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Aliases for CPSF3 Gene

Aliases for CPSF3 Gene

  • Cleavage And Polyadenylation Specific Factor 3 2 3 5
  • Cleavage And Polyadenylation Specific Factor 3, 73kDa 2 3
  • MRNA 3-End-Processing Endonuclease CPSF-73 3 4
  • CPSF73 3 4
  • Cleavage And Polyadenylation Specificity Factor 73 KDa Subunit 4
  • Cleavage And Polyadenylation Specific Factor 3, 73kD Subunit 2
  • Cleavage And Polyadenylation Specificity Factor Subunit 3 3
  • CPSF 73 KDa Subunit 4
  • EC 3.1.27.- 4
  • EC 3.1.27 61
  • CPSF-73 3

External Ids for CPSF3 Gene

Previous GeneCards Identifiers for CPSF3 Gene

  • GC02P009347
  • GC02P009615
  • GC02P009585
  • GC02P009514
  • GC02P009563

Summaries for CPSF3 Gene

Entrez Gene Summary for CPSF3 Gene

  • This gene encodes a member of the metallo-beta-lactamase family. The encoded protein is a 73kDa subunit of the cleavage and polyadenylation specificity factor and functions as an endonuclease that recognizes the pre-mRNA 3'-cleavage site AAUAAA prior to polyadenylation. It also cleaves after the pre-mRNA sequence ACCCA during histone 3'-end pre-mRNA processing. [provided by RefSeq, Oct 2012]

GeneCards Summary for CPSF3 Gene

CPSF3 (Cleavage And Polyadenylation Specific Factor 3) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include RNA binding and 5-3 exonuclease activity. An important paralog of this gene is INTS11.

UniProtKB/Swiss-Prot for CPSF3 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. Has endonuclease activity, and functions as mRNA 3-end-processing endonuclease. Also involved in the histone 3-end pre-mRNA processing. U7 snRNP-dependent protein that induces both the 3-endoribonucleolytic cleavage of histone pre-mRNAs and acts as a 5 to 3 exonuclease for degrading the subsequent downstream cleavage product (DCP) of mature histone mRNAs. Cleavage occurs after the 5-ACCCA-3 sequence in the histone pre-mRNA leaving a 3hydroxyl group on the upstream fragment containing the stem loop (SL) and 5 phosphate on the downstream cleavage product (DCP) starting with CU nucleotides. The U7-dependent 5 to 3 exonuclease activity is processive and degrades the DCP RNA substrate even after complete removal of the U7-binding site. Binds to the downstream cleavage product (DCP) of histone pre-mRNAs and the cleaved DCP RNA substrate in a U7 snRNP dependent manner.

Gene Wiki entry for CPSF3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CPSF3 Gene

Genomics for CPSF3 Gene

Regulatory Elements for CPSF3 Gene

Enhancers for CPSF3 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
GH02G009702 1.8 FANTOM5 Ensembl ENCODE 10.8 +280.0 280034 2.9 FOXA2 PKNOX1 CREB3L1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 FEZF1 RNU4-73P ENSG00000240960 LOC101929882 CPSF3 LOC100996549 KLF11 ENSG00000244260 GC02M009741
GH02G009653 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.1 +233.0 232995 6.0 PKNOX1 FOXA2 ARID4B SIN3A ZNF2 ZNF766 CBX5 FOS DEK ZNF263 YWHAQ RNU4-73P ENSG00000240960 ADAM17 LOC101929882 CPSF3 LOC105373419 LOC105373418
GH02G009546 1.8 FANTOM5 ENCODE dbSUPER 10.1 +128.6 128633 10.5 CREB3L1 AGO1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC TBX21 ADAM17 IAH1 CPSF3 ENSG00000271855 ENSG00000239300
GH02G009537 1.8 FANTOM5 Ensembl ENCODE dbSUPER 9.9 +115.2 115155 3.4 BMI1 CHAMP1 PCBP1 RELB IKZF2 CAVIN1 CEBPB TBX21 ZNF592 MEF2D ADAM17 IAH1 CPSF3 ENSG00000271855 ENSG00000239300
GH02G009167 1.5 Ensembl ENCODE dbSUPER 10.4 -255.2 -255220 2.1 PKNOX1 FOXA2 MLX CREB3L1 ZFP64 ARID4B SIN3A ZNF48 SLC30A9 ELK1 ASAP2 CPSF3 ITGB1BP1 ADAM17 LOC105373417 LOC100506317
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CPSF3 on UCSC Golden Path with GeneCards custom track

Promoters for CPSF3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000112591 -137 2001 HNRNPUL1 PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 KLF13

Genomic Location for CPSF3 Gene

Chromosome:
2
Start:
9,423,537 bp from pter
End:
9,473,110 bp from pter
Size:
49,574 bases
Orientation:
Plus strand

Genomic View for CPSF3 Gene

Genes around CPSF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CPSF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CPSF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CPSF3 Gene

