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

Gene ID: 29894, updated on 17-Jun-2019

Summary

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
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
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

Genomic context

See CPSF1 in Genome Data Viewer
Location:
8q24.3
Exon count:
39
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (144393231..144409400, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145618446..145634733, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene solute carrier family 52 member 2 Neighboring gene uncharacterized LOC101928902 Neighboring gene aarF domain containing kinase 5 Neighboring gene microRNA 939 Neighboring gene microRNA 1234 Neighboring gene microRNA 6849 Neighboring gene solute carrier family 39 member 4 Neighboring gene VPS28 subunit of ESCRT-I

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

Phenotypes

NHGRI GWAS Catalog

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

HIV-1 interactions

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 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 ...
  • 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...
  • 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
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
mRNA 3'-UTR AU-rich region binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 polyadenylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA polyadenylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
pre-mRNA cleavage required for polyadenylation IC
Inferred by Curator
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
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
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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_024302907.1
XP_024302908.1
XP_024302909.1
XP_024302910.1

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_013291.3NP_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
    Related
    ENSP00000484669.1, ENST00000616140.2
    Conserved Domains (1) summary
    cl26526
    Location:11437
    CPSF_A; CPSF A subunit region

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.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    144393231..144409400 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006716548.2XP_006716611.1  cleavage and polyadenylation specificity factor subunit 1 isoform X2

    Conserved Domains (3) summary
    COG5161
    Location:11434
    SFT1; Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]
    pfam03178
    Location:10731405
    CPSF_A; CPSF A subunit region
    pfam10433
    Location:92674
    MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term
  2. XM_024447139.1XP_024302907.1  cleavage and polyadenylation specificity factor subunit 1 isoform X1

    Conserved Domains (1) summary
    cl26526
    Location:11463
    CPSF_A; CPSF A subunit region
  3. XM_024447141.1XP_024302909.1  cleavage and polyadenylation specificity factor subunit 1 isoform X3

    Conserved Domains (1) summary
    cl26526
    Location:231385
    CPSF_A; CPSF A subunit region
  4. XM_024447142.1XP_024302910.1  cleavage and polyadenylation specificity factor subunit 1 isoform X3

    Conserved Domains (1) summary
    cl26526
    Location:231385
    CPSF_A; CPSF A subunit region
  5. XM_024447140.1XP_024302908.1  cleavage and polyadenylation specificity factor subunit 1 isoform X3

    Conserved Domains (1) summary
    cl26526
    Location:231385
    CPSF_A; CPSF A subunit region

Reference GRCh38.p13 PATCHES

Genomic

  1. NW_018654716.1 Reference GRCh38.p13 PATCHES

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