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Conserved domains on  [gi|1907195737|ref|XP_036010620|]
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RNA-binding protein 6 isoform X3 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM2_RBM6 cd12563
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup ...
 651-737 5.47e-50

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup corresponds to the RRM2 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


:

Pssm-ID: 409979 [Multi-domain]  Cd Length: 87  Bit Score: 170.03  E-value: 5.47e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 651 ESKTIMLKRIYRSTPPEVIVEVLEPYVHLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMV 730
Cdd:cd12563     1 DSKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNKTGPMGHTYGFIDLDSHAEALRLVKLLQNLDPPLYIDGRRV 80


                  ....*..
gi 1907195737 731 AVNLATG 737
Cdd:cd12563    81 YVNVATG 87
RRM1_RBM6 cd12314
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This ...
 456-533 6.49e-43

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


:

Pssm-ID: 409753 [Multi-domain]  Cd Length: 78  Bit Score: 149.64  E-value: 6.49e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907195737 456 RLIRLSGVPENATKEEILNAFRTSDGIPVKDLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIHDKEVTLEY 533
Cdd:cd12314     1 NLIRLIGVPETATKEQILNAFRVPDGMPVKNLKLKNYVPGYDYDYVCVEFSLLEDAIGCMEANQGTLKIGTKEVTLEY 78
YjbI COG1357
Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];
94-259 5.72e-06

Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];


:

Pssm-ID: 440968 [Multi-domain]  Cd Length: 178  Bit Score: 47.24  E-value: 5.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737  94 DFRGGDFSSSDFQSRDSAQLDFRNRDIhSGDFRDregppMDYRGGDGTPMDYRGRETPHMNYRDRDSHTVDFRSrdvppT 173
Cdd:COG1357     1 DLSGADLSGADLSGADLSGADLSGANL-SGALSG-----ANLSGANLSGANLTGANLSGADLSGADLSGANLSG-----A 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 174 DFRG--------RGTYDLDFRGREGSHSDFRGRDLSDLDFRSRDQSRSDFRNRDVSDLDFRDKDGTQVDFRGrgsatTDL 245
Cdd:COG1357    70 DLSGanltgadlSGANLANLSGANLSGANLSGANLRGANLSGANLSGADLSGADLSGANLSGADLSGANLSG-----ANL 144

                         170
                  ....*....|....*..
gi 1907195737 246 ---DFRNRDTPHSDFRG 259
Cdd:COG1357   145 sgaDLSGADLSGANLSG 161
 
Name Accession Description Interval E-value
RRM2_RBM6 cd12563
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup ...
 651-737 5.47e-50

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup corresponds to the RRM2 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409979 [Multi-domain]  Cd Length: 87  Bit Score: 170.03  E-value: 5.47e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 651 ESKTIMLKRIYRSTPPEVIVEVLEPYVHLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMV 730
Cdd:cd12563     1 DSKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNKTGPMGHTYGFIDLDSHAEALRLVKLLQNLDPPLYIDGRRV 80


                  ....*..
gi 1907195737 731 AVNLATG 737
Cdd:cd12563    81 YVNVATG 87
RRM1_RBM6 cd12314
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This ...
 456-533 6.49e-43

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409753 [Multi-domain]  Cd Length: 78  Bit Score: 149.64  E-value: 6.49e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907195737 456 RLIRLSGVPENATKEEILNAFRTSDGIPVKDLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIHDKEVTLEY 533
Cdd:cd12314     1 NLIRLIGVPETATKEQILNAFRVPDGMPVKNLKLKNYVPGYDYDYVCVEFSLLEDAIGCMEANQGTLKIGTKEVTLEY 78
YjbI COG1357
Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];
94-259 5.72e-06

Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];


Pssm-ID: 440968 [Multi-domain]  Cd Length: 178  Bit Score: 47.24  E-value: 5.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737  94 DFRGGDFSSSDFQSRDSAQLDFRNRDIhSGDFRDregppMDYRGGDGTPMDYRGRETPHMNYRDRDSHTVDFRSrdvppT 173
Cdd:COG1357     1 DLSGADLSGADLSGADLSGADLSGANL-SGALSG-----ANLSGANLSGANLTGANLSGADLSGADLSGANLSG-----A 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 174 DFRG--------RGTYDLDFRGREGSHSDFRGRDLSDLDFRSRDQSRSDFRNRDVSDLDFRDKDGTQVDFRGrgsatTDL 245
Cdd:COG1357    70 DLSGanltgadlSGANLANLSGANLSGANLSGANLRGANLSGANLSGADLSGADLSGANLSGADLSGANLSG-----ANL 144

                         170
                  ....*....|....*..
gi 1907195737 246 ---DFRNRDTPHSDFRG 259
Cdd:COG1357   145 sgaDLSGADLSGANLSG 161
RRM smart00360
RNA recognition motif;
458-531 5.81e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 41.81  E-value: 5.81e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907195737  458 IRLSGVPENATKEEILNAFRTSdGiPVKDLQL-KEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIHDKEVTL 531
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKF-G-KVESVRLvRDKETGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 458-530 1.46e-03

