKYDTHEEAALAIQQLNGQPF-LGRPIKCSWGKK 73
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
232-286 3.77e-03

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 35.63  E-value: 3.77e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157 232 LFNQFPGFKevrlvpgrhdiAFVEFDNEVQAGAARDALQGFKITQN-NAMKISFAK 286
Cdd:cd12422   33 IFEKGTGVQ-----------ALVQFDSVESAEAAKKALNGRNIYDGcCTLDIQFSR 77
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
215-276 3.93e-03

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 35.50  E-value: 3.93e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 551894157 215 LFLTNL-PEETNELMLSMLFNQFPGFKEVRLvpgRHDIAFVEFDNEVQAGAARDALQGFKITQ 276
Cdd:cd12233    2 LFVVGFdPGTTREEDIEKLFEPFGPLVRCDI---RKTFAFVEFEDSEDATKALEALHGSRIDG 61
RRM2_NGR1_NAM8_like cd12613
RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast ...
58-93 4.04e-03

RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins; This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 410025 [Multi-domain]  Cd Length: 80  Bit Score: 35.57  E-value: 4.04e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 551894157  58 RGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYA 93
Cdd:cd12613   44 RGYGFVRFSDENDQQRALIEMQGKYCQGRPLRISYA 79
RRM2_hnRNPM_like cd12386
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
18-91 4.98e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409820 [Multi-domain]  Cd Length: 74  Bit Score: 35.03  E-value: 4.98e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 551894157  18 IYINNLNEKIKKDELKKslyaIFSQFGQIL--DILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12386    1 IFVANLDYKVGWKKLKE----VFKLAGKVVraDIREDKDGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRVK 72
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
36-274 5.57e-03

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 37.87  E-value: 5.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157   36 LYAIFSQFGQILDILvsrIMKMRG--QAFVIFKEVTSATNALRSMQGFPFYDK--PMRIQYAKTDS-DIIAKMKGT---- 106
Cdd:TIGR01649 113 LYQIFNPYGKVLRIV---TFTKNNvfQALVEFESVNSAQHAKAALNGADIYNGccTLKIEYAKPTRlNVKYNDDDSrdyt 189
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  107 --YVERDRKREKRKPKSQETPAAKKAVQGGAAAPVVGAvqpvPGMPPMPQAPRIMHHMPGQPPYMPPPGMipppglapgq 184
Cdd:TIGR01649 190 npDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSS----HGGPLAPLAGGDRMGPPHGPPSRYRPAY---------- 255
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  185 ippGAMPPQQLMPGQMPPAqplseNPPNHILFLTNL-PEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAG 263
Cdd:TIGR01649 256 ---EAAPLAPAISSYGPAG-----GGPGSVLMVSGLhQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQ 327
                         250
                  ....*....|.
gi 551894157  264 AARDALQGFKI 274
Cdd:TIGR01649 328 LALTHLNGVKL 338
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
17-91 5.61e-03

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 34.86  E-value: 5.61e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 551894157  17 TIYINNLNEKIKKDELKKslyaIFSQFGQILDILVSRIMKM---RGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQ 91
Cdd:cd12307    1 VVYIGHLPHGFYEPELRK----YFSQFGTVTRLRLSRSKKTgksKGYAFVEFEDPEVAKIVAETMNNYLLFERLLKCK 74
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
18-94 5.64e-03

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 35.26  E-value: 5.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKKDELkkslYAIFSQFGQILDILVSR---IMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAK 94
Cdd:cd12411   12 IYIGGLPYELTEGDI----LCVFSQYGEIVDINLVRdkkTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRVDHVE 87
RRM2_CELF1_2 cd12634
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-1, CELF-2 and ...
18-93 5.71e-03

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins; This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3.


Pssm-ID: 410042 [Multi-domain]  Cd Length: 81  Bit Score: 35.03  E-value: 5.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  18 IYINNLNEKIKKDELKkslyAIFSQFGQILDilvSRIMK-----MRGQAFVIFKEVTSATNALRSM---QGFPFYDKPMR 89
Cdd:cd12634    4 LFIGMVSKKCNENDIR----VMFSPFGQIEE---CRILRgpdglSRGCAFVTFSTRAMAQNAIKAMhqsQTMEGCSSPIV 76

                 ....
gi 551894157  90 IQYA 93
Cdd:cd12634   77 VKFA 80
RRM3_RBM47 cd12497
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 47 (RBM47); This ...
214-286 5.78e-03

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409920 [Multi-domain]  Cd Length: 74  Bit Score: 34.94  E-value: 5.78e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157 214 ILFLTNLPEETNELMLSMLFNQF-PGFkeVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKItQNNAMKISFAK 286
Cdd:cd12497    3 ILYVRNLMIETTEDTIKKIFGQFnPGC--VERVKKIRDYAFVHFASRDDAVVAMNNLNGTEL-EGSCIEVTLAK 73
RRM2_hnRNPL_like cd12694
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
36-97 7.77e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both nuclear and cytoplasmic roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410094 [Multi-domain]  Cd Length: 86  Bit Score: 34.94  E-value: 7.77e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157  36 LYAIFSQFGQILDILvsrIMKMRG-QAFVIFKEVTSATNALRSMQGFPFYDK--PMRIQYAKTDS 97
Cdd:cd12694   20 IHTICSPYGKVLRIV---IFRKNGvQAMVEFDSVESAQRAKAALNGADIYSGccTLKIEYAKPTR 81
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
210-258 8.04e-03

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 34.70  E-value: 8.04e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 551894157 210 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH-----DIAFVEFDN 258
Cdd:cd12229    1 PDNHQLFVGNLPHDITEDELKEFFSRFGNVLELRINSKGGggrlpNFGFVVFDD 54
RRM_RBPMS2 cd12683
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 ...
215-278 8.08e-03

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2); This subfamily corresponds to the RRM of RBP-MS2, encoded by RBPMS2 gene, a paralog of RNA-binding protein with multiple splicing (RBP-MS). The biological function of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410084 [Multi-domain]  Cd Length: 76  Bit Score: 34.63  E-value: 8.08e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 551894157 215 LFLTNLPEETNELMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFDNEVQAGAARDALQGFKITQNN 278
Cdd:cd12683    4 LFVSGLPVDIKPRELYLLFRPFKGYEGSLIkLTSKQPVGFVTFDSRAGAEAAKNALNGIRFDPEN 68
RRM3_PTBPH3 cd12698
RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 3 ...
214-286 9.50e-03

RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subgroup corresponds to the RRM3 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410098 [Multi-domain]  Cd Length: 76  Bit Score: 34.26  E-value: 9.50e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 551894157 214 ILFLTNL-PEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITqNNAMKISFAK 286
Cdd:cd12698    3 VLLVSNLnPEKVDVDKLFNLFSLYGNIVRIKILRNKPDHALIQMSDPFQAELAVNYLKGAMLF-GKSLEVNFSK 75
RRM3_PTBPH3 cd12698
RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 3 ...
17-94 9.88e-03

RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subgroup corresponds to the RRM3 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410098 [Multi-domain]  Cd Length: 76  Bit Score: 34.26  E-value: 9.88e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 551894157  17 TIYINNLN-EKIKKDELkkslYAIFSQFGQILdilvsRIMKMRGQ---AFVIFKEVTSATNALRSMQGFPFYDKPMRIQY 92
Cdd:cd12698    3 VLLVSNLNpEKVDVDKL----FNLFSLYGNIV-----RIKILRNKpdhALIQMSDPFQAELAVNYLKGAMLFGKSLEVNF 73

                 ..
gi 551894157  93 AK 94
Cdd:cd12698   74 SK 75
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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