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 interac... See more...

Aliases for CPSF7 Gene

Aliases for CPSF7 Gene

  • Cleavage And Polyadenylation Specific Factor 7 2 3 5
  • Cleavage Factor Im Complex 59 KDa Subunit 2 3 4
  • Cleavage And Polyadenylation Specificity Factor 59 KDa Subunit 3 4
  • Cleavage And Polyadenylation Specificity Factor Subunit 7 3 4
  • Pre-MRNA Cleavage Factor Im 59 KDa Subunit 3 4
  • CPSF 59 KDa Subunit 3 4
  • CFIm59 3 4
  • Cleavage And Polyadenylation Specific Factor 7, 59kDa 2
  • Pre MRNA Cleavage Factor I, 59 KDa Subunit 2
  • Pre-MRNA Cleavage Factor I, 59 KDa Subunit 3
  • FLJ12529 2
  • CFIM59 2
  • CPSF7 5

External Ids for CPSF7 Gene

Previous GeneCards Identifiers for CPSF7 Gene

  • GC11M060928
  • GC11M061170
  • GC11M057498

Summaries for CPSF7 Gene

Entrez Gene Summary for CPSF7 Gene

  • 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]

GeneCards Summary for CPSF7 Gene

CPSF7 (Cleavage And Polyadenylation Specific Factor 7) is a Protein Coding gene. Among its related pathways are Processing of Capped Intronless Pre-mRNA and Tat-mediated elongation of the HIV-1 transcript. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is CPSF6.

UniProtKB/Swiss-Prot Summary for CPSF7 Gene

  • Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:8626397, PubMed:17024186, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:8626397, PubMed:17024186). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF7 activates directly the mRNA 3'-processing machinery (PubMed:29276085). Binds to pA signals in RNA substrates (PubMed:8626397, PubMed:17024186).

Gene Wiki entry for CPSF7 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CPSF7 Gene

Genomics for CPSF7 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CPSF7 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CPSF7 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CPSF7

Top Transcription factor binding sites by QIAGEN in the CPSF7 gene promoter:
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • E47

Genomic Locations for CPSF7 Gene

Latest Assembly
chr11:61,402,641-61,430,031
(GRCh38/hg38)
Size:
27,391 bases
Orientation:
Minus strand

Previous Assembly
chr11:61,170,201-61,197,447
(GRCh37/hg19 by Entrez Gene)
Size:
27,247 bases
Orientation:
Minus strand

chr11:61,170,121-61,197,503
(GRCh37/hg19 by Ensembl)
Size:
27,383 bases
Orientation:
Minus strand

Genomic View for CPSF7 Gene

Genes around CPSF7 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CPSF7 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CPSF7 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CPSF7 Gene

Proteins for CPSF7 Gene

  • Protein details for CPSF7 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N684-CPSF7_HUMAN
    Recommended name:
    Cleavage and polyadenylation specificity factor subunit 7
    Protein Accession:
    Q8N684
    Secondary Accessions:
    • B3KU04
    • C9K0Q4
    • Q7Z3H9
    • Q9H025
    • Q9H9V1

    Protein attributes for CPSF7 Gene

    Size:
    471 amino acids
    Molecular mass:
    52050 Da
    Quaternary structure:
    • Component of the cleavage factor Im (CFIm) complex which is a heterotetramer composed of two subunits of NUDT21/CPSF5 and two subunits of CPSF6 or CPSF7 or a heterodimer of CPSF6 and CPSF7 (PubMed:8626397, PubMed:20695905, PubMed:23187700, Ref.22). The cleavage factor Im (CFIm) complex associates with the CPSF and CSTF complexes to promote the assembly of the core mRNA 3'-processing machinery (PubMed:29276085). Interacts with NUDT21/CPSF5 (PubMed:29276085). Interacts (via Arg/Ser-rich domain) with FIP1L1 (preferentially via unphosphorylated form and Arg/Glu/Asp-rich region); this interaction mediates, at least in part, the interaction between the CFIm and CPSF complexes and may be inhibited by CPSF7 hyper-phosphorylation (PubMed:29276085).
    SequenceCaution:
    • Sequence=AAH18135.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB14118.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAD97884.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CPSF7 Gene

    Alternative splice isoforms for CPSF7 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CPSF7 Gene

Post-translational modifications for CPSF7 Gene

  • Phosphorylated (PubMed:29276085).
  • Asymmetrically dimethylated on arginine residues by PRMT1 (PubMed:20562214).
  • Ubiquitination at Lys148 and Lys379
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CPSF7 Gene

Domains & Families for CPSF7 Gene

Gene Families for CPSF7 Gene

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

Protein Domains for CPSF7 Gene

InterPro:
Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)

Suggested Antigen Peptide Sequences for CPSF7 Gene

GenScript: Design optimal peptide antigens:
  • Pre-mRNA cleavage factor Im 59 kDa subunit (CPSF7_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N684

UniProtKB/Swiss-Prot:

CPSF7_HUMAN :
  • Contains an Arg/Ser-rich domain composed of arginine-serine dipeptide repeats within the C-terminal region that is necessary and sufficient for activating mRNA 3'-processing (PubMed:29276085).
  • Belongs to the RRM CPSF6/7 family.
Domain:
  • Contains an Arg/Ser-rich domain composed of arginine-serine dipeptide repeats within the C-terminal region that is necessary and sufficient for activating mRNA 3'-processing (PubMed:29276085).
Family:
  • Belongs to the RRM CPSF6/7 family.
genes like me logo Genes that share domains with CPSF7: view

Function for CPSF7 Gene

Molecular function for CPSF7 Gene

UniProtKB/Swiss-Prot Function:
Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:8626397, PubMed:17024186, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:8626397, PubMed:17024186). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF7 activates directly the mRNA 3'-processing machinery (PubMed:29276085). Binds to pA signals in RNA substrates (PubMed:8626397, PubMed:17024186).

Phenotypes From GWAS Catalog for CPSF7 Gene

Gene Ontology (GO) - Molecular Function for CPSF7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,HDA 22658674
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with CPSF7: view
genes like me logo Genes that share phenotypes with CPSF7: view

miRNA for CPSF7 Gene

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CPSF7

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CPSF7 Gene

Localization for CPSF7 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CPSF7 Gene

Nucleus. Cytoplasm. Note=Shuttles between the nucleus and the cytoplasm in a transcription- and XPO1/CRM1-independent manner, most probably in complex with the cleavage factor Im complex (CFIm) (PubMed:19864460). {ECO:0000269 PubMed:19864460}.

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 CPSF7 gene
Compartment Confidence
nucleus 5
cytosol 3
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CPSF7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 19864460
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 19864460
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex IDA 23187700
GO:0005849 mRNA cleavage factor complex IEA,IDA 20695905
genes like me logo Genes that share ontologies with CPSF7: view

Pathways & Interactions for CPSF7 Gene

genes like me logo Genes that share pathways with CPSF7: view

Pathways by source for CPSF7 Gene

Gene Ontology (GO) - Biological Process for CPSF7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006397 mRNA processing IEA --
GO:0031124 mRNA 3'-end processing TAS --
GO:0051262 protein tetramerization IDA 20695905
genes like me logo Genes that share ontologies with CPSF7: view

No data available for SIGNOR curated interactions for CPSF7 Gene

Drugs & Compounds for CPSF7 Gene

No Compound Related Data Available

Transcripts for CPSF7 Gene

mRNA/cDNA for CPSF7 Gene

3 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
26 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CPSF7

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for CPSF7 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ·
SP1: - - - - -
SP2: - - - - - - - - - - - - - -
SP3: - - - - - - - - - - - - - -
SP4: - - - - - - - - - -
SP5: - - - - - - - - - - - - -
SP6: - - - - - - - - - - - - - -
SP7: - - - - - - - - - - - - -
SP8: - - - - - - - - - - - -
SP9: - - - - - - - - - -
SP10: - - - - -
SP11:
SP12: - - - - - - - - - - - - - - - - -
SP13: - - - - - - - - - - - - - - -
SP14: - - - - - - - - - - - - -
SP15: - - - - - - - - - - - -
SP16: - - - - - - - - - - -
SP17: - - - - - - - - -
SP18: - - - - - - -
SP19: - - - - - -
SP20: - - - - - - - -
SP21: - - - - - - - - - - -
SP22:
SP23: - - - - - - - - - - - - - - - - - - - -
SP24: - - - - - - - - -
SP25: - -
SP26:
SP27:
SP28:

ExUns: 11c · 11d · 11e · 11f · 11g ^ 12a · 12b · 12c · 12d · 12e · 12f · 12g ^ 13 ^ 14a · 14b ^ 15a · 15b ^ 16 ^ 17a · 17b · 17c ^ 18 ^ 19a · 19b · 19c
SP1: - - - - - - -
SP2: - - -
SP3: - -
SP4: - -
SP5:
SP6: - - - - -
SP7: -
SP8:
SP9: -
SP10: -
SP11: - - - - -
SP12: -
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19: -
SP20: -
SP21:
SP22:
SP23: - - - - -
SP24:
SP25:
SP26:
SP27:
SP28:

Relevant External Links for CPSF7 Gene

GeneLoc Exon Structure for
CPSF7

Expression for CPSF7 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CPSF7 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CPSF7 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (10.0), Nasal epithelium (8.4), and Lymph node (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CPSF7 Gene



Protein tissue co-expression partners for CPSF7 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CPSF7

SOURCE GeneReport for Unigene cluster for CPSF7 Gene:

Hs.718984

Evidence on tissue expression from TISSUES for CPSF7 Gene

  • Nervous system(4.9)
  • Liver(4.3)
  • Bone marrow(4.3)
  • Lung(2.6)
  • Skin(2.2)
  • Kidney(2)
  • Intestine(2)
genes like me logo Genes that share expression patterns with CPSF7: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CPSF7 Gene

Orthologs for CPSF7 Gene

This gene was present in the common ancestor of animals.

Orthologs for CPSF7 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CPSF7 29 30
  • 99.61 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CPSF7 29 30
  • 95.47 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CPSF7 29 30
  • 95.4 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Cpsf7 29 16 30
  • 93.49 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cpsf7 29
  • 92.47 (n)
Oppossum
(Monodelphis domestica)
Mammalia CPSF7 30
  • 90 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CPSF7 30
  • 83 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CPSF7 29 30
  • 78.37 (n)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.6759 29
Zebrafish
(Danio rerio)
Actinopterygii cpsf6 29
  • 58.5 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG7185 30
  • 30 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea cfim-2 30
  • 27 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 38 (a)
OneToMany
Species where no ortholog for CPSF7 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Lizard (Anolis carolinensis)
  • 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 Vase (Ciona intestinalis)
  • 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 CPSF7 Gene

ENSEMBL:
Gene Tree for CPSF7 (if available)
TreeFam:
Gene Tree for CPSF7 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CPSF7: view image
Alliance of Genome Resources:
Additional Orthologs for CPSF7

Paralogs for CPSF7 Gene

Paralogs for CPSF7 Gene

(1) SIMAP similar genes for CPSF7 Gene using alignment to 14 proteins:

  • CPSF7_HUMAN
  • C9J286_HUMAN
  • C9J323_HUMAN
  • C9JM38_HUMAN
  • F5GXA3_HUMAN
  • F5H047_HUMAN
  • F5H1W4_HUMAN
  • F5H2K8_HUMAN
  • F5H5B7_HUMAN
  • F5H669_HUMAN
  • F5H6A8_HUMAN
  • F5H6M0_HUMAN
  • F5H6P5_HUMAN
  • J3QT54_HUMAN
genes like me logo Genes that share paralogs with CPSF7: view

Variants for CPSF7 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CPSF7 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs193920985 Uncertain Significance: Malignant tumor of prostate 61,419,946(-) C/CA
NM_001142565.2(CPSF7):c.523+2dup
SPLICE_DONOR_VARIANT,NONSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CPSF7 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CPSF7 Gene

Variant ID Type Subtype PubMed ID
nsv1119883 CNV deletion 24896259
nsv520751 CNV gain 19592680
nsv832178 CNV gain+loss 17160897

Variation tolerance for CPSF7 Gene

Residual Variation Intolerance Score: 13.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.58; 12.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CPSF7 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CPSF7
Leiden Open Variation Database (LOVD)
CPSF7

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CPSF7 Gene

Disorders for CPSF7 Gene

Additional Disease Information for CPSF7

No disorders were found for CPSF7 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CPSF7 Gene

Publications for CPSF7 Gene

  1. Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation. (PMID: 29276085) Zhu Y … Shi Y (Molecular cell 2018) 3 4
  2. Cleavage factor Im is a key regulator of 3' UTR length. (PMID: 23187700) Gruber AR … Zavolan M (RNA biology 2012) 3 4
  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
  4. Mammalian pre-mRNA 3' end processing factor CF I m 68 functions in mRNA export. (PMID: 19864460) Ruepp MD … Barabino SM (Molecular biology of the cell 2009) 3 4
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4

Products for CPSF7 Gene

Sources for CPSF7 Gene