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CSTF2 cleavage stimulation factor subunit 2 [ Homo sapiens (human) ]

Gene ID: 1478, updated on 7-Apr-2024

Summary

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Official Symbol
CSTF2provided by HGNC
Official Full Name
cleavage stimulation factor subunit 2provided by HGNC
Primary source
HGNC:HGNC:2484
See related
Ensembl:ENSG00000101811 MIM:300907; AllianceGenome:HGNC:2484
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CSTF64; CstF-64; XLID113
Summary
This gene encodes a nuclear protein with an RRM (RNA recognition motif) domain. The protein is a member of the cleavage stimulation factor (CSTF) complex that is involved in the 3' end cleavage and polyadenylation of pre-mRNAs. Specifically, this protein binds GU-rich elements within the 3'-untranslated region of mRNAs. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in esophagus (RPKM 6.8), testis (RPKM 6.5) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
Xq22.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (100820391..100841520)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (99262925..99284058)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (100075380..100096509)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:100059685-100060282 Neighboring gene peptidylprolyl isomerase A pseudogene 89 Neighboring gene RAD21 pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:100067081-100067582 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:100067583-100068082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29803 Neighboring gene small nucleolar RNA SNORA9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29805 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 26 Neighboring gene NADPH oxidase 1 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 27 Neighboring gene XK related X-linked

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. Cleavage stimulation factor 2 promotes malignant progression of liver hepatocellular carcinoma by activating phosphatidylinositol 3'-kinase/protein kinase B/mammalian target of rapamycin pathway. Zhang MH, et al. Bioengineered, 2022 Apr. PMID 35412944, Free PMC Article
  2. CstF64-Induced Shortening of the BID 3'UTR Promotes Esophageal Squamous Cell Carcinoma Progression by Disrupting ceRNA Cross-talk with ZFP36L2. Lin A, et al. Cancer Res, 2021 Nov 15. PMID 34607841
  3. A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans. Grozdanov PN, et al. Nucleic Acids Res, 2020 Sep 25. PMID 32816001, Free PMC Article
  4. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Xia Z, et al. Nat Commun, 2014 Nov 20. PMID 25409906, Free PMC Article
  5. Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Yao C, et al. Proc Natl Acad Sci U S A, 2012 Nov 13. PMID 23112178, Free PMC Article

See all (115) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CSTF2 mediated mRNA N[6]-methyladenosine modification drives pancreatic ductal adenocarcinoma m[6]A subtypes.
    Title: CSTF2 mediated mRNA N(6)-methyladenosine modification drives pancreatic ductal adenocarcinoma m(6)A subtypes.
  2. Alternative polyadenylation writer CSTF2 forms a positive loop with FGF2 to promote tubular epithelial-mesenchymal transition and renal fibrosis.
    Title: Alternative polyadenylation writer CSTF2 forms a positive loop with FGF2 to promote tubular epithelial-mesenchymal transition and renal fibrosis.
  3. Cleavage stimulation factor 2 promotes malignant progression of liver hepatocellular carcinoma by activating phosphatidylinositol 3'-kinase/protein kinase B/mammalian target of rapamycin pathway.
    Title: Cleavage stimulation factor 2 promotes malignant progression of liver hepatocellular carcinoma by activating phosphatidylinositol 3'-kinase/protein kinase B/mammalian target of rapamycin pathway.
  4. CstF64-Induced Shortening of the BID 3'UTR Promotes Esophageal Squamous Cell Carcinoma Progression by Disrupting ceRNA Cross-talk with ZFP36L2.
    Title: CstF64-Induced Shortening of the BID 3'UTR Promotes Esophageal Squamous Cell Carcinoma Progression by Disrupting ceRNA Cross-talk with ZFP36L2.
  5. A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans.
    Title: A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans.
  6. CSTF2 exerts critical roles in activation of RAC1 by promoting 3'UTR shortening of RAC1 mRNAs through two transcription elongation factors, AFF1 and AFF4, in urothelial carcinoma of the bladder pathogenesis
    Title: CSTF2-Induced Shortening of the RAC1 3'UTR Promotes the Pathogenesis of Urothelial Carcinoma of the Bladder.
  7. Reverse genetics and nuclear magnetic resonance studies of recombinant CstF-64 (RRM-Hinge) and CstF-77 (monkeytail-carboxy-terminal domain) indicate that the last 30 amino acids of CstF-77 increases the stability of the RRM, thus altering the affinity of the complex for RNA. These results provide new insights into the mechanism by which CstF regulates the location of the RNA cleavage site during Cleavage/polyadenylation.
    Title: The structural basis of CstF-77 modulation of cleavage and polyadenylation through stimulation of CstF-64 activity.
  8. The findings demonstrate that constitutive Tip110 expression in human cord blood CD34(+) cells is regulated, at least in part, through its interaction with CstF64, recruitment of CstF64 to, and selective usage of two polyadenylation sites within its 3'UTR.
    Title: Regulation of Constitutive Tip110 Expression in Human Cord Blood CD34(+) Cells Through Selective Usage of the Proximal and Distal Polyadenylation Sites Within the 3'Untranslated Region.
  9. hnRNP H binds to two specific G-runs in exon 5a of ACHE and activates the distal alternative 3 splice site (ss) between exons 5a and 5b. Furthermore, hnRNP H competes for binding of CstF64 to the overlapping binding sites in exon 5a, and suppresses the selection of a cryptic polyadenylation site, which additionally ensures transcription of the distal 3 ss required for the generation of AChET isoform.
    Title: Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms.
  10. CstF-64 is dispensable for the expression/3'-end processing of Star-PAP target mRNAs.CstF-64 and 3'-UTR cis-element determine Star-PAP specificity for target mRNA selection by excluding poly A polymerase.
    Title: CstF-64 and 3'-UTR cis-element determine Star-PAP specificity for target mRNA selection by excluding PAPα.
Submit: New GeneRIF Correction See all GeneRIFs (21)

