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Conserved domains on  [gi|1207180454|ref|XP_021333263|]
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splicing factor 1 isoform X3 [Danio rerio]

Protein Classification

KH-I_SF1 and ZnF_C2HC domain-containing protein( domain architecture ID 13420122)

KH-I_SF1 and ZnF_C2HC domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MSL5 super family cl34926
Splicing factor (branch point binding protein) [RNA processing and modification];
36-257 8.51e-66

Splicing factor (branch point binding protein) [RNA processing and modification];


The actual alignment was detected with superfamily member COG5176:

Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 215.99  E-value: 8.51e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454  36 MPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDlGIPVNPEDRSPSPEPIYNSEGKRLNTREYRTRKKLEEERHSLITE 115
Cdd:COG5176    50 LPSKISGALTREQIYSYQVMMRPFEITEKLRTPD-GVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKER 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 116 MVGLNPEFKPPADYKPPaTRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQM 195
Cdd:COG5176   129 AQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPES 207

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207180454 196 LPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLRED 257
Cdd:COG5176   208 LKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLRAD 269
ZnF_C2HC smart00343
zinc finger;
279-293 9.08e-03

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 33.96  E-value: 9.08e-03
                           10
                   ....*....|....*
gi 1207180454  279 CTKCGGAGHISSDCK 293
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
 
Name Accession Description Interval E-value
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
36-257 8.51e-66

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 215.99  E-value: 8.51e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454  36 MPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDlGIPVNPEDRSPSPEPIYNSEGKRLNTREYRTRKKLEEERHSLITE 115
Cdd:COG5176    50 LPSKISGALTREQIYSYQVMMRPFEITEKLRTPD-GVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKER 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 116 MVGLNPEFKPPADYKPPaTRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQM 195
Cdd:COG5176   129 AQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPES 207

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207180454 196 LPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLRED 257
Cdd:COG5176   208 LKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLRAD 269
SF1-HH pfam16275
Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is ...
 18-130 2.62e-58

Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is mainly found in splicing factor 1 from yeast to human. It is a helix-hairpin domain, which forms a secondary, hydrophobic interface with U2AF65(UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. In this domain, it contains a highly conserved SPSP motif in its C terminal and phophorylation of SPSP motif induces a disorder-to-order transition within a novel SF1/U2AF65 interface, indicating a phosphorylation-dependent control of pre-mRNA splicing factors.


Pssm-ID: 465080  Cd Length: 114  Bit Score: 190.51  E-value: 2.62e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454  18 KRSRWSSETPD-QKTVIPGMPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDLGIPVNPEDRSPSPEPIYNSEGKRLNT 96
Cdd:pfam16275   1 RKSRWGGEPEKtDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLGVPPSPEERSPSPPPIYDANGKRTNT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1207180454  97 REYRTRKKLEEERHSLITEMVGLNPEFKPPADYK 130
Cdd:pfam16275  81 REVRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 135-227 5.21e-56

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.


Pssm-ID: 411810 [Multi-domain]  Cd Length: 93  Bit Score: 183.66  E-value: 5.21e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN 214
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGQPLPGEDEPLHALVTANTAES 80

                          90
                  ....*....|...
gi 1207180454 215 VKKAVEQIRNILK 227
Cdd:cd22382    81 VKKAVDKIKEIIK 93
KH smart00322
K homology RNA-binding domain;
134-226 1.10e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 49.22  E-value: 1.10e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454  134 TRVSDKVMIPQdeypeiNFVGLLIGPRGNTLKNIEKECCAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTME 213
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDI-------------------PGPGSEERVVEITGPPE 55

                           90
                   ....*....|...
gi 1207180454  214 NVKKAVEQIRNIL 226
Cdd:smart00322  56 NVEKAAELILEIL 68
ZnF_C2HC smart00343
zinc finger;
279-293 9.08e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 33.96  E-value: 9.08e-03
                           10
                   ....*....|....*
gi 1207180454  279 CTKCGGAGHISSDCK 293
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
 
Name Accession Description Interval E-value
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
36-257 8.51e-66

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 215.99  E-value: 8.51e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454  36 MPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDlGIPVNPEDRSPSPEPIYNSEGKRLNTREYRTRKKLEEERHSLITE 115
Cdd:COG5176    50 LPSKISGALTREQIYSYQVMMRPFEITEKLRTPD-GVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKER 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 116 MVGLNPEFKPPADYKPPaTRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQM 195
Cdd:COG5176   129 AQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPES 207

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207180454 196 LPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLRED 257
Cdd:COG5176   208 LKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLRAD 269
SF1-HH pfam16275
Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is ...
 18-130 2.62e-58

Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is mainly found in splicing factor 1 from yeast to human. It is a helix-hairpin domain, which forms a secondary, hydrophobic interface with U2AF65(UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. In this domain, it contains a highly conserved SPSP motif in its C terminal and phophorylation of SPSP motif induces a disorder-to-order transition within a novel SF1/U2AF65 interface, indicating a phosphorylation-dependent control of pre-mRNA splicing factors.


