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Conserved domains on  [gi|1834199545|ref|NP_001369136|]
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zinc finger CCCH domain-containing protein 13 isoform 1 [Homo sapiens]

Protein Classification

zinc finger CCCH domain-containing protein 13( domain architecture ID 13639077)

zinc finger CCCH domain-containing protein 13 (ZC3H13) is an zssociated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing

Gene Symbol:  ZC3H13
Gene Ontology:  GO:0008270|GO:0003723|GO:0080009
PubMed:  12665246

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 343-566 8.24e-08

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 57.22  E-value: 8.24e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  343 QRHSPSPRRKRTPSPSYQRTLTPPLRRSASPYPSHSLSSP-QRKQSPPRHRSPMREKGRHDHERTSQSHDRRHERREDTR 421
Cdd:PRK12678    59 RGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAaAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAAR 138

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  422 GKRDREKDSREEREYEQDQSSSRDHRDDREPRDGRDRRDARDTRDRRELRDSRDMRDSREmrdySRDTKESRDPRDSRST 501
Cdd:PRK12678   139 RGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGR----DGDDRDRRDRREQGDR 214

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1834199545  502 RDAHDYRDREGRDTHRKEDTYPEESRSYGRNHLREESSRTEIRNESRNESRSEIRNDRMGRSRGR 566
Cdd:PRK12678   215 REERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDG 279
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
42-63 4.95e-05

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


:

Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 41.80  E-value: 4.95e-05
                           10        20
                   ....*....|....*....|..
gi 1834199545   42 CRNWLKTGNCLYGNTCRFVHGP 63
Cdd:pfam00642    6 CRFFLRTGYCKYGDRCKFAHGQ 27
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 343-566 8.24e-08

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 57.22  E-value: 8.24e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  343 QRHSPSPRRKRTPSPSYQRTLTPPLRRSASPYPSHSLSSP-QRKQSPPRHRSPMREKGRHDHERTSQSHDRRHERREDTR 421
Cdd:PRK12678    59 RGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAaAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAAR 138

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  422 GKRDREKDSREEREYEQDQSSSRDHRDDREPRDGRDRRDARDTRDRRELRDSRDMRDSREmrdySRDTKESRDPRDSRST 501
Cdd:PRK12678   139 RGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGR----DGDDRDRRDRREQGDR 214

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1834199545  502 RDAHDYRDREGRDTHRKEDTYPEESRSYGRNHLREESSRTEIRNESRNESRSEIRNDRMGRSRGR 566
Cdd:PRK12678   215 REERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDG 279
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
42-63 4.95e-05

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 41.80  E-value: 4.95e-05
                           10        20
                   ....*....|....*....|..
gi 1834199545   42 CRNWLKTGNCLYGNTCRFVHGP 63
Cdd:pfam00642    6 CRFFLRTGYCKYGDRCKFAHGQ 27
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 470-573 3.21e-04

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: 45.30  E-value: 3.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  470 LRDSRDMRDSREMRDYSRDTKESRDpRDSRSTRDAHDYRDREgRDTHRKEDTYPEESRSYGRNHLREESSRTEIRNESRN 549
Cdd:TIGR01622   10 LRDSSSAGDRDRRRDKGRERSRDRS-RDRERSRSRRRDRHRD-RDYYRGRERRSRSRRPNRRYRPREKRRRRGDSYRRRR 87

                           90       100
                   ....*....|....*....|....
gi 1834199545  550 ESRSEIRNDRMGRSRGRVPELPEK 573
Cdd:TIGR01622   88 DDRRSRREKPRARDGTPEPLTEDE 111
ZnF_C3H1 smart00356
zinc finger;
42-63 3.39e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.45  E-value: 3.39e-03
                            10        20
                    ....*....|....*....|..
gi 1834199545    42 CRNWlKTGNCLYGNTCRFVHGP 63
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHPL 27
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 343-566 8.24e-08

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 57.22  E-value: 8.24e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  343 QRHSPSPRRKRTPSPSYQRTLTPPLRRSASPYPSHSLSSP-QRKQSPPRHRSPMREKGRHDHERTSQSHDRRHERREDTR 421
Cdd:PRK12678    59 RGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAaAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAAR 138

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  422 GKRDREKDSREEREYEQDQSSSRDHRDDREPRDGRDRRDARDTRDRRELRDSRDMRDSREmrdySRDTKESRDPRDSRST 501
Cdd:PRK12678   139 RGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGR----DGDDRDRRDRREQGDR 214

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1834199545  502 RDAHDYRDREGRDTHRKEDTYPEESRSYGRNHLREESSRTEIRNESRNESRSEIRNDRMGRSRGR 566
Cdd:PRK12678   215 REERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDG 279
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 344-558 5.62e-06

