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Conserved domains on  [gi|256985198|ref|NP_080958|]
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putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform 1 [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 ...
 36-178 8.68e-22

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: 90.70  E-value: 8.68e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256985198  36 SSSAVCNFFAKGLCVKGMLCPLRHEQGEKL--VVCKHWLRGLCRKSDCCDFLHQYDVSK--MPVCYFHSKFGNCSN-KEC 110
Cdd:COG5084   73 NTVACISRNFNSIRGSRLSTPNNHVNPVLSssVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSgPSC 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256985198 111 LFLHLKPVLKLQDCPWYN---QGFCKEvGPLCKYRHVHQVL------CPNYFTGFCPEGPQ--------------CQFGH 167
Cdd:COG5084  153 GYSHIDPDSFAGNCDQYSgatYGFCPL-GASCKFSHTLKRVsygsspCGNYTPPFSPPGTPsesvsswgygkgtsCSLSH 231

                        170
                 ....*....|....*.
gi 256985198 168 PKMS-----PPFHPSN 178
Cdd:COG5084  232 PSLNidiqqPQTAPSR 247
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 36-178 8.68e-22

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: 90.70  E-value: 8.68e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256985198  36 SSSAVCNFFAKGLCVKGMLCPLRHEQGEKL--VVCKHWLRGLCRKSDCCDFLHQYDVSK--MPVCYFHSKFGNCSN-KEC 110
Cdd:COG5084   73 NTVACISRNFNSIRGSRLSTPNNHVNPVLSssVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSgPSC 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256985198 111 LFLHLKPVLKLQDCPWYN---QGFCKEvGPLCKYRHVHQVL------CPNYFTGFCPEGPQ--------------CQFGH 167
Cdd:COG5084  153 GYSHIDPDSFAGNCDQYSgatYGFCPL-GASCKFSHTLKRVsygsspCGNYTPPFSPPGTPsesvsswgygkgtsCSLSH 231

                        170
                 ....*....|....*.
gi 256985198 168 PKMS-----PPFHPSN 178
Cdd:COG5084  232 PSLNidiqqPQTAPSR 247
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 41-117 9.45e-05

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: 40.52  E-value: 9.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256985198   41 CNFFAKGLCVKGMLCPLRHEQGE--KLVVCKHWLRGLCRKSdCCDFLH---QYDVSKMPvCYFHSKFGNCSNKECLFLHL 115
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHCEAAlgNETVCTLWQEGRCFRP-VCRFRHmeiDKNRKEIP-CYWENQPGGCQKPHCAFHHT 85


                  ..
gi 256985198  116 KP 117
Cdd:pfam15663  86 KP 87
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 36-178 8.68e-22

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: 90.70  E-value: 8.68e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256985198  36 SSSAVCNFFAKGLCVKGMLCPLRHEQGEKL--VVCKHWLRGLCRKSDCCDFLHQYDVSK--MPVCYFHSKFGNCSN-KEC 110
Cdd:COG5084   73 NTVACISRNFNSIRGSRLSTPNNHVNPVLSssVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSgPSC 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256985198 111 LFLHLKPVLKLQDCPWYN---QGFCKEvGPLCKYRHVHQVL------CPNYFTGFCPEGPQ--------------CQFGH 167
Cdd:COG5084  153 GYSHIDPDSFAGNCDQYSgatYGFCPL-GASCKFSHTLKRVsygsspCGNYTPPFSPPGTPsesvsswgygkgtsCSLSH 231

                        170
                 ....*....|....*.
gi 256985198 168 PKMS-----PPFHPSN 178
Cdd:COG5084  232 PSLNidiqqPQTAPSR 247
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 41-117 9.45e-05

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: 40.52  E-value: 9.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256985198   41 CNFFAKGLCVKGMLCPLRHEQGE--KLVVCKHWLRGLCRKSdCCDFLH---QYDVSKMPvCYFHSKFGNCSNKECLFLHL 115
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHCEAAlgNETVCTLWQEGRCFRP-VCRFRHmeiDKNRKEIP-CYWENQPGGCQKPHCAFHHT 85


                  ..
gi 256985198  116 KP 117
Cdd:pfam15663  86 KP 87
 
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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