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: 37.60  E-value: 1.46e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907195737 458 IRLSGVPENATKEEILNAFRTSdGiPVKDLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIHDKEVT 530
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKF-G-PIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGK-ELGGRELK 70
RRM smart00360
RNA recognition motif;
654-732 1.97e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.57  E-value: 1.97e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907195737  654 TIMLKRIYRSTPPEVIVEVLEPYVHLTtaNVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNldppFSIDGKMVAV 732
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVE--SVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNG----KELDGRPLKV 73
Pentapeptide_4 pfam13599
Pentapeptide repeats (9 copies);
173-235 4.90e-03

Pentapeptide repeats (9 copies);


Pssm-ID: 433339 [Multi-domain]  Cd Length: 78  Bit Score: 36.48  E-value: 4.90e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907195737 173 TDFRGRGTYDLDFRGREGSHSDFRGRDLSDLDFRSRDQSRSDFRNRDVSDLDFRDKDGTQVDF 235
Cdd:pfam13599  16 TEFYHATLKDCNFTECNLVNVNFDDCNLRDVDFLEAQLKNAQFSGCNLKNSNFSDVKLKGADF 78
 
Name Accession Description Interval E-value
RRM2_RBM6 cd12563
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup ...
 651-737 5.47e-50

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup corresponds to the RRM2 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409979 [Multi-domain]  Cd Length: 87  Bit Score: 170.03  E-value: 5.47e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 651 ESKTIMLKRIYRSTPPEVIVEVLEPYVHLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMV 730
Cdd:cd12563     1 DSKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNKTGPMGHTYGFIDLDSHAEALRLVKLLQNLDPPLYIDGRRV 80


                  ....*..
gi 1907195737 731 AVNLATG 737
Cdd:cd12563    81 YVNVATG 87
RRM1_RBM6 cd12314
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This ...
 456-533 6.49e-43

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409753 [Multi-domain]  Cd Length: 78  Bit Score: 149.64  E-value: 6.49e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907195737 456 RLIRLSGVPENATKEEILNAFRTSDGIPVKDLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIHDKEVTLEY 533
Cdd:cd12314     1 NLIRLIGVPETATKEQILNAFRVPDGMPVKNLKLKNYVPGYDYDYVCVEFSLLEDAIGCMEANQGTLKIGTKEVTLEY 78
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
 651-735 3.12e-28

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: 108.51  E-value: 3.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 651 ESKTIMLKRIYRSTPPEVIVEVLEPYVHLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMV 730
Cdd:cd12313     1 PTNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLLPPFKIDGRVV 80


                  ....*
gi 1907195737 731 AVNLA 735
Cdd:cd12313    81 SVSYA 85
RRM2_RBM5_like cd12562
RNA recognition motif 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
 654-735 3.96e-16

RNA recognition motif 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, 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. Both, RBM5 and RBM10, 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: 409978 [Multi-domain]  Cd Length: 86  Bit Score: 73.83  E-value: 3.96e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 654 TIMLKRIYRSTPPEVIVEVLEPYVHLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMVAVN 733
Cdd:cd12562     4 TIILRNINPHTTVDSILGALAPYAVLSSSNVRLIKDKQTQLNRGFAFVQLSSPIEASQLLQILQSLHPPLTIDGKTINVD 83


                  ..
gi 1907195737 734 LA 735
Cdd:cd12562    84 FA 85
RRM2_RBM10 cd12754
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This ...
 654-737 3.11e-15

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). 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. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains 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: 410148 [Multi-domain]  Cd Length: 87  Bit Score: 71.58  E-value: 3.11e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 654 TIMLKRIYRSTPPEVIVEVLEPYVHLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMVAVN 733
Cdd:cd12754     4 TIILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTINVE 83


                  ....
gi 1907195737 734 LATG 737
Cdd:cd12754    84 FAKG 87
RRM2_RBM5 cd12755
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
 652-735 2.48e-14

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410149 [Multi-domain]  Cd Length: 86  Bit Score: 68.80  E-value: 2.48e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 652 SKTIMLKRIYRSTPPEVIVEVLEPYVHLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMVA 731
Cdd:cd12755     2 SDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIG 81


                  ....
gi 1907195737 732 VNLA 735
Cdd:cd12755    82 VDFA 85
RRM1_RBM5 cd12752
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
 451-533 9.75e-10

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410146 [Multi-domain]  Cd Length: 87  Bit Score: 55.72  E-value: 9.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 451 EEKPNRLIRLSGVPENATKEEILNAFRTSDGIPVKDLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIHDKEVT 530
Cdd:cd12752     1 DEKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQDATSWMEANQKKLVIQGKTIA 80


                  ...
gi 1907195737 531 LEY 533
Cdd:cd12752    81 MHY 83
RRM1_RBM10 cd12753
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This ...
 455-533 2.49e-09