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 51.06  E-value: 5.62e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  344 RHSPSPRRKRTPSPSYQRTLTPPLRRSASPYPSHSLSSPQRKQSPPRHRSPMREKGRHDHERTSQSHDRRHERRED--TR 421
Cdd:PRK12678    76 AARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQpaTE 155

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  422 GKRDREKDSREEREYEQDQSSSRDHRDDREPRDGRDRRDARDTRDRRELRDSRDMRDSREMRDYSRDTKESRDPRDSRST 501
Cdd:PRK12678   156 ARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDR 235

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1834199545  502 RDAHDYRDREGRDTHRKEDTYPEESRSYGRNHLREESSRTeiRNESRNESRSEIRND 558
Cdd:PRK12678   236 RDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRR--GGDGGNEREPELRED 290
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
42-63 4.95e-05

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 41.80  E-value: 4.95e-05
                           10        20
                   ....*....|....*....|..
gi 1834199545   42 CRNWLKTGNCLYGNTCRFVHGP 63
Cdd:pfam00642    6 CRFFLRTGYCKYGDRCKFAHGQ 27
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 291-520 8.85e-05

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 47.21  E-value: 8.85e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  291 EEKTRDGKDRGRDFERQREKRDKPRSTSPAGQHHSPISSRHHSSSSQSGSSIQRHSPSPRRKRTPSPSYQRTLTPPLRRS 370
Cdd:PRK12678    70 PAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGG 149

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  371 ASPYPSHSLSSPQRKQSPPRHRSPMREKGRHDHERTSQSHDRRHERREDTRGKRDREKDSREEREYEQDQSSSRDHRDDR 450
Cdd:PRK12678   150 EQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGR 229

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  451 EPRDGRDRRDARDTRDRRELRDSRDMRDSREmrdysRDTKESRDPRDSRSTRDahdyRDREGRDTHRKED 520
Cdd:PRK12678   230 RRRRDRRDARGDDNREDRGDRDGDDGEGRGG-----RRGRRFRDRDRRGRRGG----DGGNEREPELRED 290
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 370-580 2.63e-04

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 45.67  E-value: 2.63e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  370 SASPYPSHSLSSPQRKQSPPRHRSPMREKGRHDHERTSQSHDRRHERREDTRGKRDREKDSREEREYEQDQSSSRdhrdd 449
Cdd:PRK12678    62 GAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEA----- 136

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  450 rEPRDGRDRRDARDTRDRRELRDSRDMRDSREMRDySRDTKESRDPRDSRSTRDAHDYRDREGRDTHRKEDTYP-EESRS 528
Cdd:PRK12678   137 -ARRGAARKAGEGGEQPATEARADAAERTEEEERD-ERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRrEQGDR 214

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1834199545  529 YGRNHLREESSRTEIRNESRNESRSEIRNDRMGRSRGRVPELPEKGSRGSRG 580
Cdd:PRK12678   215 REERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRF 266
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 42-61 3.09e-04

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 39.32  E-value: 3.09e-04
                           10        20
                   ....*....|....*....|
gi 1834199545   42 CRNWLKtGNCLYGNTCRFVH 61
Cdd:pfam18345    1 CKFFLK-GRCRYGDKCRFAH 19
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 470-573 3.21e-04

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: 45.30  E-value: 3.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  470 LRDSRDMRDSREMRDYSRDTKESRDpRDSRSTRDAHDYRDREgRDTHRKEDTYPEESRSYGRNHLREESSRTEIRNESRN 549
Cdd:TIGR01622   10 LRDSSSAGDRDRRRDKGRERSRDRS-RDRERSRSRRRDRHRD-RDYYRGRERRSRSRRPNRRYRPREKRRRRGDSYRRRR 87

                           90       100
                   ....*....|....*....|....
gi 1834199545  550 ESRSEIRNDRMGRSRGRVPELPEK 573
Cdd:TIGR01622   88 DDRRSRREKPRARDGTPEPLTEDE 111
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 315-520 3.69e-04

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 45.28  E-value: 3.69e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  315 RSTSPAGQHHSPISSRHHSSSSQSGSSIQRHSPSPRRKRTPSPSYQRTLTPPLRRSASPYPSHSLSSPQRKQSPPRHRSP 394
Cdd:PRK12678    59 RGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAAR 138

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  395 MREKGRH------------DHERTSQSHDRRHERREDTRGKRDREKDSREEREYEQDQSSSRDHRDDREPRDGRDRRDAR 462
Cdd:PRK12678   139 RGAARKAgeggeqpatearADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREER 218

