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Conserved domains on  [gi|601983512|ref|NP_001278178|]
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cleavage and polyadenylation specificity factor subunit 4 isoform b [Mus musculus]

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 ...
 25-176 1.11e-32

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: 119.98  E-value: 1.11e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 601983512  25 AQPLPFPGMDKSGAAVCEFFLKAACGKGGMCPFRHISGE--KTVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYS 100
Cdd:COG5084   62 MQNTNDNFVPGNTVACISRNFNSIRGSRLSTPNNHVNPVlsSSVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFS 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 601983512 101 KFGECSN-KECPFLHIDPESKIKDCPWYDR---GFCKHGPLCRHRHTRRVI------CVNYLVGFCPEGP---------- 160
Cdd:COG5084  142 LKGSCSSgPSCGYSHIDPDSFAGNCDQYSGatyGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTpsesvsswgy 221

                        170       180
                 ....*....|....*....|
gi 601983512 161 ----SCKFMHPRFELPMGTT 176
Cdd:COG5084  222 gkgtSCSLSHPSLNIDIQQP 241
COG5222 super family cl34947
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
192-232 3.93e-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: 38.19  E-value: 3.93e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 601983512 192 APQVIGVMQSQNSSAGNRGPRPlEQVTCYKCGEKGHYANRC 232
Cdd:COG5222  153 ATPIYKPNQHRIGAQKHNKPPP-PGYVCYRCGQKGHWIQNC 192
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 25-176 1.11e-32

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: 119.98  E-value: 1.11e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 601983512  25 AQPLPFPGMDKSGAAVCEFFLKAACGKGGMCPFRHISGE--KTVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYS 100
Cdd:COG5084   62 MQNTNDNFVPGNTVACISRNFNSIRGSRLSTPNNHVNPVlsSSVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFS 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 601983512 101 KFGECSN-KECPFLHIDPESKIKDCPWYDR---GFCKHGPLCRHRHTRRVI------CVNYLVGFCPEGP---------- 160
Cdd:COG5084  142 LKGSCSSgPSCGYSHIDPDSFAGNCDQYSGatyGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTpsesvsswgy 221

                        170       180
                 ....*....|....*....|
gi 601983512 161 ----SCKFMHPRFELPMGTT 176
Cdd:COG5084  222 gkgtSCSLSHPSLNIDIQQP 241
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 41-119 3.50e-07

Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically between 155 and 169 amino acids in length.


Pssm-ID: 464787 [Multi-domain]  Cd Length: 110  Bit Score: 47.46  E-value: 3.50e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 601983512   41 CEFFLKAACGKGGMCPFRHIS---GEKTvVCKHWLRGLCKKgDQCEFLHEYDMTKMPE--CYFYSKFGECSNKECPFLHI 115
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHCEaalGNET-VCTLWQEGRCFR-PVCRFRHMEIDKNRKEipCYWENQPGGCQKPHCAFHHT 85


                  ....
gi 601983512  116 DPES 119
Cdd:pfam15663  86 KPRY 89
ZnF_C3H1 smart00356
zinc finger;
63-88 1.70e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 37.99  E-value: 1.70e-04
                           10        20
                   ....*....|....*....|....*.
gi 601983512    63 EKTVVCKHWLRGLCKKGDQCEFLHEY 88
Cdd:smart00356   2 YKTELCKFFKRGYCPRGDRCKFAHPL 27
COG5222 COG5222
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
192-232 3.93e-03

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


Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 38.19  E-value: 3.93e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 601983512 192 APQVIGVMQSQNSSAGNRGPRPlEQVTCYKCGEKGHYANRC 232
Cdd:COG5222  153 ATPIYKPNQHRIGAQKHNKPPP-PGYVCYRCGQKGHWIQNC 192
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 25-176 1.11e-32

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: 119.98  E-value: 1.11e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 601983512  25 AQPLPFPGMDKSGAAVCEFFLKAACGKGGMCPFRHISGE--KTVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYS 100
Cdd:COG5084   62 MQNTNDNFVPGNTVACISRNFNSIRGSRLSTPNNHVNPVlsSSVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFS 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 601983512 101 KFGECSN-KECPFLHIDPESKIKDCPWYDR---GFCKHGPLCRHRHTRRVI------CVNYLVGFCPEGP---------- 160
Cdd:COG5084  142 LKGSCSSgPSCGYSHIDPDSFAGNCDQYSGatyGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTpsesvsswgy 221

                        170       180
                 ....*....|....*....|
gi 601983512 161 ----SCKFMHPRFELPMGTT 176
Cdd:COG5084  222 gkgtSCSLSHPSLNIDIQQP 241
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 41-119 3.50e-07

Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically between 155 and 169 amino acids in length.


Pssm-ID: 464787 [Multi-domain]  Cd Length: 110  Bit Score: 47.46  E-value: 3.50e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 601983512   41 CEFFLKAACGKGGMCPFRHIS---GEKTvVCKHWLRGLCKKgDQCEFLHEYDMTKMPE--CYFYSKFGECSNKECPFLHI 115
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHCEaalGNET-VCTLWQEGRCFR-PVCRFRHMEIDKNRKEipCYWENQPGGCQKPHCAFHHT 85


                  ....
gi 601983512  116 DPES 119
Cdd:pfam15663  86 KPRY 89
ZnF_C3H1 smart00356
zinc finger;
63-88 1.70e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 37.99  E-value: 1.70e-04
                           10        20
                   ....*....|....*....|....*.
gi 601983512    63 EKTVVCKHWLRGLCKKGDQCEFLHEY 88
Cdd:smart00356   2 YKTELCKFFKRGYCPRGDRCKFAHPL 27
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 68-86 2.82e-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: 34.31  E-value: 2.82e-03
                          10
                  ....*....|....*....
gi 601983512   68 CKHWLRGLCKKGDQCEFLH 86
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
ZnF_C3H1 smart00356
zinc finger;
143-168 3.43e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 34.14  E-value: 3.43e-03
                           10        20
                   ....*....|....*....|....*.
gi 601983512   143 TRRVICVNYLVGFCPEGPSCKFMHPR 168
Cdd:smart00356   2 YKTELCKFFKRGYCPRGDRCKFAHPL 27
COG5222 COG5222
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
192-232 3.93e-03

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


Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 38.19  E-value: 3.93e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 601983512 192 APQVIGVMQSQNSSAGNRGPRPlEQVTCYKCGEKGHYANRC 232
Cdd:COG5222  153 ATPIYKPNQHRIGAQKHNKPPP-PGYVCYRCGQKGHWIQNC 192
 
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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