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). 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. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains 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: 410147 [Multi-domain]  Cd Length: 84  Bit Score: 54.56  E-value: 2.49e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907195737 455 NRLIRLSGVPENATKEEILNAFRTSDGIPVKDLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIHDKEVTLEY 533
Cdd:cd12753     1 SNIIMLRMLPQSATENDIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVSMHY 79
RRM1_RBM5_like cd12561
RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
 454-533 7.55e-09

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, 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. Both, RBM5 and RBM10, 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: 409977 [Multi-domain]  Cd Length: 81  Bit Score: 53.14  E-value: 7.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 454 PNRLIRLSGVPENATKEEILNAFrTSDGIPVKDLQL-KEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIHDKEVTLE 532
Cdd:cd12561     1 PNNTIMLRGLPLSVTEEDIRNAL-VSHGVQPKDVRLmRRKTTGASRGFAFVEFMSLEEATRWMEANQGKLQLQGYKITLH 79


                  .
gi 1907195737 533 Y 533
Cdd:cd12561    80 Y 80
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
 454-533 7.97e-07

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: 47.65  E-value: 7.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 454 PNRLIRLSGVPENATKEEILNAFRTSDGIPVKDLQL-KEYNTGYDYGYVCVEFSLLEDAIGCMEANQGT---LMIHDKEV 529
Cdd:cd12313     1 PTNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLiRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLlppFKIDGRVV 80


                  ....
gi 1907195737 530 TLEY 533
Cdd:cd12313    81 SVSY 84
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 458-532 1.79e-06

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: 46.12  E-value: 1.79e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907195737 458 IRLSGVPENATKEEILNAFRTSDgiPVKDLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIHDKEVTLE 532
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFG--EVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGT-ELGGRPLKVS 72
YjbI COG1357
Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];
94-259 5.72e-06

Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];


Pssm-ID: 440968 [Multi-domain]  Cd Length: 178  Bit Score: 47.24  E-value: 5.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737  94 DFRGGDFSSSDFQSRDSAQLDFRNRDIhSGDFRDregppMDYRGGDGTPMDYRGRETPHMNYRDRDSHTVDFRSrdvppT 173
Cdd:COG1357     1 DLSGADLSGADLSGADLSGADLSGANL-SGALSG-----ANLSGANLSGANLTGANLSGADLSGADLSGANLSG-----A 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195737 174 DFRG--------RGTYDLDFRGREGSHSDFRGRDLSDLDFRSRDQSRSDFRNRDVSDLDFRDKDGTQVDFRGrgsatTDL 245
Cdd:COG1357    70 DLSGanltgadlSGANLANLSGANLSGANLSGANLRGANLSGANLSGADLSGADLSGANLSGADLSGANLSG-----ANL 144

                         170
                  ....*....|....*..
gi 1907195737 246 ---DFRNRDTPHSDFRG 259
Cdd:COG1357   145 sgaDLSGADLSGANLSG 161
RRM smart00360
RNA recognition motif;
458-531 5.81e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 41.81  E-value: 5.81e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907195737  458 IRLSGVPENATKEEILNAFRTSdGiPVKDLQL-KEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIHDKEVTL 531
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKF-G-KVESVRLvRDKETGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 458-530 1.46e-03

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: 37.60  E-value: 1.46e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907195737 458 IRLSGVPENATKEEILNAFRTSdGiPVKDLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIHDKEVT 530
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKF-G-PIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGK-ELGGRELK 70
RRM smart00360
RNA recognition motif;
654-732 1.97e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.57  E-value: 1.97e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907195737  654 TIMLKRIYRSTPPEVIVEVLEPYVHLTtaNVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNldppFSIDGKMVAV 732
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVE--SVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNG----KELDGRPLKV 73
Pentapeptide_4 pfam13599
Pentapeptide repeats (9 copies);
173-235 4.90e-03

Pentapeptide repeats (9 copies);


Pssm-ID: 433339 [Multi-domain]  Cd Length: 78  Bit Score: 36.48  E-value: 4.90e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907195737 173 TDFRGRGTYDLDFRGREGSHSDFRGRDLSDLDFRSRDQSRSDFRNRDVSDLDFRDKDGTQVDF 235
Cdd:pfam13599  16 TEFYHATLKDCNFTECNLVNVNFDDCNLRDVDFLEAQLKNAQFSGCNLKNSNFSDVKLKGADF 78
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
 463-533 5.75e-03

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. 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 also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 36.61  E-value: 5.75e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907195737 463 VPENATKEEILNAFRTSDgiPVKDLQL-KEYNTGYDYGYVCVEFSLLEDAIGCMEANQGtLMIHDKEVTLEY 533
Cdd:cd12649     8 LPQDLTDREFRALFRAIG--PVNTCKIvRDKKTGYSYGFGFVDFTSEEDAQRAIKTLNG-LQLQNKRLKVAY 76
 
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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