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1834199545  463 DTRDRRELRDSRDMRDSREMRDysrdtKESRDPRDSRSTRDAHDYRDREGRDTHRKED 520
Cdd:PRK12678   219 GRRDGGDRRGRRRRRDRRDARG-----DDNREDRGDRDGDDGEGRGGRRGRRFRDRDR 271
2a38euk TIGR00934
potassium uptake protein, Trk family; The proteins of the Trk family are derived from ...
 302-566 1.14e-03

potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 130009 [Multi-domain]  Cd Length: 800  Bit Score: 43.82  E-value: 1.14e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  302 RDFERQREKRDKPRSTSPAGQHHSPISSRHHSSSSQSGSSIQRHSPSPRRKRTPSPSYQRTLTPP---LRRSASPYPSHS 378
Cdd:TIGR00934  156 RELEDRPETGVAGRVTVPHGSAKRRDFQDKLFSGEFVKRDEPDQNSPDVKSDTRADESISDLEFEkfaKRRGSRDVDPED 235

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  379 LsspqrkqspprHRSPMREKGRHDHERTSQSHDRRHERREdtrgkrdrEKDSREEREYEQDQSSSRDHRDDREPRDGRDR 458
Cdd:TIGR00934  236 L-----------YRSIMMLQGIHERIREKSSANSRSDERS--------SESIQEQVERRPSTSDIERNSQSLTRRYDDKS 296

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  459 RDARDTRDRRELRDSRDMRDSREMRDYsRDTKESRDPRDSRSTRDAHDYRDREGRDTHRKEDTYPEESRS---YGRNHLR 535
Cdd:TIGR00934  297 FDKAVRLRRSKTIDRAEACDLEELDRA-KDFEKMTYDNWKAHHRKKKNFRPRGWNLKFRKASRFPKDSDRnyeDNGNHLS 375

                          250       260       270
                   ....*....|....*....|....*....|..
gi 1834199545  536 EESSRT-EIRNESRNESRSEIRNDRMGRSRGR 566
Cdd:TIGR00934  376 ASSSFGsEEPSLSSEENLYPTYNKKREDSRHT 407
ZnF_C3H1 smart00356
zinc finger;
42-63 3.39e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.45  E-value: 3.39e-03
                            10        20
                    ....*....|....*....|..
gi 1834199545    42 CRNWlKTGNCLYGNTCRFVHGP 63
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHPL 27
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 382-490 3.46e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 41.80  E-value: 3.46e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  382 PQRKQSPPRHRSPMREKGRHDHERTSQSHDRRHERREDTRGKRDREKDsREEREYEQDQSSSRDHRDDREPRDGRDRRDA 461
Cdd:TIGR01642    5 PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRP-RDRRRYDSRSPRSLRYSSVRRSRDRPRRRSR 83

                           90       100
                   ....*....|....*....|....*....
gi 1834199545  462 RDTRDRRELRDSRDMRDSREMRDYSRDTK 490
Cdd:TIGR01642   84 SVRSIEQHRRRLRDRSPSNQWRKDDKKRS 112
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 392-508 4.12e-03

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: 41.83  E-value: 4.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  392 RSPMREKGRHDHERTSQSHDRRHERreDTRGKRDREKDSREEREYEQDQSSSRDHRDDREPRDGRDRRDARDTRDRRELR 471
Cdd:TIGR01622    1 RYRDRERERLRDSSSAGDRDRRRDK--GRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPREKRRR 78

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1834199545  472 DSRDMRDSREMRDYSRDTKESRDPRDSRSTRDAHDYR 508
Cdd:TIGR01622   79 RGDSYRRRRDDRRSRREKPRARDGTPEPLTEDERDRR 115
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 412-551 5.00e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 41.42  E-value: 5.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  412 RRHERREDTRGKRDREKDSREEREYEQDQSSSRDhrddreprdgrdrrdardtrdrrelRDSRDMRDSREMRDYSRDTKE 491
Cdd:TIGR01642    1 RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRF-------------------------RDRHRRSRERSYREDSRPRDR 55

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  492 SRdpRDSRSTRDAHDYRDREGRDTHRKeDTYPEESRSYGRNHLREESSRTEIRNESRNES 551
Cdd:TIGR01642   56 RR--YDSRSPRSLRYSSVRRSRDRPRR-RSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRS 112
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 409-553 9.76e-03

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: 40.29  E-value: 9.76e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1834199545  409 SHDRRHERREDTRGKRDREKDSREEREYEQDQSSSRDhrddreprdgrdrrdardtrdrrelRDSRDMRDSREMRDYSRD 488
Cdd:TIGR01622    2 YRDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRE-------------------------RSRSRRRDRHRDRDYYRG 56

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1834199545  489 TK-ESRDPRDSRSTRDAHDYRDREGRDTHRKEDtypeesRSYGRNHLREESSRTEIRNESRNESRS 553
Cdd:TIGR01622   57 RErRSRSRRPNRRYRPREKRRRRGDSYRRRRDD------RRSRREKPRARDGTPEPLTEDERDRRT 116
 
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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