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CPSF4 cleavage and polyadenylation specific factor 4 [ Homo sapiens (human) ]

Gene ID: 10898, updated on 7-Jun-2020

Summary

Official Symbol
CPSF4provided by HGNC
Official Full Name
cleavage and polyadenylation specific factor 4provided by HGNC
Primary source
HGNC:HGNC:2327
See related
Ensembl:ENSG00000160917 MIM:603052
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NAR; NEB1; NEB-1; CPSF30
Summary
Inhibition of the nuclear export of poly(A)-containing mRNAs caused by the influenza A virus NS1 protein requires its effector domain. The NS1 effector domain functionally interacts with the cellular 30 kDa subunit of cleavage and polyadenylation specific factor 4, an essential component of the 3' end processing machinery of cellular pre-mRNAs. In influenza virus-infected cells, the NS1 protein is physically associated with cleavage and polyadenylation specific factor 4, 30kD subunit. Binding of the NS1 protein to the 30 kDa protein in vitro prevents CPSF binding to the RNA substrate and inhibits 3' end cleavage and polyadenylation of host pre-mRNAs. Thus the NS1 protein selectively inhibits the nuclear export of cellular, and not viral, mRNAs. Multiple alternatively spliced transcript variants that encode different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 7.2), lymph node (RPKM 4.8) and 25 other tissues See more
Orthologs

Genomic context

See CPSF4 in Genome Data Viewer
Location:
7q22.1
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (99438912..99457377)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99036563..99054996)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene microRNA 12119 Neighboring gene BUD31 homolog Neighboring gene ATP5MF-PTCD1 readthrough Neighboring gene pentatricopeptide repeat domain 1 Neighboring gene SAP domain containing ribonucleoprotein pseudogene Neighboring gene ATP synthase membrane subunit f Neighboring gene tRNA-Trp (anticodon CCA) 5-1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
mRNA 3'-end processing TAS
Traceable Author Statement
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
modification by virus of host mRNA processing TAS
Traceable Author Statement
more info
 
pre-mRNA cleavage required for polyadenylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tRNA splicing, via endonucleolytic cleavage and ligation TAS
Traceable Author Statement
more info
 
termination of RNA polymerase II transcription TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
mRNA cleavage and polyadenylation specificity factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA cleavage and polyadenylation specificity factor complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
cleavage and polyadenylation specificity factor subunit 4
Names
CPSF 30 kDa subunit
NS1 effector domain-binding protein 1
cleavage and polyadenylation specific factor 4, 30kDa
cleavage and polyadenylation specificity factor 30 kDa subunit
no arches homolog
no arches-like zinc finger protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001081559.2NP_001075028.1  cleavage and polyadenylation specificity factor subunit 4 isoform 2

    See identical proteins and their annotated locations for NP_001075028.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AA040394, AI076832, AW512538, BM757197, BM787372, BQ052009
    Consensus CDS
    CCDS47652.1
    UniProtKB/Swiss-Prot
    O95639
    Related
    ENSP00000395311.2, ENST00000436336.6
    Conserved Domains (2) summary
    COG5084
    Location:25176
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
    cl26688
    Location:201233
    DWNN; DWNN domain
  2. NM_001318160.1NP_001305089.1  cleavage and polyadenylation specificity factor subunit 4 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AW512538, BC003101, BC050738, BM757197
    UniProtKB/Swiss-Prot
    O95639
    Related
    ENSP00000396060.1, ENST00000451876.5
    Conserved Domains (2) summary
    COG5084
    Location:25176
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
    cl26688
    Location:200232
    DWNN; DWNN domain
  3. NM_001318161.1NP_001305090.1  cleavage and polyadenylation specificity factor subunit 4 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has multiple differences in the coding region, one of which results in a frameshift, compared to variant 1. The encoded isoform (4) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AW512538, BC003101, BE388179, BM757197
    UniProtKB/Swiss-Prot
    O95639
    Related
    ENSP00000392584.1, ENST00000452047.1
    Conserved Domains (2) summary
    smart00356
    Location:6388
    ZnF_C3H1; zinc finger
    COG5084
    Location:25159
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
  4. NM_001318162.1NP_001305091.1  cleavage and polyadenylation specificity factor subunit 4 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate 5'-terminal exon, uses an alternate splice site in the 3' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
    Source sequence(s)
    AK301745, AW512538, BC003101, BX358595
    Consensus CDS
    CCDS83205.1
    UniProtKB/Swiss-Prot
    O95639
    UniProtKB/TrEMBL
    B7Z7B0
    Related
    ENSP00000402224.1, ENST00000441580.5
    Conserved Domains (2) summary
    COG5084
    Location:2123
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
    COG5222
    Location:148180
    COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
  5. NM_006693.4NP_006684.1  cleavage and polyadenylation specificity factor subunit 4 isoform 1

    See identical proteins and their annotated locations for NP_006684.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA040394, BM757197, BQ641871, CX754488, U79569
    Consensus CDS
    CCDS5664.1
    UniProtKB/Swiss-Prot
    O95639
    Related
    ENSP00000292476.5, ENST00000292476.10
    Conserved Domains (2) summary
    COG5084
    Location:25211
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
    cl26688
    Location:226258
    DWNN; DWNN domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    99438912..99457377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011700.2XP_016867189.1  cleavage and polyadenylation specificity factor subunit 4 isoform X2

  2. XM_017011701.2XP_016867190.1  cleavage and polyadenylation specificity factor subunit 4 isoform X5

  3. XM_011515755.3XP_011514057.1  cleavage and polyadenylation specificity factor subunit 4 isoform X1

    Conserved Domains (2) summary
    smart00356
    Location:6388
    ZnF_C3H1; zinc finger
    COG5084
    Location:25161
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
  4. XM_011515757.2XP_011514059.1  cleavage and polyadenylation specificity factor subunit 4 isoform X4

    Conserved Domains (2) summary
    smart00356
    Location:6388
    ZnF_C3H1; zinc finger
    COG5084
    Location:25161
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
  5. XM_011515756.3XP_011514058.1  cleavage and polyadenylation specificity factor subunit 4 isoform X3

    Conserved Domains (2) summary
    smart00356
    Location:6388
    ZnF_C3H1; zinc finger
    COG5084
    Location:25161
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
  6. XM_017011702.1XP_016867191.1  cleavage and polyadenylation specificity factor subunit 4 isoform X6

  7. XM_017011703.2XP_016867192.1  cleavage and polyadenylation specificity factor subunit 4 isoform X6

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