Pssm-ID: 465080  Cd Length: 114  Bit Score: 190.51  E-value: 2.62e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454  18 KRSRWSSETPD-QKTVIPGMPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDLGIPVNPEDRSPSPEPIYNSEGKRLNT 96
Cdd:pfam16275   1 RKSRWGGEPEKtDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLGVPPSPEERSPSPPPIYDANGKRTNT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1207180454  97 REYRTRKKLEEERHSLITEMVGLNPEFKPPADYK 130
Cdd:pfam16275  81 REVRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 135-227 5.21e-56

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.


Pssm-ID: 411810 [Multi-domain]  Cd Length: 93  Bit Score: 183.66  E-value: 5.21e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN 214
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGQPLPGEDEPLHALVTANTAES 80

                          90
                  ....*....|...
gi 1207180454 215 VKKAVEQIRNILK 227
Cdd:cd22382    81 VKKAVDKIKEIIK 93
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
 135-226 7.37e-38

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.


Pssm-ID: 411805 [Multi-domain]  Cd Length: 92  Bit Score: 135.04  E-value: 7.37e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKvGRKDGQMLPGEDEPLHALVTANTMEN 214
Cdd:cd02395     1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGK-GRSDPQPDPDEEEDLHVLITADTEEK 79

                          90
                  ....*....|..
gi 1207180454 215 VKKAVEQIRNIL 226
Cdd:cd02395    80 VDKAAKLIEKLL 91
KH-I_Hqk_like cd22383
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk ...
 136-227 1.61e-25

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411811 [Multi-domain]  Cd Length: 101  Bit Score: 100.89  E-value: 1.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 136 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEG-KVGRKDGQmlPGE---DEPLHALVTANT 211
Cdd:cd22383     2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKkKEEANRGK--PNWehlNDDLHVLITVED 79

                          90       100
                  ....*....|....*....|.
gi 1207180454 212 MEN-----VKKAVEQIRNILK 227
Cdd:cd22383    80 TENrahikLAKAVEEVKKLLI 100
KH-I_HOW cd22466
type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and ...
 132-226 4.62e-18

type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and similar proteins; How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411894 [Multi-domain]  Cd Length: 105  Bit Score: 79.96  E-value: 4.62e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 132 PATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKV-----GRKDGQMLpgeDEPLHAL 206
Cdd:cd22466     2 PSVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKedlnrGKPNWEHL---NDELHVL 78

                          90       100
                  ....*....|....*....|....*
gi 1207180454 207 VTANTMEN-----VKKAVEQIRNIL 226
Cdd:cd22466    79 ITVEDTENrakvkLQRAVEEVRKLL 103
KH-I_Hqk cd22465
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; ...
 135-226 6.52e-17

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia.


Pssm-ID: 411893 [Multi-domain]  Cd Length: 103  Bit Score: 76.52  E-value: 6.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKV-----GRKDGQMLpgeDEPLHALVTA 209
Cdd:cd22465     1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKeeqnrGKPNWEHL---NEDLHVLITV 77

                          90       100
                  ....*....|....*....|..
gi 1207180454 210 NTMEN-----VKKAVEQIRNIL 226
Cdd:cd22465    78 EDAQNraeikLKRAVEEVKKLL 99
KH-I_KHDRBS cd22384
type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, ...
 135-209 1.92e-16

type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family; The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411812 [Multi-domain]  Cd Length: 102  Bit Score: 75.01  E-value: 1.92e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1207180454 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSV----KEGKVGRKDGQMLPGEDEPLHALVTA 209
Cdd:cd22384     4 KLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMrdkaKEEELRKSGDPKYAHLNEDLHVLIEA 82
KH-I_SPIN1_like cd22467
type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 ...
 142-227 1.37e-15

type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 (SPIN1) and similar proteins; SPIN1 is a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11. It is involved in flowering time control in rice. SPIN1 binds DNA and RNA in vitro.


Pssm-ID: 411895  Cd Length: 101  Bit Score: 72.52  E-value: 1.37e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 142 IPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKE-GKVGRKDGQmlPGED---EPLHALVTANTMENV-- 215
Cdd:cd22467     8 VPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDtAKEEKLRDK--PGYEhlnEPLHVLIEAELPANIid 85

                          90
                  ....*....|....*
gi 1207180454 216 ---KKAVEQIRNILK 227
Cdd:cd22467    86 arlQHAQEIIEDLLK 100
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 136-227 4.93e-13

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411814 [Multi-domain]  Cd Length: 102  Bit Score: 65.27  E-value: 4.93e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 136 VSDKVMIPQDEYPE-INFVGLLIGPRGNTLKNIEKECCAKIMIRGKGS-VKEGKVGRKDgqmlpgeDEPLHALVTANTME 213
Cdd:cd22386     3 YQEKVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGSgFIEPASGREA-------DEPLHLLISHPDPE 75

                          90
                  ....*....|....
gi 1207180454 214 NVKKAVEQIRNILK 227
Cdd:cd22386    76 GLQQAKKLCEDLLQ 89
KH-I_KHDRBS2 cd22469
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 135-243 1.06e-11

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins; KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis.


Pssm-ID: 411897 [Multi-domain]  Cd Length: 118  Bit Score: 62.06  E-value: 1.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGS----VKEGKVGRKDGQMLPGEDEPLHALVT-- 208
Cdd:cd22469     6 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSmrdkAKEEELRKSGEAKYAHLSDELHVLIEvf 85

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1207180454 209 ---ANTMENVKKAVEQIRNILkqgieTPEDQNDLRKMQ 243
Cdd:cd22469    86 appGEAYSRMSHALEEIKKFL-----VPDYNDEIRQEQ 118
KH-I_KHDRBS1 cd22468
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 135-185 5.82e-11

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins; KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors.


Pssm-ID: 411896 [Multi-domain]  Cd Length: 106  Bit Score: 59.64  E-value: 5.82e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1207180454 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKE 185
Cdd:cd22468     4 KLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRD 54
KH-I_KHDRBS3 cd22470
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 135-185 7.47e-10

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins; KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411898 [Multi-domain]  Cd Length: 113  Bit Score: 56.60  E-value: 7.47e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1207180454 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKE 185
Cdd:cd22470     8 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRD 58
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 138-223 9.93e-08

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 48.83  E-value: 9.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 138 DKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSvkegkvgrkdgqmlpgEDEPLHALVTAnTMENVKK 217
Cdd:cd00105     1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE----------------GSGERVVTITG-TPEAVEK 57


                  ....*.
gi 1207180454 218 AVEQIR 223
Cdd:cd00105    58 AKELIE 63
KH smart00322
K homology RNA-binding domain;
134-226 1.10e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 49.22  E-value: 1.10e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454  134 TRVSDKVMIPQdeypeiNFVGLLIGPRGNTLKNIEKECCAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTME 213
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDI-------------------PGPGSEERVVEITGPPE 55

                           90
                   ....*....|...
gi 1207180454  214 NVKKAVEQIRNIL 226
Cdd:smart00322  56 NVEKAAELILEIL 68
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 137-224 6.62e-06

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 43.81  E-value: 6.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 137 SDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECCAKImirgkgsvkegkvgrkdgQMLPGEDEPLHALVT-ANTMENV 215
Cdd:pfam00013   1 TVEILVPSS------LVGLIIGKGGSNIKEIREETGAKI------------------QIPPSESEGNERIVTiTGTPEAV 56


                  ....*....
gi 1207180454 216 KKAVEQIRN 224
Cdd:pfam00013  57 EAAKALIEE 65
KH-I_KHDC4_rpt1 cd22385
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 160-226 6.05e-05

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411813  Cd Length: 84  Bit Score: 41.81  E-value: 6.05e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1207180454 160 RGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGqmlpgeDEPLHALVTANTMENVKKAVEQIRNIL 226
Cdd:cd22385    24 KGSTQEEIQKESGAAVSTRGRYMPPEEKATFNPG------ERPLYLHVQAPTKEAVDRAVNKINEII 84
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 139-227 7.07e-05

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.


Pssm-ID: 411803 [Multi-domain]  Cd Length: 70  Bit Score: 41.31  E-value: 7.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 139 KVMIPQDeypeinFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKegkvgrkdgqmlpgedeplhalVTANTMENVKKA 218
Cdd:cd02393     7 TIKIPPD------KIGDVIGPGGKTIRAIIEETGAKIDIEDDGTVT----------------------IFATDKESAEAA 58


                  ....*....
gi 1207180454 219 VEQIRNILK 227
Cdd:cd02393    59 KAMIEDIVA 67
KH-I_Dim2p_like_rpt1 cd22389
first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 140-180 1.10e-03

first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins; The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411817 [Multi-domain]  Cd Length: 70  Bit Score: 37.95  E-value: 1.10e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1207180454 140 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECCAKIMIRGK 180
Cdd:cd22389     3 VKIPKER------IGVLIGKKGETKREIEERTGVKITVDSE 37
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 136-228 1.84e-03

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.


Pssm-ID: 411879 [Multi-domain]  Cd Length: 69  Bit Score: 37.05  E-value: 1.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180454 136 VSDKVMIPQDEYpeinfvGLLIGPRGNTLKNIEKECCAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTMENV 215
Cdd:cd22451     1 ASIDIDIPKEYH------RAIIGKGGAVLRELEAETGCRIQV-------------------PKKDDPSGKIRITGARDGV 55

                          90
                  ....*....|...
gi 1207180454 216 KKAVEQIRNILKQ 228
Cdd:cd22451    56 EAATAKILNISDE 68
ZnF_C2HC smart00343
zinc finger;
279-293 9.08e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 33.96  E-value: 9.08e-03
                           10
                   ....*....|....*
gi 1207180454  279 CTKCGGAGHISSDCK 293
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
 
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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