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 Ref... See more...

Aliases for CPSF3 Gene

Aliases for CPSF3 Gene

  • Cleavage And Polyadenylation Specific Factor 3 2 3 5
  • CPSF73 2 3 4
  • Cleavage And Polyadenylation Specificity Factor Subunit 3 3 4
  • Cleavage And Polyadenylation Specific Factor 3, 73kDa 2 3
  • MRNA 3'-End-Processing Endonuclease CPSF-73 3 4
  • CPSF-73 2 3
  • Cleavage And Polyadenylation Specificity Factor 73 KDa Subunit 4
  • Cleavage And Polyadenylation Specific Factor 3, 73kD Subunit 2
  • CPSF 73 KDa Subunit 4
  • EC 3.1.27.- 4
  • EC 3.1.27 51
  • CPSF3 5
  • YSH1 2

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 Cleavage of Growing Transcript in the Termination Region and Transport of Mature Transcript to Cytoplasm. Gene Ontology (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 Summary 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 3'hydroxyl 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. Required for the selective processing of microRNAs (miRNAs) during embryonic stem cell differentiation via its interaction with ISY1 (By similarity). Required for the biogenesis of all miRNAs from the pri-miR-17-92 primary transcript except miR-92a (By similarity). Only required for the biogenesis of miR-290 and miR-96 from the pri-miR-290-295 and pri-miR-96-183 primary transcripts, respectively (By similarity).

Gene Wiki entry for CPSF3 Gene

Additional gene information for CPSF3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CPSF3 Gene

Genomics for CPSF3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CPSF3 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 CPSF3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CPSF3

Top Transcription factor binding sites by QIAGEN in the CPSF3 gene promoter:
  • Egr-1
  • HNF-1
  • HNF-1A
  • MAZR
  • Olf-1
  • p53
  • Pax-4a
  • POU2F1
  • POU2F1a
  • RSRFC4

Genomic Locations for CPSF3 Gene

Genomic Locations for CPSF3 Gene
chr2:9,423,537-9,473,110
(GRCh38/hg38)
Size:
49,574 bases
Orientation:
Plus strand
chr2:9,563,697-9,613,230
(GRCh37/hg19)
Size:
49,534 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 3'UTR 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, Lys306, Lys428, and Lys487
  • Modification sites at PhosphoSitePlus

Other Protein References for CPSF3 Gene

Domains & Families for CPSF3 Gene

Gene Families for CPSF3 Gene

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

Protein Domains for CPSF3 Gene

InterPro:
Blocks:
  • RNA-metabolising metallo-beta-lactamase
ProtoNet:

Suggested Antigen Peptide Sequences for CPSF3 Gene

GenScript: Design optimal peptide antigens:
  • mRNA 3'-end-processing endonuclease CPSF-73 (CPSF3_HUMAN)
  • CPSF3 protein (Q05BZ5_HUMAN)

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

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 3'hydroxyl 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. Required for the selective processing of microRNAs (miRNAs) during embryonic stem cell differentiation via its interaction with ISY1 (By similarity). Required for the biogenesis of all miRNAs from the pri-miR-17-92 primary transcript except miR-92a (By similarity). Only required for the biogenesis of miR-290 and miR-96 from the pri-miR-290-295 and pri-miR-96-183 primary transcripts, respectively (By similarity).

Enzyme Numbers (IUBMB) for CPSF3 Gene

Phenotypes From GWAS Catalog for CPSF3 Gene

Gene Ontology (GO) - Molecular Function for CPSF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA,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:
  • Cpsf3 Cpsf3<tm1a(EUCOMM)Wtsi>
  • Cpsf3 Cpsf3<tm1b(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

miRNA for CPSF3 Gene

miRTarBase miRNAs that target CPSF3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CPSF3

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
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 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 IEA,IDA 18305108
genes like me logo Genes that share ontologies with CPSF3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CPSF3 Gene

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,IBA 21873635
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

mRNA/cDNA for CPSF3 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CPSF3

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

Expression for CPSF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for CPSF3 Gene



Protein tissue co-expression partners for CPSF3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CPSF3

SOURCE GeneReport for Unigene cluster for CPSF3 Gene:

Hs.515972

Evidence on tissue expression from TISSUES for CPSF3 Gene

  • Nervous system(4.9)
  • Liver(4.3)
  • Kidney(2.8)
  • Skin(2.4)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with CPSF3: 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 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 30 31
  • 99.42 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CPSF3 31
  • 96 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CPSF3 31
  • 96 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia CPSF3 30 31
  • 93.13 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CPSF3 30 31
  • 92.74 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Cpsf3 30 17 31
  • 89.04 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cpsf3 30
  • 88.56 (n)
Chicken
(Gallus gallus)
Aves CPSF3 30 31
  • 82.86 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CPSF3 31
  • 93 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cpsf3 30
  • 78.61 (n)
Str.6057 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.16076 30
Zebrafish
(Danio rerio)
Actinopterygii cpsf3 30 31
  • 75.9 (n)
OneToOne
wufc32f10 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12326 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG7698 32
  • 65 (a)
Cpsf73 30 31
  • 62.58 (n)
OneToOne
CG1972 32
  • 40 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001224 30
  • 61.87 (n)
Worm
(Caenorhabditis elegans)
Secernentea cpsf-3 30 31
  • 61.52 (n)
OneToOne
Y67H2A.1 32
  • 58 (a)
F10B5.8 32
  • 39 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YSH1 30 31 33
  • 56.13 (n)
OneToMany
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C04598g 30
  • 55.37 (n)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AGR279C 30
  • 54.43 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons CPSF73-I 30
  • 57.06 (n)
Rice
(Oryza sativa)
Liliopsida Os03g0852900 30
  • 56.39 (n)
Os.9048 30
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes ysh1 30
  • 55.77 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU03479 30
  • 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for CPSF3: view image

Paralogs for CPSF3 Gene

Paralogs for CPSF3 Gene

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

  • CPSF3_HUMAN
  • C9JZH6_HUMAN
  • G5E9W3_HUMAN
  • Q05BZ5_HUMAN
genes like me logo Genes that share paralogs with CPSF3: view

Variants for CPSF3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CPSF3 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
VAR_035873 A breast cancer sample p.Asp578Asn
rs17850770 - p.Glu142Gly

Additional dbSNP identifiers (rs#s) for CPSF3 Gene

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)

Additional Variant Information for CPSF3 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for CPSF3 Gene

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 NG … Steitz JA (EMBO reports 2008) 3 4 23
  2. Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. (PMID: 17128255) Mandel CR … Tong L (Nature 2006) 3 4 23
  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 (The EMBO journal 2004) 3 4 23
  4. The poly A polymerase Star-PAP controls 3'-end cleavage by promoting CPSF interaction and specificity toward the pre-mRNA. (PMID: 21102410) Laishram RS … Anderson RA (The EMBO journal 2010) 3 4
  5. Inositol 1,4,5-triphosphate receptor-binding protein released with inositol 1,4,5-triphosphate (IRBIT) associates with components of the mRNA 3' processing machinery in a phosphorylation-dependent manner and inhibits polyadenylation. (PMID: 19224921) Kiefer H … Mikoshiba K (The Journal of biological chemistry 2009) 3 23

Products for CPSF3 Gene

Sources for CPSF3 Gene