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    CPSF2 cleavage and polyadenylation specific factor 2 [ Homo sapiens (human) ]

    Gene ID: 53981, updated on 28-Oct-2024

    Summary

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    Official Symbol
    CPSF2provided by HGNC
    Official Full Name
    cleavage and polyadenylation specific factor 2provided by HGNC
    Primary source
    HGNC:HGNC:2325
    See related
    Ensembl:ENSG00000165934 MIM:606028; AllianceGenome:HGNC:2325
    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
    CPSF100
    Summary
    Predicted to enable RNA binding activity. Involved in mRNA 3'-end processing by stem-loop binding activity and cleavage. Located in membrane. Part of mRNA cleavage and polyadenylation specificity factor complex. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in testis (RPKM 13.0), thyroid (RPKM 12.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CPSF2 in Genome Data Viewer
    Location:
    14q32.12
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (92121969..92172145)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (86351804..86401990)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (92588313..92638489)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903363 Neighboring gene MPRA-validated peak2235 silencer Neighboring gene MPRA-validated peak2236 silencer Neighboring gene ataxin 3 repeat instability region Neighboring gene ataxin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6031 Neighboring gene NANOG hESC enhancer GRCh37_chr14:92566141-92566677 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:92572215-92573149 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:92574354-92575164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:92586481-92587470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8927 Neighboring gene NADH:ubiquinone oxidoreductase subunit B1 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:92624044-92624245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92673090-92673696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92673697-92674303 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:92719434-92719934 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:92719935-92720435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8929 Neighboring gene RNA, U6 small nuclear 366, pseudogene Neighboring gene uncharacterized LOC105370627

    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 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. Assembly of a processive messenger RNA polyadenylation complex. Bienroth S, et al. EMBO J, 1993 Feb. PMID 8440247, Free PMC Article
    2. Negative Expression of CPSF2 Predicts a Poorer Clinical Outcome in Patients with Papillary Thyroid Carcinoma. Sung TY, et al. Thyroid, 2015 Sep. PMID 26148673
    3. Assignment of the 100-kDa subunit of cleavage and polyadenylation specificity factor (CPSF2) to human chromosome 14q31.3 by radiation hybrid mapping. Samiotaki M, et al. Cytogenet Cell Genet, 2000. PMID 11124543
    4. Loss of CPSF2 expression is associated with increased thyroid cancer cellular invasion and cancer stem cell population, and more aggressive disease. Nilubol N, et al. J Clin Endocrinol Metab, 2014 Jul. PMID 24654752, Free PMC Article
    5. CPEB phosphorylation and cytoplasmic polyadenylation are catalyzed by the kinase IAK1/Eg2 in maturing mouse oocytes. Hodgman R, et al. Development, 2001 Jul. PMID 11526086

    See all (126) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CPSF2 may have a role in Papillary Thyroid Carcinoma
      Title: Negative Expression of CPSF2 Predicts a Poorer Clinical Outcome in Patients with Papillary Thyroid Carcinoma.
    2. CPSF2 and SYMPK, are RBFOX2 cofactors for both inclusion and exclusion of internal exons.
      Title: Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors.
    3. Decreased CPSF2 expression is associated with increased cellular invasion and cancer stem cell population, and more aggressive disease in papillary thyroid cancer.
      Title: Loss of CPSF2 expression is associated with increased thyroid cancer cellular invasion and cancer stem cell population, and more aggressive disease.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
    5. Conserved residues in CPSF2 and CPSF-73 are required for assembly of the endonuclease activity that cleaves histone pre-mRNAs.
      Title: Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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
    Rev rev HIV-1 Rev interacting protein, cleavage and polyadenylation specific factor 2 (CPSF2), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with CPSF2 is increased by RRE 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

    Clone Names

    • KIAA1367

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA 3'-end processing by stem-loop binding and cleavage IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA 3'-end processing by stem-loop binding and cleavage IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    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 membrane HDA PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cleavage and polyadenylation specificity factor subunit 2
    Names
    CPSF 100 kDa subunit
    CPSF 100kDa subunit
    cleavage and polyadenylation specific factor 2, 100kDa
    cleavage and polyadenylation specificity factor 100 kDa subunit

    NCBI Reference Sequences (RefSeq)

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    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_001322270.2 → NP_001309199.1  cleavage and polyadenylation specificity factor subunit 2 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL121773
      UniProtKB/TrEMBL
      B3KN45
      Conserved Domains (4) summary
      smart01027
      Location:243 → 368
      Beta-Casp; Beta-Casp domain
      cd16293
      Location:7 → 204
      CPSF2-like_MBL-fold; cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; MBL-fold metallo-hydrolase domain
      pfam13299
      Location:557 → 728
      CPSF100_C; Cleavage and polyadenylation factor 2 C-terminal
      pfam07521
      Location:480 → 540
      RMMBL; Zn-dependent metallo-hydrolase RNA specificity domain

    2. NM_001322271.2 → NP_001309200.1  cleavage and polyadenylation specificity factor subunit 2 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL121773
      UniProtKB/TrEMBL
      B3KN45
      Conserved Domains (4) summary
      smart01027
      Location:90 → 215
      Beta-Casp; Beta-Casp domain
      pfam07521
      Location:376 → 438
      RMMBL; Zn-dependent metallo-hydrolase RNA specificity domain
      pfam13299
      Location:455 → 626
      CPSF100_C; Cleavage and polyadenylation factor 2 C-terminal
      cl23716
      Location:1 → 51
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

    3. NM_001322272.2 → NP_001309201.1  cleavage and polyadenylation specificity factor subunit 2 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL121773
      Consensus CDS
      CCDS9902.1
      UniProtKB/Swiss-Prot
      B3KME1, Q6NSJ1, Q9H3W7, Q9P2I0
      UniProtKB/TrEMBL
      B3KN45
      Conserved Domains (4) summary
      smart01027
      Location:243 → 368
      Beta-Casp; Beta-Casp domain
      cd16293
      Location:7 → 204
      CPSF2-like_MBL-fold; cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; MBL-fold metallo-hydrolase domain
      pfam07521
      Location:529 → 591
      RMMBL; Zn-dependent metallo-hydrolase RNA specificity domain
      pfam13299
      Location:608 → 779
      CPSF100_C; Cleavage and polyadenylation factor 2 C-terminal

    4. NM_017437.3 → NP_059133.1  cleavage and polyadenylation specificity factor subunit 2 isoform 1

      See identical proteins and their annotated locations for NP_059133.1

      Status: VALIDATED

      Source sequence(s)
      AB037788, AL121773, BC060854, BC070095, DB081880
      Consensus CDS
      CCDS9902.1
      UniProtKB/Swiss-Prot
      B3KME1, Q6NSJ1, Q9H3W7, Q9P2I0
      UniProtKB/TrEMBL
      B3KN45
      Related
      ENSP00000298875.4, ENST00000298875.9
      Conserved Domains (4) summary
      smart01027
      Location:243 → 368
      Beta-Casp; Beta-Casp domain
      cd16293
      Location:7 → 204
      CPSF2-like_MBL-fold; cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; MBL-fold metallo-hydrolase domain
      pfam07521
      Location:529 → 591
      RMMBL; Zn-dependent metallo-hydrolase RNA specificity domain
      pfam13299
      Location:608 → 779
      CPSF100_C; Cleavage and polyadenylation factor 2 C-terminal

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      92121969..92172145
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      86351804..86401990
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P2I0.2 GenPept UniProtKB/Swiss-Prot:Q9P2I0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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