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Conserved domains on  [gi|2462612148|ref|XP_054213122|]
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cleavage and polyadenylation specificity factor subunit 4 isoform X6 [Homo sapiens]

Protein Classification

zinc finger CCCH domain-containing protein( domain architecture ID 708395)

zinc finger CCCH domain-containing protein similar to cleavage and polyadenylation specificity factor (CPSF) subunit 4, which is part of the complex that plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YTH1 super family cl25862
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 2-123 3.23e-31

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


The actual alignment was detected with superfamily member COG5084:

Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 114.58  E-value: 3.23e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462612148   2 CPFRHISGE--KTVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYSKFGECSN-KECPFLHIDPESKIKDCPWYDR 76
Cdd:COG5084    92 TPNNHVNPVlsSSVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSgPSCGYSHIDPDSFAGNCDQYSG 171

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462612148  77 ---GFCKHGPLCRHRHTRRVI------CVNYLVGFCPEGP--------------SCKFMHPRFELPMGTT 123
Cdd:COG5084   172 atyGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTpsesvsswgygkgtSCSLSHPSLNIDIQQP 241
COG5222 super family cl34947
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
147-179 2.98e-03

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


The actual alignment was detected with superfamily member COG5222:

Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 37.42  E-value: 2.98e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2462612148 147 QSQNSSAGNRGPRPlEQVTCYKCGEKGHYANRC 179
Cdd:COG5222   161 QHRIGAQKHNKPPP-PGYVCYRCGQKGHWIQNC 192
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 2-123 3.23e-31

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 114.58  E-value: 3.23e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462612148   2 CPFRHISGE--KTVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYSKFGECSN-KECPFLHIDPESKIKDCPWYDR 76
Cdd:COG5084    92 TPNNHVNPVlsSSVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSgPSCGYSHIDPDSFAGNCDQYSG 171

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462612148  77 ---GFCKHGPLCRHRHTRRVI------CVNYLVGFCPEGP--------------SCKFMHPRFELPMGTT 123
Cdd:COG5084   172 atyGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTpsesvsswgygkgtSCSLSHPSLNIDIQQP 241
ZnF_C3H1 smart00356
zinc finger;
10-35 5.31e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.07  E-value: 5.31e-04
                           10        20
                   ....*....|....*....|....*.
gi 2462612148   10 EKTVVCKHWLRGLCKKGDQCEFLHEY 35
Cdd:smart00356   2 YKTELCKFFKRGYCPRGDRCKFAHPL 27
COG5222 COG5222
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
147-179 2.98e-03

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 37.42  E-value: 2.98e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2462612148 147 QSQNSSAGNRGPRPlEQVTCYKCGEKGHYANRC 179
Cdd:COG5222   161 QHRIGAQKHNKPPP-PGYVCYRCGQKGHWIQNC 192
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 15-33 6.36e-03

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: 32.77  E-value: 6.36e-03
                          10
                  ....*....|....*....
gi 2462612148  15 CKHWLRGLCKKGDQCEFLH 33
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 2-123 3.23e-31

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 114.58  E-value: 3.23e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462612148   2 CPFRHISGE--KTVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYSKFGECSN-KECPFLHIDPESKIKDCPWYDR 76
Cdd:COG5084    92 TPNNHVNPVlsSSVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSgPSCGYSHIDPDSFAGNCDQYSG 171

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462612148  77 ---GFCKHGPLCRHRHTRRVI------CVNYLVGFCPEGP--------------SCKFMHPRFELPMGTT 123
Cdd:COG5084   172 atyGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTpsesvsswgygkgtSCSLSHPSLNIDIQQP 241
ZnF_C3H1 smart00356
zinc finger;
10-35 5.31e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.07  E-value: 5.31e-04
                           10        20
                   ....*....|....*....|....*.
gi 2462612148   10 EKTVVCKHWLRGLCKKGDQCEFLHEY 35
Cdd:smart00356   2 YKTELCKFFKRGYCPRGDRCKFAHPL 27
COG5222 COG5222
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
147-179 2.98e-03

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 37.42  E-value: 2.98e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2462612148 147 QSQNSSAGNRGPRPlEQVTCYKCGEKGHYANRC 179
Cdd:COG5222   161 QHRIGAQKHNKPPP-PGYVCYRCGQKGHWIQNC 192
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 15-33 6.36e-03

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: 32.77  E-value: 6.36e-03
                          10
                  ....*....|....*....
gi 2462612148  15 CKHWLRGLCKKGDQCEFLH 33
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
ZnF_C3H1 smart00356
zinc finger;
90-115 9.63e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 32.60  E-value: 9.63e-03
                           10        20
                   ....*....|....*....|....*.
gi 2462612148   90 TRRVICVNYLVGFCPEGPSCKFMHPR 115
Cdd:smart00356   2 YKTELCKFFKRGYCPRGDRCKFAHPL 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.
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