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CPSF6 cleavage and polyadenylation specific factor 6 [ Homo sapiens (human) ]

Gene ID: 11052, updated on 11-Apr-2024

Summary

Official Symbol
CPSF6provided by HGNC
Official Full Name
cleavage and polyadenylation specific factor 6provided by HGNC
Primary source
HGNC:HGNC:13871
See related
Ensembl:ENSG00000111605 MIM:604979; AllianceGenome:HGNC:13871
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
CFIM; CFIM68; CFIM72; HPBRII-4; HPBRII-7
Summary
The protein encoded by this gene is one subunit of a cleavage factor required for 3' RNA cleavage and polyadenylation processing. The interaction of the protein with the RNA is one of the earliest steps in the assembly of the 3' end processing complex and facilitates the recruitment of other processing factors. The cleavage factor complex is composed of four polypeptides. This gene encodes the 68kD subunit. It has a domain organization reminiscent of spliceosomal proteins. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 16.3), lymph node (RPKM 15.0) and 25 other tissues See more
Orthologs
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Genomic context

Location:
12q15
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (69239569..69274358)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (69218652..69253462)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (69633349..69668138)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene carboxypeptidase M Neighboring gene PRELI domain containing 2 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:69401223-69401916 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:69417938-69419137 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:69420279-69420508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:69436381-69436882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:69436883-69437382 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:69447351-69447948 Neighboring gene transcript overexpressed in dedifferentiated liposarcoma Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:69461643-69462842 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:69509413-69510201 Neighboring gene MPRA-validated peak1782 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:69633505-69634085 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:69634086-69634665 Neighboring gene Sharpr-MPRA regulatory region 12312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:69639551-69640050 Neighboring gene MPRA-validated peak1783 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6648 Neighboring gene C1GALT1 pseudogene 1 Neighboring gene microRNA 1279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:69725950-69726664 Neighboring gene lysozyme

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
A genome-wide association study identifies susceptibility loci of silica related pneumoconiosis in Han Chinese.
EBI GWAS Catalog
Many sequence variants affecting diversity of adult human height.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 incorporates CPSF6 into virions PubMed
Knockdown of CPSF6, TNPO3, or NUP153 through siRNA leads to decreased CA and viral DNA nuclear entry PubMed
HIV-1 CA binds CPSF6 to enhance nuclear entry PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, cleavage and polyadenylation specific factor 6, (CPSF6), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with CPSF6 is increased by RRE PubMed
capsid gag HIV-1 CA binds CPSF6; this interaction is inhibited by the inhibitor BI-2 PubMed
gag HIV-1 CA binds CPSF6 to enhance HIV-1 nuclear entry PubMed
gag HIV-1 CA relocalizes RANBP2 (NUP358) into the cytoplasm of infected cells, which requires CPSF6 and KIF5B PubMed
gag HIV-1 CA binds to CPSF6, which is abrogated by mutation A77V in CA and confers a significant viral fitness advantage PubMed
gag HIV-1 CA binds CPSF6; HIV-1 CA mutations S41A, Q67H, V165I and V172I in combination abrogate this interaction PubMed
gag CPSF6 (313-327) F321N mutant impairs to bind to HIV-1 CA monomers and hexamers, and is inactive in the functional Epic assay PubMed
gag CPSF6 binds to the CA hexamer more tightly than the isolated CA NTD or unassembled CA, and the binding of CPSF6 to the hexamer involves energetically significant contacts with both the NTD and CTD in CA PubMed
gag Truncated CPSF6-358 binds HIV-1 core complexes and N74D CA mutant impairs the interaction between CPSF6-358 and CA PubMed
gag HIV-1 inhibition by TNPO3 knockdown and CPSF6-358 is CA-dependent and cytoplasmic localization of CPSF6-358 is required to inhibit HIV-1 PubMed
gag Crystal structure analysis demonstrates that helixes 3, 4, 8, and 9 in HIV-1 CA are involved in its binding to the CPSF6 peptide (residues 313-327) PubMed
gag Five substitutions Q67H, K70R, H87P, T107N, and L111I in HIV-1 CA resistant to PF74 reduce the binding of the host protein CPSF6 to assembled CA complexes in vitro and permit infection of cells expressing the inhibitory protein CPSF6-358 PubMed
gag Endogenously expressed CPSF6 binds and stabilizes in vitro-assembled HIV-1 CA-NC complexes, but the CPSF6-FG284AA mutant loses the ability to bind and stabilize the CA-NC complexes PubMed
gag The C-terminal residues 314-322 of CPSF6-358 contribute to binding with HIV-1 CA and mutations within this region fail to restrict HIV-1 PubMed
gag Residues N57, M66, Q67, K70, N74, and T107 in the N-terminal domain of HIV-1 CA are important for the binding to CPSF6. Mutations on these residues lead to the loss or reduction of dependency on TNPO3 and RanBP2 PubMed
gag HIV-1 CA mutants N74D and P90A fail to bind to CPSF6 and cyclophilins (Nup358 and CypA), respectively, and trigger innate sensors, leading to nuclear translocation of NFkappaB and IRF3, production of type 1 IFN and induction of an antiviral state PubMed
gag HIV-1 CA T107I and N74D substitutions can rescue the CA mutant RKLM by reducing the binding to CPSF6, while the CA S41A substitution resuces RKLM from CPSF6 inhibition without significantly changing the extent of CPSF6 binding PubMed
gag The HIV-1 CA mutant T54A infection is inhibited by CPSF6, but the A106T substitution in CA reduces the association of CPSF6 with CA to resuce the mutant T54A PubMed
gag Cytoplasmic CPSF6 stabilizes the HIV-1 CA core and TNPO3 is required for CPSF6 localization to the nucleus and the HIV-1 permissiveness. However, some studies indicate depletion of TNPO3 does not change the cellular distribution of CPSF6 PubMed
nucleocapsid gag Endogenously expressed CPSF6 binds and stabilizes in vitro-assembled HIV-1 CA-NC complexes, but the CPSF6-FG284AA mutant loses the ability to bind and stabilize the CA-NC complexes PubMed
reverse transcriptase gag-pol Mutational analyses reveal that the residues encoded by exon 6, but not the C-terminal 54 residues in hCPSF6-375, is responsible for inhibition of HIV-1 RT-mediated viral cDNA synthesis PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
contributes_to RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables exon-exon junction complex binding IDA
Inferred from Direct Assay
more info
PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables ribosomal large subunit binding IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
cleavage and polyadenylation specificity factor subunit 6
Names
CPSF 68 kDa subunit
cleavage and polyadenylation specific factor 6, 68kDa
cleavage and polyadenylation specificity factor 68 kDa subunit
cleavage factor Im complex 68 kDa subunit
pre-mRNA cleavage factor I, 68kD subunit
pre-mRNA cleavage factor Im (68kD)
pre-mRNA cleavage factor Im 68 kDa subunit
protein HPBRII-4/7

