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

Gene ID: 10898, updated on 6-Jan-2019

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 current GRCh38.p12 (GCF_000001405.38) 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 actin related protein 2/3 complex subunit 1B Neighboring gene PDGFA associated protein 1 Neighboring gene ATP5MF-PTCD1 readthrough Neighboring gene BUD31 homolog Neighboring gene pentatricopeptide repeat domain 1 Neighboring gene SAP domain containing ribonucleoprotein pseudogene Neighboring gene ATP synthase membrane subunit f Neighboring gene transfer RNA-Trp (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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Cleavage of Growing Transcript in the Termination Region, organism-specific biosystem (from REACTOME)
    Cleavage of Growing Transcript in the Termination Region, organism-specific biosystemThis section includes the cleavage of both polyadenylated and non-polyadenylated transcripts. In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is ...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Host Interactions with Influenza Factors, organism-specific biosystem (from REACTOME)
    Host Interactions with Influenza Factors, organism-specific biosystemInfection of a human host cell with influenza virus triggers an array of host processes that interfere with viral replication, notably the production of type I interferon. The viral NS1 protein plays...
  • Infectious disease, organism-specific biosystem (from REACTOME)
    Infectious disease, organism-specific biosystem
    Infectious disease
  • Influenza A, organism-specific biosystem (from KEGG)
    Influenza A, organism-specific biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Influenza A, conserved biosystem (from KEGG)
    Influenza A, conserved biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Influenza Infection, organism-specific biosystem (from REACTOME)
    Influenza Infection, organism-specific biosystemFor centuries influenza epidemics have plagued man, and influenza was probably the disease described by Hippocrates in 412 BC. Today it remains a major cause of morbidity and mortality worldwide with...
  • Inhibition of Host mRNA Processing and RNA Silencing, organism-specific biosystem (from REACTOME)
    Inhibition of Host mRNA Processing and RNA Silencing, organism-specific biosystemThe Influenza Virus NS1 protein inhibits the cleavage and polyadenylation specificity factor CPSF and the PABII components of the host cell 3' end processing machinery, preventing efficient 3' end pr...
  • NS1 Mediated Effects on Host Pathways, organism-specific biosystem (from REACTOME)
    NS1 Mediated Effects on Host Pathways, organism-specific biosystemViral NS1 protein is a nuclear, dimeric protein that is highly expressed in infected cells and has dsRNA-binding activity. The RNA-binding domain lies within the N-terminal portion of the protein. Th...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Processing of Capped Intronless Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intronless Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Processing of Intronless Pre-mRNAs, organism-specific biosystem (from REACTOME)
    Processing of Intronless Pre-mRNAs, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3' processing consists of two steps: The mRNA is first cleaved ...
  • RNA Polymerase II Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription, organism-specific biosystem
    RNA Polymerase II Transcription
  • RNA Polymerase II Transcription Termination, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription Termination, organism-specific biosystemThe detailed annotation of this section will be completed in the next release.
  • Transport of Mature Transcript to Cytoplasm, organism-specific biosystem (from REACTOME)
    Transport of Mature Transcript to Cytoplasm, organism-specific biosystemTransport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this tran...
  • Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing.
  • Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystemTransport of mature mRNAs derived from intronless transcripts require some of the same protein complexes as mRNAs derived from intron containing complexes, including TAP and Aly/Ref. However a number...
  • mRNA 3'-end processing, organism-specific biosystem (from REACTOME)
    mRNA 3'-end processing, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first ...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
    mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • mRNA surveillance pathway, conserved biosystem (from KEGG)
    mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • tRNA processing, organism-specific biosystem (from REACTOME)
    tRNA processing, organism-specific biosystemGenes encoding transfer RNAs (tRNAs) are transcribed by RNA polymerase III in the nucleus and by mitochondrial RNA polymerase in the mitochondrion.In the nucleus transcription reactions produce precu...
  • tRNA processing in the nucleus, organism-specific biosystem (from REACTOME)
    tRNA processing in the nucleus, organism-specific biosystemGenes encoding transfer RNAs are transcribed in the nucleus by RNA polymerase III. (Distinct processes of transcription and processing also occur in mitochondria.) The initial transcripts, pre-tRNAs,...

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 
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]
    cl26688
    Location:148180
    DWNN; DWNN domain
  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, ENST00000292476.9
    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 Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p12 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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