Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	51692
Gene name	Cleavage and polyadenylation specific factor 3
Gene symbol	CPSF3
Synonyms (NCBI Gene)	CPSF-73CPSF73NEDMHSNEDMHSN
Chromosome	2
Chromosome location	2p25.1
Summary	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 p

Show/Hide all (23)

miRTarBase ID	miRNA	Experiments	Reference
MIRT023534	hsa-miR-1-3p	Proteomics	18668040
MIRT028443	hsa-miR-30a-5p	Proteomics	18668040
MIRT037757	hsa-miR-708-5p	CLASH	23622248
MIRT907229	hsa-miR-1297	CLIP-seq
MIRT907230	hsa-miR-1305	CLIP-seq
MIRT907231	hsa-miR-26a	CLIP-seq
MIRT907232	hsa-miR-26b	CLIP-seq
MIRT907233	hsa-miR-3973	CLIP-seq
MIRT907234	hsa-miR-4465	CLIP-seq
MIRT907235	hsa-miR-520g	CLIP-seq
MIRT907236	hsa-miR-520h	CLIP-seq
MIRT907237	hsa-miR-607	CLIP-seq
MIRT907233	hsa-miR-3973	CLIP-seq
MIRT907235	hsa-miR-520g	CLIP-seq
MIRT907236	hsa-miR-520h	CLIP-seq
MIRT907230	hsa-miR-1305	CLIP-seq
MIRT2204946	hsa-miR-331-5p	CLIP-seq
MIRT907233	hsa-miR-3973	CLIP-seq
MIRT2204947	hsa-miR-495	CLIP-seq
MIRT907235	hsa-miR-520g	CLIP-seq
MIRT907236	hsa-miR-520h	CLIP-seq
MIRT2204948	hsa-miR-548n	CLIP-seq
MIRT907237	hsa-miR-607	CLIP-seq

Show/Hide all (29)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IEA
GO:0003723	Function	RNA binding	ISS
GO:0004518	Function	Nuclease activity	IEA
GO:0004519	Function	Endonuclease activity	IEA
GO:0004521	Function	RNA endonuclease activity	IBA
GO:0004521	Function	RNA endonuclease activity	IEA
GO:0004521	Function	RNA endonuclease activity	IMP	30507380
GO:0004521	Function	RNA endonuclease activity	ISS
GO:0004534	Function	5'-3' RNA exonuclease activity	IBA
GO:0004534	Function	5'-3' RNA exonuclease activity	IEA
GO:0004534	Function	5'-3' RNA exonuclease activity	ISS
GO:0005515	Function	Protein binding	IPI	18288197, 18688255, 21102410, 32814053
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS	7969155
GO:0005847	Component	MRNA cleavage and polyadenylation specificity factor complex	IBA
GO:0005847	Component	MRNA cleavage and polyadenylation specificity factor complex	IDA	8929409, 18305108, 21102410
GO:0005847	Component	MRNA cleavage and polyadenylation specificity factor complex	IEA
GO:0006397	Process	MRNA processing	IEA
GO:0006398	Process	MRNA 3'-end processing by stem-loop binding and cleavage	IBA
GO:0006398	Process	MRNA 3'-end processing by stem-loop binding and cleavage	IDA	18688255
GO:0006398	Process	MRNA 3'-end processing by stem-loop binding and cleavage	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0031124	Process	MRNA 3'-end processing	IMP	30507380
GO:0046872	Function	Metal ion binding	IEA
GO:0046872	Function	Metal ion binding	IMP	30507380
GO:0180010	Process	Co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway	IDA	8929409
GO:1900087	Process	Positive regulation of G1/S transition of mitotic cell cycle	IMP	30507380
GO:1990904	Component	Ribonucleoprotein complex	IEA

MIM	HGNC	e!Ensembl
606029	2326	ENSG00000119203

Q9UKF6

Protein name

Cleavage and polyadenylation specificity factor subunit 3 (EC 3.1.27.-) (Cleavage and polyadenylation specificity factor 73 kDa subunit) (CPSF 73 kDa subunit) (mRNA 3'-end-processing endonuclease CPSF-73)

Protein function

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that plays 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 c

PDB

2I7T , 2I7V , 6M8Q , 6V4X , 8T1Q , 8T1R

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00753	Lactamase_B	20 → 262	Metallo-beta-lactamase superfamily	Domain
PF10996	Beta-Casp	246 → 367	Beta-Casp domain	Domain
PF07521	RMMBL	381 → 448	Zn-dependent metallo-hydrolase RNA specificity domain	Motif
PF11718	CPSF73-100_C	479 → 682		Domain

Sequence

MSAIPAEESDQLLIRPLGAGQEVGRSCIILEFKGRKIMLDCGIHPGLEGMDALPYIDLID
PAEIDLLLISHFHLDHCGALPWFLQKTSFKGRTFMTHATKAIYRWLLSDYVKVSNISADD
MLYTETDLEESMDKIETINFHEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDF
SRQEDRHLMAAEIPNIKPDILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPV
FALGRAQELLLILDEYWQNHPELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQININ
NPFVFKHISNLKSMDHFDDIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVE
GTLAKHIMSEPEEITTMSGQKLPLKMSVDYISFSAHTDYQQTSEFIRALKPPHVILVHGE
QNEMARLKAALIREYEDNDEVHIEVHNPRNTEAVTLNFRGEKLAKVMGFLADKKPEQGQR
VSGILVKRNFNYHILSPCDLSNYTDLAMSTVKQTQAIPYTGPFNLLCYQLQKLTGDVEEL
EIQEKPALKVFKNITVIQEPGMVVLEWLANPSNDMYADTVTTVILEVQSNPKIRKGAVQK
VSKKLEMHVYSKRLEIMLQDIFGEDCVSVKDDSILSVTVDGKTANLNLETRTVECEEGSE
DDESLREMVELAAQRLYEALTPVH

Sequence length

684

Interactions

View interactions

	KEGG		Reactome
	mRNA surveillance pathway		Transport of Mature mRNA Derived from an Intronless Transcript mRNA Splicing - Major Pathway mRNA 3'-end processing RNA Polymerase II Transcription Termination Processing of Intronless Pre-mRNAs

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Neurodevelopmental disorder with hypotonia, microcephaly, and seizures	Pathogenic	rs765749321	RCV002248348	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures	Uncertain significance	ClinVar ClinVar, Disgenet, GWAS catalog, HPO ClinVar, Disgenet, GWAS catalog, HPO ClinVar, Disgenet, GWAS catalog, HPO	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (12)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	31452762		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	25230976	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	31186036		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	31186036	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	35121750	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	Pubtator	35121750	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	31452762		★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	31452762		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	37992178	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	35121750	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	36175880	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

CPSF3 (cleavage and polyadenylation specific factor 3)