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CPSF1 cleavage and polyadenylation specific factor 1 [ Homo sapiens (human) ]

Gene ID: 29894, updated on 11-Apr-2024

Summary

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Official Symbol
CPSF1provided by HGNC
Official Full Name
cleavage and polyadenylation specific factor 1provided by HGNC
Primary source
HGNC:HGNC:2324
See related
Ensembl:ENSG00000071894 MIM:606027; AllianceGenome:HGNC:2324
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
MYP27; CPSF160; P/cl.18; HSU37012
Summary
Cleavage and polyadenylation specificity factor (CPSF) is a multisubunit complex that plays a central role in 3-prime processing of pre-mRNAs. CPSF recognizes the AAUAAA signal in the pre-mRNA and interacts with other proteins to facilitate both RNA cleavage and poly(A) synthesis. CPSF1 is the largest subunit of the CPSF complex (Murthy and Manley, 1995 [PubMed 7590244]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in testis (RPKM 31.8), duodenum (RPKM 25.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
8q24.3
Exon count:
43
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144393231..144409335, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145562868..145579148, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145618446..145634719, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145583746-145584281 Neighboring gene solute carrier family 52 member 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145589246-145589414 Neighboring gene uncharacterized LOC101928902 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:145593027-145593528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145595436-145595936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19680 Neighboring gene aarF domain containing kinase 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145613649-145614150 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145619396-145619557 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145620910-145621123 Neighboring gene microRNA 939 Neighboring gene microRNA 1234 Neighboring gene microRNA 6849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28098 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145638844-145639041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145639267-145640084 Neighboring gene uncharacterized LOC124902041 Neighboring gene solute carrier family 39 member 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145647393-145648164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145648165-145648934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145651263-145652026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19684 Neighboring gene VPS28 subunit of ESCRT-I

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Clerici M, et al. Nat Struct Mol Biol, 2018 Feb. PMID 29358758, Free PMC Article
  2. Targeting cleavage and polyadenylation specific factor 1 via shRNA inhibits cell proliferation in human ovarian cancer. Zhang B, et al. J Biosci, 2017 Sep. PMID 29358555
  3. Cleavage and polyadenylation specificity factor (CPSF)-derived peptides can induce HLA-A2-restricted and tumor-specific CTLs in the majority of gastrointestinal cancer patients. Maeda Y, et al. Int J Cancer, 2002 May 20. PMID 11992410
  4. Assignment of the 160-kDa subunit of cleavage and polyadenylation specificity factor (CPSF1) to human chromosome 8q24.23 by radiation hybrid mapping. Samiotaki M, et al. Cytogenet Cell Genet, 2000. PMID 11124521
  5. m(6)A-induced repression of SIAH1 facilitates alternative splicing of androgen receptor variant 7 by regulating CPSF1. Xia L, et al. Mol Ther Nucleic Acids, 2022 Jun 14. PMID 35402071, Free PMC Article