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_001300947.2NP_001287876.1  cleavage and polyadenylation specificity factor subunit 6 isoform 2

    See identical proteins and their annotated locations for NP_001287876.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) represents the longer transcript and encodes the longer isoform (2).
    Source sequence(s)
    AC020656, AW189370, BC000714, DA365448
    Consensus CDS
    CCDS73494.1
    UniProtKB/Swiss-Prot
    Q16630
    Related
    ENSP00000266679.8, ENST00000266679.8
    Conserved Domains (2) summary
    COG0724
    Location:9152
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12643
    Location:82158
    RRM_CFIm68; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins
  2. NM_007007.3NP_008938.2  cleavage and polyadenylation specificity factor subunit 6 isoform 1

    See identical proteins and their annotated locations for NP_008938.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon in the central coding region, compared to variant 2. The encoded isoform (1) is shorter than isoform 2.
    Source sequence(s)
    AC020656, AK223568, AW189370, DA365448
    Consensus CDS
    CCDS8988.1
    UniProtKB/Swiss-Prot
    A8K7K9, Q16630, Q53ES1, Q9BSJ7, Q9BW18
    Related
    ENSP00000391774.2, ENST00000435070.7
    Conserved Domains (1) summary
    cd12643
    Location:82158
    RRM_CFIm68; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    69239569..69274358
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005268588.4XP_005268645.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

    See identical proteins and their annotated locations for XP_005268645.1

    Conserved Domains (2) summary
    COG0724
    Location:9152
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12643
    Location:82158
    RRM_CFIm68; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins
  2. XM_005268590.4XP_005268647.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

    See identical proteins and their annotated locations for XP_005268647.1

    Conserved Domains (1) summary
    cd12643
    Location:82158
    RRM_CFIm68; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins
  3. XM_047428132.1XP_047284088.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    69218652..69253462
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370842.1XP_054226817.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

  2. XM_054370844.1XP_054226819.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

  3. XM_054370843.1XP_054226818.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1