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

    Gene ID: 10898, updated on 17-Jun-2024

    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; AllianceGenome:HGNC:2327
    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
    NEW
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    Try the new Transcript table

    Genomic context

    See CPSF4 in Genome Data Viewer
    Location:
    7q22.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (99438943..99457373)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (100677844..100696279)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99036566..99054996)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene BUD31 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18409 Neighboring gene ATP5MF-PTCD1 readthrough Neighboring gene pentatricopeptide repeat domain 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99020619-99021120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99027477-99028073 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:99032915-99033062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99034189-99034714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18410 Neighboring gene SAP domain containing ribonucleoprotein pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99049670-99050230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99053345-99054147 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99058948-99059448 Neighboring gene ATP synthase membrane subunit f Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99062959-99063576 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99063577-99064192 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    part_of mRNA cleavage and polyadenylation specificity factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of mRNA cleavage and polyadenylation specificity factor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in 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)

    NEW Try the new Transcript table

    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_001081559.3NP_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, BM757197, BM787372, BQ052009
      Consensus CDS
      CCDS47652.1
      UniProtKB/TrEMBL
      C9JEV9
      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]
      COG5222
      Location:201233
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
    2. NM_001318160.2NP_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)
      BC003101, BC050738, BM757197
      UniProtKB/TrEMBL
      C9JEV9
      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]
      COG5222
      Location:200232
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
    3. NM_001318161.2NP_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)
      BC003101, BE388179, BM757197
      UniProtKB/TrEMBL
      H7C016
      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_001318162.2NP_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, BC003101
      Consensus CDS
      CCDS83205.1
      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
      D6W5S8, O95639, Q6FGE6, Q86TF8, Q9BTW6
      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]
      COG5222
      Location:226258
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      99438943..99457373
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      Conserved Domains (2) summary
      COG5084
      Location:25161
      YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
      COG5222
      Location:231263
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
    2. XM_011515756.4XP_011514058.1  cleavage and polyadenylation specificity factor subunit 4 isoform X2

      UniProtKB/TrEMBL
      C9JEV9
      Conserved Domains (2) summary
      COG5084
      Location:25161
      YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
      COG5222
      Location:206238
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
    3. XM_011515757.3XP_011514059.1  cleavage and polyadenylation specificity factor subunit 4 isoform X3

      UniProtKB/TrEMBL
      C9JEV9
      Conserved Domains (2) summary
      COG5084
      Location:25161
      YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
      COG5222
      Location:205237
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
    4. XM_047419827.1XP_047275783.1  cleavage and polyadenylation specificity factor subunit 4 isoform X7

    5. XM_047419824.1XP_047275780.1  cleavage and polyadenylation specificity factor subunit 4 isoform X4

    6. XM_047419825.1XP_047275781.1  cleavage and polyadenylation specificity factor subunit 4 isoform X5

    7. XM_047419826.1XP_047275782.1  cleavage and polyadenylation specificity factor subunit 4 isoform X6

    8. XM_017011703.3XP_016867192.1  cleavage and polyadenylation specificity factor subunit 4 isoform X4

      Conserved Domains (2) summary
      COG5084
      Location:2108
      YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
      COG5222
      Location:178210
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      100677844..100696279
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357141.1XP_054213116.1  cleavage and polyadenylation specificity factor subunit 4 isoform X1

    2. XM_054357142.1XP_054213117.1  cleavage and polyadenylation specificity factor subunit 4 isoform X2

      UniProtKB/TrEMBL
      C9JEV9
    3. XM_054357143.1XP_054213118.1  cleavage and polyadenylation specificity factor subunit 4 isoform X3

      UniProtKB/TrEMBL
      C9JEV9
    4. XM_054357148.1XP_054213123.1  cleavage and polyadenylation specificity factor subunit 4 isoform X7

    5. XM_054357144.1XP_054213119.1  cleavage and polyadenylation specificity factor subunit 4 isoform X4

    6. XM_054357146.1XP_054213121.1  cleavage and polyadenylation specificity factor subunit 4 isoform X5

    7. XM_054357147.1XP_054213122.1  cleavage and polyadenylation specificity factor subunit 4 isoform X6

    8. XM_054357145.1XP_054213120.1  cleavage and polyadenylation specificity factor subunit 4 isoform X4