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
Intellectual developmental disorder, x-linked 113
MedGen: CN376362 OMIM: 301116 GeneReviews: Not available
not available

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 stimulation factor, subunit 2 (CSTF2), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with CSTF2 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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables mRNA 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 cellular response to nerve growth factor stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA 3'-end processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cleavage body IDA
Inferred from Direct Assay
more info
 PubMed 
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 nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
cleavage stimulation factor subunit 2
Names
CF-1 64 kDa subunit
CSTF 64 kDa subunit
cleavage stimulation factor 64 kDa subunit
cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kD
cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa

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.

Genomic

  1. NG_015848.1 RefSeqGene

    Range
    5033..26162
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001306206.2 → NP_001293135.1  cleavage stimulation factor subunit 2 isoform 1

    See identical proteins and their annotated locations for NP_001293135.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AI826277, AK095684, AK300600, BX384743, EU616679
    Consensus CDS
    CCDS78498.1
    UniProtKB/TrEMBL
    B3V096, E7EWR4
    Related
    ENSP00000387996.2, ENST00000415585.7
    Conserved Domains (5) summary
    TIGR01628
    Location:4 → 352
    PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
    PRK14718
    Location:412 → 469
    PRK14718; ribonuclease III; Provisional
    cd12671
    Location:18 → 92
    RRM_CSTF2_CSTF2T; RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins
    pfam14304
    Location:553 → 593
    CSTF_C; Transcription termination and cleavage factor C-terminal
    pfam14327
    Location:112 → 191
    CSTF2_hinge; Hinge domain of cleavage stimulation factor subunit 2

  2. NM_001306209.2 → NP_001293138.1  cleavage stimulation factor subunit 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region and lacks an alternate in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
    Source sequence(s)
    AI826277, AK300600, BC033135, BX384743
    UniProtKB/TrEMBL
    B4DUD5
    Conserved Domains (4) summary
    PRK07764
    Location:202 → 419
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    cd12671
    Location:18 → 92
    RRM_CSTF2_CSTF2T; RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins
    pfam14304
    Location:516 → 556
    CSTF_C; Transcription termination and cleavage factor C-terminal
    pfam14327
    Location:112 → 191
    CSTF2_hinge; Hinge domain of cleavage stimulation factor subunit 2

  3. NM_001325.3 → NP_001316.1  cleavage stimulation factor subunit 2 isoform 2

    See identical proteins and their annotated locations for NP_001316.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AW016125, M85085, Z83819, Z95327
    Consensus CDS
    CCDS14473.1
    UniProtKB/Swiss-Prot
    P33240, Q5H951, Q6LA74, Q8N502
    UniProtKB/TrEMBL
    B4DUD5
    Related
    ENSP00000362063.2, ENST00000372972.7
    Conserved Domains (5) summary
    TIGR01628
    Location:5 → 318
    PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
    PRK07764
    Location:241 → 436
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    cd12671
    Location:18 → 92
    RRM_CSTF2_CSTF2T; RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins
    pfam14304
    Location:533 → 573
    CSTF_C; Transcription termination and cleavage factor C-terminal
    pfam14327
    Location:112 → 191
    CSTF2_hinge; Hinge domain of cleavage stimulation factor subunit 2

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    100820391..100841520
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047441854.1 → XP_047297810.1  cleavage stimulation factor subunit 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    99262925..99284058
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326526.1 → XP_054182501.1  cleavage stimulation factor subunit 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P33240.1 GenPept UniProtKB/Swiss-Prot:P33240

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