See all (115) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration.
    Title: Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration.
  2. Heterozygous loss-of-function mutations in CPSF1 are associated with early-onset high myopia and that CPSF1 may play an important role in the development of retinal ganglion cell axon projection.
    Title: CPSF1 mutations are associated with early-onset high myopia and involved in retinal ganglion cell axon projection.
  3. cryo-electron microscopic analysis of a core CPSF module bound to the polyadenylation signal hexamer motif
    Title: Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex.
  4. Knockdown of CPSF inhibits the proliferation, migration and invasion of ovarian carcinoma cells.
    Title: Targeting cleavage and polyadenylation specific factor 1 via shRNA inhibits cell proliferation in human ovarian cancer.
  5. The authors define the molecular architecture of the core human CPSF complex comprising CPSF160, WDR33, CPSF30 and Fip1 and identify specific domains involved in inter-subunit interactions. Together, these results shed light on the function of CPSF in mediating polyA signal-dependent RNA cleavage and polyadenylation.
    Title: Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex.
  6. CPSF1 was identified among protein-binding candidates. A consensus polyadenylation signal AAUAAA is present in intron 6 of IL7 receptor directly downstream from the 5' splice site. Mutations to this site and CPSF1 knockdown increased exon 6 inclusion.
    Title: Cleavage and polyadenylation specificity factor 1 (CPSF1) regulates alternative splicing of interleukin 7 receptor (IL7R) exon 6.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Myopia 27
MedGen: C5394215 OMIM: 618827 GeneReviews: Not available
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EBI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify cleavage and polyadenylation specific factor 1 (CPSF1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify cleavage and polyadenylation specific factor 1 (CPSF1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify cleavage and polyadenylation specific factor 1 (CPSF1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify cleavage and polyadenylation specific factor 1 (CPSF1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables mRNA 3'-UTR AU-rich region binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway IC
Inferred by Curator
more info
 PubMed 
Component Evidence Code Pubs
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
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
cleavage and polyadenylation specificity factor subunit 1
Names
CPSF 160 kDa subunit
cleavage and polyadenylation specific factor 1, 160kDa
cleavage and polyadenylation specificity factor 160 kDa subunit
polyadenylation specificity factor
NP_037423.2
XP_006716611.1
XP_047277688.1
XP_047277689.1
XP_047277690.1
XP_047277691.1
XP_047277692.1
XP_054188162.1
XP_054188163.1
XP_054188164.1
XP_054188165.1
XP_054188166.1
XP_054188167.1
XP_054216355.1
XP_054216356.1
XP_054216357.1
XP_054216358.1
XP_054216359.1
XP_054216360.1
XP_054216361.1
XP_054216362.1

NCBI Reference Sequences (RefSeq)

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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_013291.3 → NP_037423.2  cleavage and polyadenylation specificity factor subunit 1

    See identical proteins and their annotated locations for NP_037423.2

    Status: VALIDATED

    Source sequence(s)
    BC017232, CD299980
    Consensus CDS
    CCDS34966.1
    UniProtKB/Swiss-Prot
    Q10570, Q96AF0
    Related
    ENSP00000484669.1, ENST00000616140.2
    Conserved Domains (1) summary
    COG5161
    Location:1 → 1437
    SFT1; Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    144393231..144409335 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006716548.3 → XP_006716611.1  cleavage and polyadenylation specificity factor subunit 1 isoform X1

    Conserved Domains (1) summary
    COG5161
    Location:1 → 1434
    SFT1; Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]

  2. XM_047421733.1 → XP_047277689.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  3. XM_047421735.1 → XP_047277691.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  4. XM_047421734.1 → XP_047277690.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  5. XM_047421732.1 → XP_047277688.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  6. XM_047421736.1 → XP_047277692.1  cleavage and polyadenylation specificity factor subunit 1 isoform X3

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654716.1 Reference GRCh38.p14 PATCHES

    Range
    123834..139938 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332187.1 → XP_054188162.1  cleavage and polyadenylation specificity factor subunit 1 isoform X1

  2. XM_054332191.1 → XP_054188166.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  3. XM_054332190.1 → XP_054188165.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  4. XM_054332189.1 → XP_054188164.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  5. XM_054332188.1 → XP_054188163.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  6. XM_054332192.1 → XP_054188167.1  cleavage and polyadenylation specificity factor subunit 1 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    145562868..145579148 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054360382.1 → XP_054216357.1  cleavage and polyadenylation specificity factor subunit 1 isoform X5

  2. XM_054360380.1 → XP_054216355.1  cleavage and polyadenylation specificity factor subunit 1 isoform X4

  3. XM_054360381.1 → XP_054216356.1  cleavage and polyadenylation specificity factor subunit 1 isoform X1

  4. XM_054360386.1 → XP_054216361.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  5. XM_054360385.1 → XP_054216360.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  6. XM_054360384.1 → XP_054216359.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  7. XM_054360383.1 → XP_054216358.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

  8. XM_054360387.1 → XP_054216362.1  cleavage and polyadenylation specificity factor subunit 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q10570.2 GenPept UniProtKB/Swiss-Prot:Q10570

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