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Conserved domains on  [gi|568974750|ref|XP_006533764|]
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putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X4 [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 ...
 82-230 1.80e-23

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: 96.48  E-value: 1.80e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974750  82 STSCLRESSSAVCNFFAKGLCVKGMLCPLRHEQGEKL--VVCKHWLRGLCRKSDCCDFLHQYDVSK--MPVCYFHSKFGN 157
Cdd:COG5084   66 NDNFVPGNTVACISRNFNSIRGSRLSTPNNHVNPVLSssVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGS 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974750 158 CSN-KECLFLHLKPVLKLQDCPWYN---QGFCKEGPLCKYRHVHQVL------CPNYFTGFCPEGPQ------------- 214
Cdd:COG5084  146 CSSgPSCGYSHIDPDSFAGNCDQYSgatYGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTPsesvsswgygkgt 225

                        170       180
                 ....*....|....*....|..
gi 568974750 215 -CQFGHPKMS-----PPFHPSN 230
Cdd:COG5084  226 sCSLSHPSLNidiqqPQTAPSR 247
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 82-230 1.80e-23

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: 96.48  E-value: 1.80e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974750  82 STSCLRESSSAVCNFFAKGLCVKGMLCPLRHEQGEKL--VVCKHWLRGLCRKSDCCDFLHQYDVSK--MPVCYFHSKFGN 157
Cdd:COG5084   66 NDNFVPGNTVACISRNFNSIRGSRLSTPNNHVNPVLSssVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGS 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974750 158 CSN-KECLFLHLKPVLKLQDCPWYN---QGFCKEGPLCKYRHVHQVL------CPNYFTGFCPEGPQ------------- 214
Cdd:COG5084  146 CSSgPSCGYSHIDPDSFAGNCDQYSgatYGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTPsesvsswgygkgt 225

                        170       180
                 ....*....|....*....|..
gi 568974750 215 -CQFGHPKMS-----PPFHPSN 230
Cdd:COG5084  226 sCSLSHPSLNidiqqPQTAPSR 247
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 94-170 1.80e-04

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: 40.14  E-value: 1.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974750   94 CNFFAKGLCVKGMLCPLRHEQGE--KLVVCKHWLRGLCRKSdCCDFLH---QYDVSKMPvCYFHSKFGNCSNKECLFLHL 168
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHCEAAlgNETVCTLWQEGRCFRP-VCRFRHmeiDKNRKEIP-CYWENQPGGCQKPHCAFHHT 85


                  ..
gi 568974750  169 KP 170
Cdd:pfam15663  86 KP 87
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 82-230 1.80e-23

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: 96.48  E-value: 1.80e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974750  82 STSCLRESSSAVCNFFAKGLCVKGMLCPLRHEQGEKL--VVCKHWLRGLCRKSDCCDFLHQYDVSK--MPVCYFHSKFGN 157
Cdd:COG5084   66 NDNFVPGNTVACISRNFNSIRGSRLSTPNNHVNPVLSssVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGS 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974750 158 CSN-KECLFLHLKPVLKLQDCPWYN---QGFCKEGPLCKYRHVHQVL------CPNYFTGFCPEGPQ------------- 214
Cdd:COG5084  146 CSSgPSCGYSHIDPDSFAGNCDQYSgatYGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTPsesvsswgygkgt 225

                        170       180
                 ....*....|....*....|..
gi 568974750 215 -CQFGHPKMS-----PPFHPSN 230
Cdd:COG5084  226 sCSLSHPSLNidiqqPQTAPSR 247
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 94-170 1.80e-04

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: 40.14  E-value: 1.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974750   94 CNFFAKGLCVKGMLCPLRHEQGE--KLVVCKHWLRGLCRKSdCCDFLH---QYDVSKMPvCYFHSKFGNCSNKECLFLHL 168
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHCEAAlgNETVCTLWQEGRCFRP-VCRFRHmeiDKNRKEIP-CYWENQPGGCQKPHCAFHHT 85


                  ..
gi 568974750  169 KP 170
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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