Proteins for CPSF3 Gene

  • Protein details for CPSF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UKF6-CPSF3_HUMAN
    Recommended name:
    Cleavage and polyadenylation specificity factor subunit 3
    Protein Accession:
    Q9UKF6
    Secondary Accessions:
    • O14769
    • Q53RS2
    • Q96F36

    Protein attributes for CPSF3 Gene

    Size:
    684 amino acids
    Molecular mass:
    77486 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Component of the cleavage and polyadenylation specificity factor (CPSF) complex, composed of CPSF1, CPSF2, CPSF3, CPSF4 and FIP1L1. Interacts with CPSF2, CSTF2 and SYMPK. Interacts with TUT1; the interaction is direct and mediates the recruitment of the CPSF complex on the 3UTR of pre-mRNAs. Interacts with WDR33. Interacts with ZC3H3 (By similarity).

    Three dimensional structures from OCA and Proteopedia for CPSF3 Gene

neXtProt entry for CPSF3 Gene

Selected DME Specific Peptides for CPSF3 Gene

Q9UKF6:
  • TKAIYRWL
  • LGAGQEVGRSC
  • MTHATKAIY
  • SHFHLDH
  • HFHLDHCGALP
  • PVFALGRAQEL
  • LYTGDFSRQEDRHLM
  • NPFVFKHISNL
  • YHAGHVLGA
  • FDDIGPSV
  • VEGTLAKHIMSEP
  • LILDEYW
  • MSVDYISFSAH
  • AGHVLGAAM

Post-translational modifications for CPSF3 Gene

  • Sumoylated on Lys-462, Lys-465 and Lys-545, preferentially by SUMO3.
  • Ubiquitination at Lys295, isoforms=306, Lys428, and Lys487
  • Modification sites at PhosphoSitePlus

Other Protein References for CPSF3 Gene

Domains & Families for CPSF3 Gene

Protein Domains for CPSF3 Gene

Suggested Antigen Peptide Sequences for CPSF3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UKF6

UniProtKB/Swiss-Prot:

CPSF3_HUMAN :
  • Belongs to the metallo-beta-lactamase superfamily. RNA-metabolizing metallo-beta-lactamase-like family. CPSF3 subfamily.
Family:
  • Belongs to the metallo-beta-lactamase superfamily. RNA-metabolizing metallo-beta-lactamase-like family. CPSF3 subfamily.
genes like me logo Genes that share domains with CPSF3: view

No data available for Gene Families for CPSF3 Gene

Function for CPSF3 Gene

Molecular function for CPSF3 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. Has endonuclease activity, and functions as mRNA 3-end-processing endonuclease. Also involved in the histone 3-end pre-mRNA processing. U7 snRNP-dependent protein that induces both the 3-endoribonucleolytic cleavage of histone pre-mRNAs and acts as a 5 to 3 exonuclease for degrading the subsequent downstream cleavage product (DCP) of mature histone mRNAs. Cleavage occurs after the 5-ACCCA-3 sequence in the histone pre-mRNA leaving a 3hydroxyl group on the upstream fragment containing the stem loop (SL) and 5 phosphate on the downstream cleavage product (DCP) starting with CU nucleotides. The U7-dependent 5 to 3 exonuclease activity is processive and degrades the DCP RNA substrate even after complete removal of the U7-binding site. Binds to the downstream cleavage product (DCP) of histone pre-mRNAs and the cleaved DCP RNA substrate in a U7 snRNP dependent manner.

Enzyme Numbers (IUBMB) for CPSF3 Gene

Gene Ontology (GO) - Molecular Function for CPSF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding ISS --
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0004521 endoribonuclease activity IEA,ISS --
GO:0005515 protein binding IPI 18288197
genes like me logo Genes that share ontologies with CPSF3: view
genes like me logo Genes that share phenotypes with CPSF3: view

Animal Models for CPSF3 Gene

MGI Knock Outs for CPSF3:

Animal Model Products

CRISPR Products

miRNA for CPSF3 Gene

miRTarBase miRNAs that target CPSF3

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CPSF3 Gene

Localization for CPSF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CPSF3 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 CPSF3 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1

Gene Ontology (GO) - Cellular Components for CPSF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex IDA 18305108
GO:0030529 intracellular ribonucleoprotein complex IEA --
genes like me logo Genes that share ontologies with CPSF3: view

Pathways & Interactions for CPSF3 Gene

genes like me logo Genes that share pathways with CPSF3: view

Pathways by source for CPSF3 Gene

Gene Ontology (GO) - Biological Process for CPSF3 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 TAS 8929409
GO:0006379 mRNA cleavage TAS 8929409
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with CPSF3: view

No data available for SIGNOR curated interactions for CPSF3 Gene

Drugs & Compounds for CPSF3 Gene

(1) Drugs for CPSF3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for CPSF3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CPSF3: view

Transcripts for CPSF3 Gene

Unigene Clusters for CPSF3 Gene

Cleavage and polyadenylation specific factor 3, 73kDa:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CPSF3 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20
SP1: - - - - - - -
SP2: - - -
SP3: -
SP4: - -
SP5:
SP6:

Relevant External Links for CPSF3 Gene

GeneLoc Exon Structure for
CPSF3
ECgene alternative splicing isoforms for
CPSF3

Expression for CPSF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CPSF3 Gene

Protein differential expression in normal tissues from HIPED for CPSF3 Gene

This gene is overexpressed in Lymph node (15.8), Fetal ovary (6.6), and CD8 Tcells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CPSF3 Gene



Protein tissue co-expression partners for CPSF3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CPSF3 Gene:

CPSF3

SOURCE GeneReport for Unigene cluster for CPSF3 Gene:

Hs.515972

Evidence on tissue expression from TISSUES for CPSF3 Gene

  • Nervous system(4.8)
  • Liver(4.2)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with CPSF3: 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 CPSF3 Gene

Orthologs for CPSF3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CPSF3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CPSF3 34 35
  • 99.42 (n)
oppossum
(Monodelphis domestica)
Mammalia CPSF3 35
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CPSF3 35
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CPSF3 34 35
  • 93.13 (n)
dog
(Canis familiaris)
Mammalia CPSF3 34 35
  • 92.74 (n)
mouse
(Mus musculus)
Mammalia Cpsf3 34 16 35
  • 89.04 (n)
rat
(Rattus norvegicus)
Mammalia Cpsf3 34
  • 88.56 (n)
chicken
(Gallus gallus)
Aves CPSF3 34 35
  • 82.86 (n)
lizard
(Anolis carolinensis)
Reptilia CPSF3 35
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cpsf3 34
  • 78.61 (n)
Str.6057 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.16076 34
zebrafish
(Danio rerio)
Actinopterygii cpsf3 34 35
  • 75.9 (n)
wufc32f10 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12326 34
fruit fly
(Drosophila melanogaster)
Insecta CG7698 36
  • 65 (a)
Cpsf73 34 35
  • 62.58 (n)
CG1972 36
  • 40 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001224 34
  • 61.87 (n)
worm
(Caenorhabditis elegans)
Secernentea cpsf-3 34 35
  • 61.52 (n)
Y67H2A.1 36
  • 58 (a)
F10B5.8 36
  • 39 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YSH1 34 35 37
  • 56.13 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C04598g 34
  • 55.37 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR279C 34
  • 54.43 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons CPSF73-I 34
  • 57.06 (n)
rice
(Oryza sativa)
Liliopsida Os03g0852900 34
  • 56.39 (n)
Os.9048 34
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes ysh1 34
  • 55.77 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU03479 34
  • 51.5 (n)
Species where no ortholog for CPSF3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CPSF3 Gene

ENSEMBL:
Gene Tree for CPSF3 (if available)
TreeFam:
Gene Tree for CPSF3 (if available)

Paralogs for CPSF3 Gene

Paralogs for CPSF3 Gene

(1) SIMAP similar genes for CPSF3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with CPSF3: view

Variants for CPSF3 Gene

Sequence variations from dbSNP and Humsavar for CPSF3 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
VAR_035873 A breast cancer sample
rs1000032243 -- 9,429,088(+) CCACT(A/C)CTGAA intron-variant
rs1000075612 -- 9,423,385(+) CCGCG(A/G)GCCCA nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs1000140703 -- 9,466,366(+) CACGC(A/G)CACAC intron-variant
rs1000151459 -- 9,469,174(+) CAGAG(A/G)GCTCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CPSF3 Gene

Variant ID Type Subtype PubMed ID
esv3589774 CNV loss 21293372
nsv1114050 CNV deletion 24896259
nsv1123295 CNV deletion 24896259
nsv2602 CNV deletion 18451855
nsv514992 CNV gain 21397061
nsv580915 CNV gain 21841781

Variation tolerance for CPSF3 Gene

Residual Variation Intolerance Score: 9.17% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.08; 21.96% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CPSF3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CPSF3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CPSF3 Gene

Disorders for CPSF3 Gene

Relevant External Links for CPSF3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CPSF3

No disorders were found for CPSF3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CPSF3 Gene

Publications for CPSF3 Gene

  1. Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation. (PMID: 18688255) Kolev N.G. … Steitz J.A. (EMBO Rep. 2008) 3 4 22 64
  2. Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. (PMID: 17128255) Mandel C.R. … Tong L. (Nature 2006) 3 4 22 64
  3. 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 22 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. The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors. (PMID: 19136632) Rozenblatt-Rosen O. … Meyerson M. (Proc. Natl. Acad. Sci. U.S.A. 2009) 3 22 64

Products for CPSF3 Gene

Sources for CPSF3 Gene

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