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

    Gene ID: 29894, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See CPSF1 in Genome Data Viewer
    Location:
    8q24.3
    Exon count:
    43
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144393231..144409335, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145562868..145579148, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. 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
    3. 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
    4. 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
    5. Cleavage and polyadenylation factor CPF specifically interacts with the pre-mRNA 3' processing signal AAUAAA. Keller W, et al. EMBO J, 1991 Dec. PMID 1756731, Free PMC Article

    See all (140) 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
    		Compare labs

    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)

    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 
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    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_2024_08

    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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