NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|982940795|ref|XP_015329287|]
View 

zinc finger CCCH domain-containing protein 13 isoform X1 [Bos taurus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 344-570 1.21e-07

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 56.45  E-value: 1.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795  344 QRHSPSPRRKRTPSPSYQRTITPPLRRSASPYPSHSLASPQRKQSPPRHRSPVREKGrhdHERASQSHDRRHERREETRG 423
Cdd:PRK12678   59 RGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAA---AEAASAPEAAQARERRERGE 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795  424 KRDREKDTREEREYEQDQSSSRDHRDDREPRDGRDRRDARDTRDRRELRDSRDVRDSREMRDYSRDNKESRDPRDSRSTR 503
Cdd:PRK12678  136 AARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRR 215

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 982940795  504 DAHDYRDRESRDAHRKEDAYQEESRSYGRNHLREESSRAEIRNDSRNESRSEIRNDRMGRSRGRAPE 570
Cdd:PRK12678  216 EERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNE 282
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
42-63 4.57e-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: 4.57e-05
                           10        20
                   ....*....|....*....|..
gi 982940795    42 CRNWLKTGNCLYGNTCRFVHGP 63
Cdd:pfam00642    6 CRFFLRTGYCKYGDRCKFAHGQ 27
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 344-570 1.21e-07

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 56.45  E-value: 1.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795  344 QRHSPSPRRKRTPSPSYQRTITPPLRRSASPYPSHSLASPQRKQSPPRHRSPVREKGrhdHERASQSHDRRHERREETRG 423
Cdd:PRK12678   59 RGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAA---AEAASAPEAAQARERRERGE 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795  424 KRDREKDTREEREYEQDQSSSRDHRDDREPRDGRDRRDARDTRDRRELRDSRDVRDSREMRDYSRDNKESRDPRDSRSTR 503
Cdd:PRK12678  136 AARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRR 215

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 982940795  504 DAHDYRDRESRDAHRKEDAYQEESRSYGRNHLREESSRAEIRNDSRNESRSEIRNDRMGRSRGRAPE 570
Cdd:PRK12678  216 EERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNE 282
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
42-63 4.57e-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: 4.57e-05
                           10        20
                   ....*....|....*....|..
gi 982940795    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 ...
 471-579 1.85e-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: 46.07  E-value: 1.85e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795   471 LRDSRDVRDSREMRDYSRDNKESRDpRDSRSTRDAHDYRDREsRDAHRKEDAYQEESRSYGRNHLREESSRAEIRNDSRN 550
Cdd:TIGR01622   10 LRDSSSAGDRDRRRDKGRERSRDRS-RDRERSRSRRRDRHRD-RDYYRGRERRSRSRRPNRRYRPREKRRRRGDSYRRRR 87

                           90       100
                   ....*....|....*....|....*....
gi 982940795   551 ESRSEIRNDRMGRSRGRAPEMPEKGSRGT 579
Cdd:TIGR01622   88 DDRRSRREKPRARDGTPEPLTEDERDRRT 116
ZnF_C3H1 smart00356
zinc finger;
42-63 3.72e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.45  E-value: 3.72e-03
                            10        20
                    ....*....|....*....|..
gi 982940795     42 CRNWlKTGNCLYGNTCRFVHGP 63
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHPL 27
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 344-570 1.21e-07

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 56.45  E-value: 1.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795  344 QRHSPSPRRKRTPSPSYQRTITPPLRRSASPYPSHSLASPQRKQSPPRHRSPVREKGrhdHERASQSHDRRHERREETRG 423
Cdd:PRK12678   59 RGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAA---AEAASAPEAAQARERRERGE 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795  424 KRDREKDTREEREYEQDQSSSRDHRDDREPRDGRDRRDARDTRDRRELRDSRDVRDSREMRDYSRDNKESRDPRDSRSTR 503
Cdd:PRK12678  136 AARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRR 215

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 982940795  504 DAHDYRDRESRDAHRKEDAYQEESRSYGRNHLREESSRAEIRNDSRNESRSEIRNDRMGRSRGRAPE 570
Cdd:PRK12678  216 EERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNE 282
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
42-63 4.57e-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: 4.57e-05
                           10        20
                   ....*....|....*....|..
gi 982940795    42 CRNWLKTGNCLYGNTCRFVHGP 63
Cdd:pfam00642    6 CRFFLRTGYCKYGDRCKFAHGQ 27
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 292-521 1.04e-04

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 47.21  E-value: 1.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795  292 EEKPRDGKDRGRDFERQREKRDKPRSTSPAGQHHSPISSRHHSSSSQSGSSIQRHSPSPRRKRTPSPSYQRTITPPLRRS 371
Cdd:PRK12678   70 PAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGG 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795  372 ASPYPSHSLASPQRKQSPPRHRSPVREKGRHDHERASQSHDRRHERREETRGKRDREKDTREEREYEQDQSSSRDHRDDR 451
Cdd:PRK12678  150 EQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGR 229

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795  452 EPRDGRDRRDARDTRDRRELRDSRDVRDSREmrdysRDNKESRDPRDSRSTRDahdyRDRESRDAHRKED 521
Cdd:PRK12678  230 RRRRDRRDARGDDNREDRGDRDGDDGEGRGG-----RRGRRFRDRDRRGRRGG----DGGNEREPELRED 290
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 471-579 1.85e-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: 46.07  E-value: 1.85e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 982940795   471 LRDSRDVRDSREMRDYSRDNKESRDpRDSRSTRDAHDYRDREsRDAHRKEDAYQEESRSYGRNHLREESSRAEIRNDSRN 550
Cdd:TIGR01622   10 LRDSSSAGDRDRRRDKGRERSRDRS-RDRERSRSRRRDRHRD-RDYYRGRERRSRSRRPNRRYRPREKRRRRGDSYRRRR 87

                           90       100
                   ....*....|....*....|....*....
gi 982940795   551 ESRSEIRNDRMGRSRGRAPEMPEKGSRGT 579
Cdd:TIGR01622   88 DDRRSRREKPRARDGTPEPLTEDERDRRT 116
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 42-61 3.11e-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: 3.11e-04
                           10        20
                   ....*....|....*....|
gi 982940795    42 CRNWLKtGNCLYGNTCRFVH 61
Cdd:pfam18345    1 CKFFLK-GRCRYGDKCRFAH 19
ZnF_C3H1 smart00356
zinc finger;
42-63 3.72e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.45  E-value: 3.72e-03
                            10        20
                    ....*....|....*....|..
gi 982940795     42 CRNWlKTGNCLYGNTCRFVHGP 63
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHPL 27
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH