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Aliases for CPSF4 Gene

Aliases for CPSF4 Gene

  • Cleavage And Polyadenylation Specific Factor 4 2 3 5
  • Cleavage And Polyadenylation Specificity Factor 30 KDa Subunit 3 4
  • Cleavage And Polyadenylation Specific Factor 4, 30kDa 2 3
  • NS1 Effector Domain-Binding Protein 1 3 4
  • CPSF 30 KDa Subunit 3 4
  • No Arches Homolog 3 4
  • CPSF30 3 4
  • NEB-1 3 4
  • NEB1 3 4
  • NAR 3 4
  • Cleavage And Polyadenylation Specific Factor 4, 30kD Subunit 2
  • Cleavage And Polyadenylation Specificity Factor Subunit 4 3
  • No Arches-Like Zinc Finger Protein 3

External Ids for CPSF4 Gene

Previous GeneCards Identifiers for CPSF4 Gene

  • GC07P097571
  • GC07P098634
  • GC07P098647
  • GC07P098619
  • GC07P098682
  • GC07P098874
  • GC07P099036
  • GC07P093673

Summaries for CPSF4 Gene

Entrez Gene Summary for CPSF4 Gene

  • Inhibition of the nuclear export of poly(A)-containing mRNAs caused by the influenza A virus NS1 protein requires its effector domain. The NS1 effector domain functionally interacts with the cellular 30 kDa subunit of cleavage and polyadenylation specific factor 4, an essential component of the 3' end processing machinery of cellular pre-mRNAs. In influenza virus-infected cells, the NS1 protein is physically associated with cleavage and polyadenylation specific factor 4, 30kD subunit. Binding of the NS1 protein to the 30 kDa protein in vitro prevents CPSF binding to the RNA substrate and inhibits 3' end cleavage and polyadenylation of host pre-mRNAs. Thus the NS1 protein selectively inhibits the nuclear export of cellular, and not viral, mRNAs. Multiple alternatively spliced transcript variants that encode different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for CPSF4 Gene

CPSF4 (Cleavage And Polyadenylation Specific Factor 4) is a Protein Coding gene. Diseases associated with CPSF4 include Influenza and Benign Essential Hypertension. Among its related pathways are mRNA Splicing - Major Pathway and Processing of Capped Intronless Pre-mRNA. GO annotations related to this gene include nucleic acid binding and poly(A) RNA binding. An important paralog of this gene is CPSF4L.

UniProtKB/Swiss-Prot for CPSF4 Gene

  • Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. CPSF4 binds RNA polymers with a preference for poly(U).

Gene Wiki entry for CPSF4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CPSF4 Gene

Genomics for CPSF4 Gene

Regulatory Elements for CPSF4 Gene

Enhancers for CPSF4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07G099324 1.2 ENCODE 8.1 -110.3 -110284 7.3 CREB3L1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 NFYC MEF2D ARPC1B BUD31 PDAP1 TRRAP MBLAC1 ENSG00000242798 TMEM225B CPSF4 CYP3A5 ATP5J2
GH07G099504 1.4 ENCODE dbSUPER 6.8 +66.8 66772 3.3 HDGF PKNOX1 CREB3L1 AGO1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B TMEM225B CPSF4 ZSCAN25 BUD31 ATP5J2 TRIM4 ZKSCAN5 GC07P099532
GH07G099579 1.5 FANTOM5 Ensembl ENCODE 5.4 +141.5 141479 1.2 AGO1 ZNF2 RAD21 ZBTB40 ZNF354C ZNF366 ZNF263 ZNF202 ZNF680 ELF4 ZSCAN25 LOC100131859 TRRAP AP4M1 ZNF655 LOC101927550 LOC100419643 ENSG00000242798 STAG3L5P SMURF1
GH07G099371 1.8 FANTOM5 Ensembl ENCODE dbSUPER 4.3 -66.2 -66172 1.6 ATF1 MLX ZFP64 ARID4B DMAP1 ZNF48 SP5 MXD4 NFYC MIER2 ARPC1B ATP5J2 PILRB CPSF4 PTCD1 PIR48819
GH07G099207 1.9 FANTOM5 Ensembl ENCODE dbSUPER 1.5 -228.9 -228905 5.9 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 YY1 ZNF121 FOS SMURF1 ARPC1B TRIM4 PDAP1 BUD31 ARPC1A FAM200A ZNF655 PTCD1 KPNA7
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CPSF4 on UCSC Golden Path with GeneCards custom track

Promoters for CPSF4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000215666 78 1601 HDGF HNRNPUL1 PKNOX1 MLX CREB3L1 ARNT AGO1 ARID4B SIN3A DMAP1

Genomic Location for CPSF4 Gene

Chromosome:
7
Start:
99,438,922 bp from pter
End:
99,457,373 bp from pter
Size:
18,452 bases
Orientation:
Plus strand

Genomic View for CPSF4 Gene

Genes around CPSF4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CPSF4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CPSF4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CPSF4 Gene

Proteins for CPSF4 Gene

  • Protein details for CPSF4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95639-CPSF4_HUMAN
    Recommended name:
    Cleavage and polyadenylation specificity factor subunit 4
    Protein Accession:
    O95639
    Secondary Accessions:
    • D6W5S8
    • Q6FGE6
    • Q86TF8
    • Q9BTW6

    Protein attributes for CPSF4 Gene

    Size:
    269 amino acids
    Molecular mass:
    30255 Da
    Quaternary structure:
    • Component of the cleavage and polyadenylation specificity factor (CPSF) complex, composed of CPSF1, CPSF2, CPSF3, CPSF4 and FIP1L1. Interacts with FIP1L1. Association with influenza A virus NS1 blocks processing of pre-mRNAs, thereby preventing nuclear export of host cell mRNAs.

    Three dimensional structures from OCA and Proteopedia for CPSF4 Gene

    Alternative splice isoforms for CPSF4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CPSF4 Gene

Post-translational modifications for CPSF4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CPSF4 Gene

Domains & Families for CPSF4 Gene

Protein Domains for CPSF4 Gene

Suggested Antigen Peptide Sequences for CPSF4 Gene

Graphical View of Domain Structure for InterPro Entry

O95639

UniProtKB/Swiss-Prot:

CPSF4_HUMAN :
  • Belongs to the CPSF4/YTH1 family.
Family:
  • Belongs to the CPSF4/YTH1 family.
genes like me logo Genes that share domains with CPSF4: view

No data available for Gene Families for CPSF4 Gene

Function for CPSF4 Gene

Molecular function for CPSF4 Gene

UniProtKB/Swiss-Prot Function:
Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. CPSF4 binds RNA polymers with a preference for poly(U).

Gene Ontology (GO) - Molecular Function for CPSF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,IDA 22681889
GO:0004521 endoribonuclease activity IBA --
GO:0005515 protein binding IPI 28169297
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with CPSF4: view
genes like me logo Genes that share phenotypes with CPSF4: view

Animal Model Products

miRNA for CPSF4 Gene

miRTarBase miRNAs that target CPSF4

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CPSF4 Gene

Localization for CPSF4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CPSF4 Gene

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 CPSF4 gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 1

Gene Ontology (GO) - Cellular Components for CPSF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex IDA 21102410
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with CPSF4: view

Pathways & Interactions for CPSF4 Gene

genes like me logo Genes that share pathways with CPSF4: view

Pathways by source for CPSF4 Gene

Gene Ontology (GO) - Biological Process for CPSF4 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:0006378 mRNA polyadenylation IBA --
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation TAS --
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with CPSF4: view

No data available for SIGNOR curated interactions for CPSF4 Gene

Drugs & Compounds for CPSF4 Gene

(1) Additional Compounds for CPSF4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CPSF4: view

Transcripts for CPSF4 Gene

Unigene Clusters for CPSF4 Gene

Cleavage and polyadenylation specific factor 4, 30kDa:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for CPSF4 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e ^ 11a · 11b · 11c · 11d
SP1: - - - - - - - - - -
SP2: - - - - - - - - - - -
SP3: - - - - - - - - - - -
SP4: - - - - - - - -
SP5: - - - - - -
SP6: - - - - - - -
SP7: - - - -
SP8: - - - -
SP9: - -
SP10: -
SP11: - -

Relevant External Links for CPSF4 Gene

GeneLoc Exon Structure for
CPSF4
ECgene alternative splicing isoforms for
CPSF4

Expression for CPSF4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CPSF4 Gene

Protein differential expression in normal tissues from HIPED for CPSF4 Gene

This gene is overexpressed in Liver (49.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CPSF4 Gene



Protein tissue co-expression partners for CPSF4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CPSF4 Gene:

CPSF4

SOURCE GeneReport for Unigene cluster for CPSF4 Gene:

Hs.489287

Evidence on tissue expression from TISSUES for CPSF4 Gene

  • Nervous system(4.6)
  • Eye(4.1)
  • Lung(2)
genes like me logo Genes that share expression patterns with CPSF4: view

Primer Products

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 CPSF4 Gene

Orthologs for CPSF4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CPSF4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CPSF4 34 35
  • 99.63 (n)
oppossum
(Monodelphis domestica)
Mammalia CPSF4 35
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CPSF4 34 35
  • 95.17 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CPSF4 35
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CPSF4 34 35
  • 91.36 (n)
mouse
(Mus musculus)
Mammalia Cpsf4 34 16 35
  • 89.57 (n)
rat
(Rattus norvegicus)
Mammalia Cpsf4 34
  • 89.3 (n)
chicken
(Gallus gallus)
Aves CPSF4 34 35
  • 83.68 (n)
lizard
(Anolis carolinensis)
Reptilia CPSF4 35
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cpsf4 34
  • 77.94 (n)
Str.3196 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.25683 34
zebrafish
(Danio rerio)
Actinopterygii cpsf4 34 35
  • 72.99 (n)
nar 34
fruit fly
(Drosophila melanogaster)
Insecta Clp 36 34 35
  • 60.97 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP013044 34
  • 59.48 (n)
worm
(Caenorhabditis elegans)
Secernentea F11A10.3 36
  • 61 (a)
cpsf-4 34 35
  • 53.41 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YTH1 35 37
  • 36 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9063 35
  • 50 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3252 34
Species where no ortholog for CPSF4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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 CPSF4 Gene

ENSEMBL:
Gene Tree for CPSF4 (if available)
TreeFam:
Gene Tree for CPSF4 (if available)

Paralogs for CPSF4 Gene

Paralogs for CPSF4 Gene

(1) SIMAP similar genes for CPSF4 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with CPSF4: view

Variants for CPSF4 Gene

Sequence variations from dbSNP and Humsavar for CPSF4 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs1000236639 -- 99,440,374(+) GAGAC(-/AG)GGGCC intron-variant, upstream-variant-2KB
rs1000357355 -- 99,445,716(+) TCGTC(C/T)CTACT intron-variant
rs1000512264 -- 99,438,954(+) CCTCG(-/GGCGGCGGC)GGCGG intron-variant, upstream-variant-2KB, cds-indel
rs1000711537 -- 99,438,279(+) AACCC(C/T)GCCGT intron-variant, upstream-variant-2KB
rs1000858065 -- 99,444,334(+) CACCT(G/T)TAATC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CPSF4 Gene

Variant ID Type Subtype PubMed ID
nsv5864 CNV insertion 18451855
nsv831069 CNV loss 17160897
nsv951383 CNV deletion 24416366

Variation tolerance for CPSF4 Gene

Residual Variation Intolerance Score: 40.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.45; 9.78% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CPSF4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CPSF4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CPSF4 Gene

Disorders for CPSF4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CPSF4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
influenza
  • flu
benign essential hypertension
- elite association - COSMIC cancer census association via MalaCards
Search CPSF4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CPSF4

Genetic Association Database (GAD)
CPSF4
Human Genome Epidemiology (HuGE) Navigator
CPSF4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CPSF4
genes like me logo Genes that share disorders with CPSF4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CPSF4 Gene

Publications for CPSF4 Gene

  1. Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 3'end formation of cellular pre-mRNAs. (PMID: 9651582) Nemeroff M.E. … Krug R.M. (Mol. Cell 1998) 2 3 4 64
  2. The 30-kD subunit of mammalian cleavage and polyadenylation specificity factor and its yeast homolog are RNA-binding zinc finger proteins. (PMID: 9224719) Barabino S.M.L. … Keller W. (Genes Dev. 1997) 2 3 4 64
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  4. The poly A polymerase Star-PAP controls 3'-end cleavage by promoting CPSF interaction and specificity toward the pre-mRNA. (PMID: 21102410) Laishram R.S. … Anderson R.A. (EMBO J. 2010) 3 4 64
  5. Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase. (PMID: 14749727) Kaufmann I. … Keller W. (EMBO J. 2004) 3 4 64

Products for CPSF4 Gene

Sources for CPSF4 Gene

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