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Aliases for CPSF6 Gene

Aliases for CPSF6 Gene

  • Cleavage And Polyadenylation Specific Factor 6 2 3 5
  • Cleavage And Polyadenylation Specificity Factor 68 KDa Subunit 3 4
  • Cleavage And Polyadenylation Specific Factor 6, 68kDa 2 3
  • Pre-MRNA Cleavage Factor Im 68 KDa Subunit 3 4
  • Cleavage Factor Im Complex 68 KDa Subunit 2 3
  • CPSF 68 KDa Subunit 3 4
  • Protein HPBRII-4/7 3 4
  • CFIM68 3 4
  • Cleavage And Polyadenylation Specific Factor 6, 68kD Subunit 2
  • Cleavage And Polyadenylation Specificity Factor Subunit 6 3
  • Pre-MRNA Cleavage Factor I, 68kD Subunit 3
  • Pre-MRNA Cleavage Factor Im (68kD) 3
  • HPBRII-4 3
  • HPBRII-7 3
  • CFIM72 3
  • CFIM 3

External Ids for CPSF6 Gene

Previous GeneCards Identifiers for CPSF6 Gene

  • GC12M069604
  • GC12P069573
  • GC12P069350
  • GC12P067919
  • GC12P069633

Summaries for CPSF6 Gene

Entrez Gene Summary for CPSF6 Gene

  • 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]

GeneCards Summary for CPSF6 Gene

CPSF6 (Cleavage And Polyadenylation Specific Factor 6) is a Protein Coding gene. Among its related pathways are Signaling by FGFR2 in disease and FGFR1 mutant receptor activation. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is CPSF7.

UniProtKB/Swiss-Prot for CPSF6 Gene

  • Component of the cleavage factor Im complex (CFIm) that plays a key role in pre-mRNA 3-processing. Involved in association with NUDT21/CPSF5 in pre-MRNA 3-end poly(A) site cleavage and poly(A) addition. CPSF6 binds to cleavage and polyadenylation RNA substrates and promotes RNA looping.

Gene Wiki entry for CPSF6 Gene

Additional gene information for CPSF6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CPSF6 Gene

Genomics for CPSF6 Gene

GeneHancer (GH) Regulatory Elements for CPSF6 Gene

Promoters and enhancers for CPSF6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12I069238 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 559.7 +0.5 493 3.1 HDGF CLOCK SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B CPSF6 LYZ RAP1B NUP107 MDM2 YEATS4 FRS2 CCT2 SLC35E3 RAB3IP
GH12I068685 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 33.9 -552.7 -552707 3 MLX DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC ZC3H11A NUP107 LOC100507250 CPSF6 KRT8P39 RPL10P12 MDM2 RPL7P42
GH12I068803 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE 24.4 -432.8 -432835 7 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 MDM2 LOC100130075 NUP107 CPSF6 RPL10P12 RAP1B KRT8P39 C1GALT1P1 SLC35E3 CPM
GH12I068609 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15.4 -626.9 -626866 6.7 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 RAP1B NUP107 CPSF6 MDM2 KRT8P39 CPM LINC02384 MDM1 RPL10P12 IFNG
GH12I068932 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 15.5 -306.6 -306641 1.8 PKNOX1 SIN3A RAD21 ZNF335 SCRT2 IKZF2 EGR2 CEBPB SMARCB1 ZFP69B CPM CPSF6 NUP107 KRT8P39 MDM2 RPL10P12 ENSG00000257289 PRELID2P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CPSF6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CPSF6 gene promoter:

Genomic Locations for CPSF6 Gene

Genomic Locations for CPSF6 Gene
chr12:69,239,537-69,274,358
(GRCh38/hg38)
Size:
34,822 bases
Orientation:
Plus strand
chr12:69,633,317-69,668,138
(GRCh37/hg19)

Genomic View for CPSF6 Gene

Genes around CPSF6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CPSF6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CPSF6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CPSF6 Gene

