NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1384072052|ref|NP_001349735|]
View 

putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform 4 [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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 36-177 2.33e-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: 94.94  E-value: 2.33e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384072052  36 SSSAVCNFFAKGLCVKGMLCPLRHEQGEKL--VVCKHWLRGLCRKSDCCDFLHQYDVSK--MPVCYFHSKFGNCSN-KEC 110
Cdd:COG5084    73 NTVACISRNFNSIRGSRLSTPNNHVNPVLSssVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSgPSC 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384072052 111 LFLHLKPVLKLQDCPWYN---QGFCKEGPLCKYRHVHQVL------CPNYFTGFCPEGPQ--------------CQFGHP 167
Cdd:COG5084   153 GYSHIDPDSFAGNCDQYSgatYGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTPsesvsswgygkgtsCSLSHP 232

                         170
                  ....*....|....*
gi 1384072052 168 KMS-----PPFHPSN 177
Cdd:COG5084   233 SLNidiqqPQTAPSR 247
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 36-177 2.33e-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: 94.94  E-value: 2.33e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384072052  36 SSSAVCNFFAKGLCVKGMLCPLRHEQGEKL--VVCKHWLRGLCRKSDCCDFLHQYDVSK--MPVCYFHSKFGNCSN-KEC 110
Cdd:COG5084    73 NTVACISRNFNSIRGSRLSTPNNHVNPVLSssVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSgPSC 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384072052 111 LFLHLKPVLKLQDCPWYN---QGFCKEGPLCKYRHVHQVL------CPNYFTGFCPEGPQ--------------CQFGHP 167
Cdd:COG5084   153 GYSHIDPDSFAGNCDQYSgatYGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTPsesvsswgygkgtsCSLSHP 232

                         170
                  ....*....|....*
gi 1384072052 168 KMS-----PPFHPSN 177
Cdd:COG5084   233 SLNidiqqPQTAPSR 247
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 41-117 1.10e-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: 40.52  E-value: 1.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384072052  41 CNFFAKGLCVKGMLCPLRHEQGE--KLVVCKHWLRGLCRKSdCCDFLH---QYDVSKMPvCYFHSKFGNCSNKECLFLHL 115
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHCEAAlgNETVCTLWQEGRCFRP-VCRFRHmeiDKNRKEIP-CYWENQPGGCQKPHCAFHHT 85


                  ..
gi 1384072052 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 ...
 36-177 2.33e-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: 94.94  E-value: 2.33e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384072052  36 SSSAVCNFFAKGLCVKGMLCPLRHEQGEKL--VVCKHWLRGLCRKSDCCDFLHQYDVSK--MPVCYFHSKFGNCSN-KEC 110
Cdd:COG5084    73 NTVACISRNFNSIRGSRLSTPNNHVNPVLSssVVCKFFLRGLCKSGFSCEFLHEYDLRSsqGPPCRSFSLKGSCSSgPSC 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384072052 111 LFLHLKPVLKLQDCPWYN---QGFCKEGPLCKYRHVHQVL------CPNYFTGFCPEGPQ--------------CQFGHP 167
Cdd:COG5084   153 GYSHIDPDSFAGNCDQYSgatYGFCPLGASCKFSHTLKRVsygsspCGNYTPPFSPPGTPsesvsswgygkgtsCSLSHP 232

                         170
                  ....*....|....*
gi 1384072052 168 KMS-----PPFHPSN 177
Cdd:COG5084   233 SLNidiqqPQTAPSR 247
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 41-117 1.10e-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: 40.52  E-value: 1.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384072052  41 CNFFAKGLCVKGMLCPLRHEQGE--KLVVCKHWLRGLCRKSdCCDFLH---QYDVSKMPvCYFHSKFGNCSNKECLFLHL 115
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHCEAAlgNETVCTLWQEGRCFRP-VCRFRHmeiDKNRKEIP-CYWENQPGGCQKPHCAFHHT 85


                  ..
gi 1384072052 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH