CPSF7 cleavage and polyadenylation specific factor 7 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CPSF7provided by HGNC
Official Full Name: cleavage and polyadenylation specific factor 7provided by HGNC
Primary source: HGNC:HGNC:30098
See related: Ensembl:ENSG00000149532 AllianceGenome:HGNC:30098
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: CFIm59
Summary: Cleavage factor Im (CFIm) is one of six factors necessary for correct cleavage and polyadenylation of pre-mRNAs. CFIm is composed of three different subunits of 25, 59, and 68 kDa, and it functions as a heterotetramer, with a dimer of the 25 kDa subunit binding to two of the 59 or 68 kDa subunits. The protein encoded by this gene represents the 59 kDa subunit, which can interact with the splicing factor U2 snRNP Auxiliary Factor (U2AF) 65 to link the splicing and polyadenylation complexes. [provided by RefSeq, Oct 2016]
Expression: Ubiquitous expression in ovary (RPKM 25.0), testis (RPKM 24.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q12.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (61402729..61429975, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (61391627..61418874, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (61170201..61197447, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CPSF7 promoted WWP2-FL due to the presence of PTEN ubiquitination sites in this longer transcript and regulates liver cancer growth by targeting WWP2-FL that in turn regulates AKT activation in a PTEN-dependent manner.
Title: CPSF7 regulates liver cancer growth and metastasis by facilitating WWP2-FL and targeting the WWP2/PTEN/AKT signaling pathway.
The authors demonstrate that CFIm functions as an enhancer-dependent activator of mRNA 3' processing. CFIm regulates global alternative polyadenylation by specifically binding and activating enhancer-containing poly(A) sites.
Title: Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.
Data provide evidence that CFIm exists as a heterotetramer of 25-kD, 59-kD and 68-kD subunits of CFIm: CFIm25, CFIm59 and CFIm68.
Title: Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation.

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

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 59kDa cleavage and polyadenylation specific factor 7 (CPSF7), 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 59kDa cleavage and polyadenylation specific factor 7 (CPSF7), 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 59kDa cleavage and polyadenylation specific factor 7 (CPSF7), 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 59kDa cleavage and polyadenylation specific factor 7 (CPSF7), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Rev	rev	HIV-1 Rev interacting protein, cleavage and polyadenylation specific factor 7 (CPSF7), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa. The interaction of Rev with CPSF7 is increased by RRE	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48364 (e-PCR)
- UniSTS:43790

WI-16090 (e-PCR)
- UniSTS:71190

Bda87b01 (e-PCR)
- UniSTS:5144

RH12455 (e-PCR)
- UniSTS:22438

WI-17061 (e-PCR)
- UniSTS:1711

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA 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 mRNA 3'-end processing	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA alternative polyadenylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA alternative polyadenylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein heterotetramerization	IDA Inferred from Direct Assay more info	PubMed
involved_in protein tetramerization	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	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
part_of mRNA cleavage factor complex	IDA Inferred from Direct Assay more info	PubMed
part_of mRNA cleavage factor complex	IPI Inferred from Physical Interaction more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cleavage and polyadenylation specificity factor subunit 7

Names: CPSF 59 kDa subunit; cleavage and polyadenylation specificity factor 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; pre-mRNA cleavage factor I, 59 kDa subunit; pre-mRNA cleavage factor Im 59 kDa subunit

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

NG_051815.1 RefSeqGene

Range

5018..32264

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001136040.4 → NP_001129512.1 cleavage and polyadenylation specificity factor subunit 7 isoform 2

See identical proteins and their annotated locations for NP_001129512.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an alternate 5' exon, which results in a downstream AUG start codon, as compared to variant 1. The resulting isoform (2) has a shorter N-terminus, as compared to isoform 1.

Source sequence(s)

AP003108

Consensus CDS

CCDS44619.1

UniProtKB/Swiss-Prot

B3KU04, C9K0Q4, Q7Z3H9, Q8N684, Q9H025, Q9H9V1

UniProtKB/TrEMBL

B4DGF8

Related

ENSP00000378352.4, ENST00000394888.8

Conserved Domains (2) summary

COG0724
Location:50 → 231

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12644
Location:81 → 170

RRM_CFIm59; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins
NM_001142565.3 → NP_001136037.1 cleavage and polyadenylation specificity factor subunit 7 isoform 3

See identical proteins and their annotated locations for NP_001136037.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) has an alternate 5' exon, which results in a downstream AUG start codon, and lacks an in-frame coding segment, as compared to variant 1. The resulting isoform (3) has a shorter N-terminus and lacks an internal segment, as compared to isoform 1.

Source sequence(s)

AP003108

Consensus CDS

CCDS44620.1

UniProtKB/TrEMBL

B4DGF8

Related

ENSP00000397203.3, ENST00000439958.8

Conserved Domains (1) summary

cd12644
Location:81 → 170

RRM_CFIm59; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins
NM_024811.4 → NP_079087.3 cleavage and polyadenylation specificity factor subunit 7 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AP003108

Consensus CDS

CCDS8006.2

UniProtKB/TrEMBL

B4DGF8

Related

ENSP00000345412.4, ENST00000340437.8

Conserved Domains (1) summary

cd12644
Location:124 → 213

RRM_CFIm59; RNA recognition motif of pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins

RNA

NR_165413.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003108
NR_165414.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003108
NR_165415.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003108
NR_165416.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003108
NR_165417.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003108
NR_165418.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003108
NR_165419.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003108
NR_165420.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003108

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

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

61402729..61429975 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047427623.1 → XP_047283579.1 cleavage and polyadenylation specificity factor subunit 7 isoform X8

Related

ENSP00000437860.1, ENST00000477890.6
XM_047427622.1 → XP_047283578.1 cleavage and polyadenylation specificity factor subunit 7 isoform X7
XM_047427624.1 → XP_047283580.1 cleavage and polyadenylation specificity factor subunit 7 isoform X8
XM_011545259.3 → XP_011543561.1 cleavage and polyadenylation specificity factor subunit 7 isoform X4

See identical proteins and their annotated locations for XP_011543561.1

UniProtKB/TrEMBL

B4DGF8

Conserved Domains (1) summary

cd12644
Location:81 → 170

RRM_CFIm59; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins
XM_011545258.3 → XP_011543560.1 cleavage and polyadenylation specificity factor subunit 7 isoform X3

See identical proteins and their annotated locations for XP_011543560.1

UniProtKB/Swiss-Prot

B3KU04, C9K0Q4, Q7Z3H9, Q8N684, Q9H025, Q9H9V1

UniProtKB/TrEMBL

B4DGF8

Conserved Domains (2) summary

COG0724
Location:50 → 231

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12644
Location:81 → 170

RRM_CFIm59; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins
XM_047427620.1 → XP_047283576.1 cleavage and polyadenylation specificity factor subunit 7 isoform X8
XM_047427618.1 → XP_047283574.1 cleavage and polyadenylation specificity factor subunit 7 isoform X4
XM_047427619.1 → XP_047283575.1 cleavage and polyadenylation specificity factor subunit 7 isoform X7
XM_005274299.5 → XP_005274356.1 cleavage and polyadenylation specificity factor subunit 7 isoform X3

See identical proteins and their annotated locations for XP_005274356.1

UniProtKB/Swiss-Prot

B3KU04, C9K0Q4, Q7Z3H9, Q8N684, Q9H025, Q9H9V1

UniProtKB/TrEMBL

B4DGF8

Conserved Domains (2) summary

COG0724
Location:50 → 231

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12644
Location:81 → 170

RRM_CFIm59; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins
XM_017018345.2 → XP_016873834.1 cleavage and polyadenylation specificity factor subunit 7 isoform X6

UniProtKB/TrEMBL

F5H669
XM_005274298.5 → XP_005274355.1 cleavage and polyadenylation specificity factor subunit 7 isoform X2

UniProtKB/TrEMBL

B4DGF8

Conserved Domains (1) summary

cd12644
Location:124 → 213

RRM_CFIm59; RNA recognition motif of pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins
XM_011545257.3 → XP_011543559.1 cleavage and polyadenylation specificity factor subunit 7 isoform X5

UniProtKB/TrEMBL

F5H669

Conserved Domains (1) summary

cd12644
Location:124 → 213

RRM_CFIm59; RNA recognition motif of pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins
XM_047427625.1 → XP_047283581.1 cleavage and polyadenylation specificity factor subunit 7 isoform X9
XM_047427617.1 → XP_047283573.1 cleavage and polyadenylation specificity factor subunit 7 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

61391627..61418874 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054370010.1 → XP_054225985.1 cleavage and polyadenylation specificity factor subunit 7 isoform X8
XM_054370008.1 → XP_054225983.1 cleavage and polyadenylation specificity factor subunit 7 isoform X7
XM_054370004.1 → XP_054225979.1 cleavage and polyadenylation specificity factor subunit 7 isoform X4
XM_054370007.1 → XP_054225982.1 cleavage and polyadenylation specificity factor subunit 7 isoform X6
XM_054370001.1 → XP_054225976.1 cleavage and polyadenylation specificity factor subunit 7 isoform X2
XM_054370006.1 → XP_054225981.1 cleavage and polyadenylation specificity factor subunit 7 isoform X5
XM_054370002.1 → XP_054225977.1 cleavage and polyadenylation specificity factor subunit 7 isoform X3

UniProtKB/Swiss-Prot

B3KU04, C9K0Q4, Q7Z3H9, Q8N684, Q9H025, Q9H9V1
XM_054370011.1 → XP_054225986.1 cleavage and polyadenylation specificity factor subunit 7 isoform X8
XM_054370009.1 → XP_054225984.1 cleavage and polyadenylation specificity factor subunit 7 isoform X7
XM_054370012.1 → XP_054225987.1 cleavage and polyadenylation specificity factor subunit 7 isoform X8
XM_054370005.1 → XP_054225980.1 cleavage and polyadenylation specificity factor subunit 7 isoform X4
XM_054370003.1 → XP_054225978.1 cleavage and polyadenylation specificity factor subunit 7 isoform X3

UniProtKB/Swiss-Prot

B3KU04, C9K0Q4, Q7Z3H9, Q8N684, Q9H025, Q9H9V1
XM_054370013.1 → XP_054225988.1 cleavage and polyadenylation specificity factor subunit 7 isoform X9
XM_054370000.1 → XP_054225975.1 cleavage and polyadenylation specificity factor subunit 7 isoform X1