Proteins for CPSF6 Gene

  • Protein details for CPSF6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q16630-CPSF6_HUMAN
    Recommended name:
    Cleavage and polyadenylation specificity factor subunit 6
    Protein Accession:
    Q16630
    Secondary Accessions:
    • A8K7K9
    • Q53ES1
    • Q9BSJ7
    • Q9BW18

    Protein attributes for CPSF6 Gene

    Size:
    551 amino acids
    Molecular mass:
    59210 Da
    Quaternary structure:
    • Component of the cleavage factor Im (CFIm) complex, composed at least of NUDT21/CPSF5 and CPSF6 or CPSF7. Within the cleavage factor Im complex, the NUDT21/CPSF5 homodimer is at the core of a heterotetramer, and is clasped by two additional subunits (CPSF6 or CPSF7). Interacts with NUDT21/CPSF5, SFRS3, SFRS7, SNRNP70 and TRA2B/SFRS10.

    Three dimensional structures from OCA and Proteopedia for CPSF6 Gene

    Alternative splice isoforms for CPSF6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CPSF6 Gene

Post-translational modifications for CPSF6 Gene

  • Ubiquitination at Lys79, Lys161, and posLast=185185

No data available for DME Specific Peptides for CPSF6 Gene

Domains & Families for CPSF6 Gene

Gene Families for CPSF6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CPSF6 Gene

Suggested Antigen Peptide Sequences for CPSF6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q16630

UniProtKB/Swiss-Prot:

CPSF6_HUMAN :
  • Belongs to the RRM CPSF6/7 family.
Family:
  • Belongs to the RRM CPSF6/7 family.
genes like me logo Genes that share domains with CPSF6: view

Function for CPSF6 Gene

Molecular function for CPSF6 Gene

UniProtKB/Swiss-Prot Function:
Component of the cleavage factor Im complex (CFIm) that plays a key role in pre-mRNA 3-processing. Involved in association with NUDT21/CPSF5 in pre-MRNA 3-end poly(A) site cleavage and poly(A) addition. CPSF6 binds to cleavage and polyadenylation RNA substrates and promotes RNA looping.

Phenotypes From GWAS Catalog for CPSF6 Gene

Gene Ontology (GO) - Molecular Function for CPSF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 contributes_to RNA binding IEA,IDA 15169763
GO:0003729 mRNA binding IDA 21295486
GO:0005515 protein binding IPI 14561889
genes like me logo Genes that share ontologies with CPSF6: view
genes like me logo Genes that share phenotypes with CPSF6: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CPSF6 Gene

Localization for CPSF6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CPSF6 Gene

Nucleus. Note=In punctate subnuclear structures localized adjacent to nuclear speckles, called paraspeckles.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CPSF6 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CPSF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 20695905
GO:0005654 nucleoplasm IDA --
GO:0005849 mRNA cleavage factor complex IDA 9659921
GO:0016020 membrane IDA,HDA 19946888
GO:0016607 nuclear speck IDA --
genes like me logo Genes that share ontologies with CPSF6: view

Pathways & Interactions for CPSF6 Gene

genes like me logo Genes that share pathways with CPSF6: view

Gene Ontology (GO) - Biological Process for CPSF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006378 mRNA polyadenylation IMP 20695905
GO:0006397 mRNA processing IEA,IDA 14690600
GO:0051262 protein tetramerization IDA 20695905
genes like me logo Genes that share ontologies with CPSF6: view

No data available for SIGNOR curated interactions for CPSF6 Gene

Drugs & Compounds for CPSF6 Gene

No Compound Related Data Available

Transcripts for CPSF6 Gene

Unigene Clusters for CPSF6 Gene

Cleavage and polyadenylation specific factor 6, 68kDa:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CPSF6 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15
SP1: - -
SP2: - - -
SP3: -
SP4:
SP5:
SP6: -
SP7:
SP8:

Relevant External Links for CPSF6 Gene

GeneLoc Exon Structure for
CPSF6
ECgene alternative splicing isoforms for
CPSF6

Expression for CPSF6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CPSF6 Gene

Protein differential expression in normal tissues from HIPED for CPSF6 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CPSF6 Gene



Protein tissue co-expression partners for CPSF6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CPSF6 Gene:

CPSF6

SOURCE GeneReport for Unigene cluster for CPSF6 Gene:

Hs.369606

Evidence on tissue expression from TISSUES for CPSF6 Gene

  • Pancreas(5)
  • Heart(4.3)
  • Kidney(4.3)
  • Liver(4.3)
  • Spleen(4.3)
  • Nervous system(3.9)
genes like me logo Genes that share expression patterns with CPSF6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CPSF6 Gene

Orthologs for CPSF6 Gene

This gene was present in the common ancestor of animals.

Orthologs for CPSF6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CPSF6 33 34
  • 99.58 (n)
oppossum
(Monodelphis domestica)
Mammalia CPSF6 34
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CPSF6 33 34
  • 96.13 (n)
rat
(Rattus norvegicus)
Mammalia Cpsf6 33
  • 93.47 (n)
dog
(Canis familiaris)
Mammalia CPSF6 33 34
  • 92.96 (n)
mouse
(Mus musculus)
Mammalia Cpsf6 33 16 34
  • 92.56 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CPSF6 34
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves CPSF6 33 34
  • 84.74 (n)
lizard
(Anolis carolinensis)
Reptilia CPSF6 34
  • 95 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.17115 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.7296 33
zebrafish
(Danio rerio)
Actinopterygii cpsf6 34
  • 83 (a)
OneToOne
Dr.28441 33
fruit fly
(Drosophila melanogaster)
Insecta CG7185 34
  • 40 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cfim-2 34
  • 32 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 49 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3009 33
Species where no ortholog for CPSF6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CPSF6 Gene

ENSEMBL:
Gene Tree for CPSF6 (if available)
TreeFam:
Gene Tree for CPSF6 (if available)

Paralogs for CPSF6 Gene

Paralogs for CPSF6 Gene

(1) SIMAP similar genes for CPSF6 Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for CPSF6 Gene

genes like me logo Genes that share paralogs with CPSF6: view

Variants for CPSF6 Gene

Sequence variations from dbSNP and Humsavar for CPSF6 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000036530 -- 69,242,320(+) A/T intron_variant
rs1000088484 -- 69,242,652(+) C/G intron_variant
rs1000199292 -- 69,257,205(+) T/C intron_variant
rs1000206522 -- 69,267,505(+) A/C intron_variant
rs1000241726 -- 69,248,727(+) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CPSF6 Gene

Variant ID Type Subtype PubMed ID
esv3394226 CNV duplication 20981092

Variation tolerance for CPSF6 Gene

Residual Variation Intolerance Score: 21.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.29; 6.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CPSF6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CPSF6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CPSF6 Gene

Disorders for CPSF6 Gene

Additional Disease Information for CPSF6

No disorders were found for CPSF6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CPSF6 Gene

Publications for CPSF6 Gene

  1. Human pre-mRNA cleavage factor Im is related to spliceosomal SR proteins and can be reconstituted in vitro from recombinant subunits. (PMID: 9659921) Rüegsegger U … Keller W (Molecular cell 1998) 2 3 4 58
  2. Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping. (PMID: 21295486) Yang Q … Doublié S (Structure (London, England : 1993) 2011) 3 4 58
  3. Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation. (PMID: 20695905) Kim S … Yamaguchi Y (Genes to cells : devoted to molecular & cellular mechanisms 2010) 3 4 58
  4. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson DF … Stefansson K (Nature genetics 2008) 3 44 58
  5. Subnuclear localization and dynamics of the Pre-mRNA 3' end processing factor mammalian cleavage factor I 68-kDa subunit. (PMID: 17267687) Cardinale S … Barabino SM (Molecular biology of the cell 2007) 2 3 58

Products for CPSF6 Gene

Sources for CPSF6 Gene

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