CPSF3 (cleavage and polyadenylation specific factor 3)

Gene

• Entrez ID: 51692
• Gene name: Cleavage and polyadenylation specific factor 3
• Gene symbol: CPSF3
• Synonyms (NCBI Gene): CPSF-73, CPSF73, NEDMHS, NEDMHSN
• 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

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 606029
• HGNC: 2326
• e!Ensembl: ENSG00000119203

Protein

• UniProt ID: 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

Pathways

KEGG:

mRNA surveillance pathway

Reactome:

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

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Neurodevelopmental disorder with hypotonia, microcephaly, and seizures	Pathogenic	rs765749321	RCV002248348

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Uncertain significance	rs750132422	RCV005929210
Neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures	Uncertain significance	rs924983689, rs750067417	RCV003493384 RCV003989386

Associations from Text Mining
Disease Name	Relationship Type	References
Abortion Spontaneous	Associate	35121750
Adenocarcinoma of Lung	Associate	38213773
Carcinoma Renal Cell	Associate	25230976
Colorectal Neoplasms	Associate	31186036
Embryo Loss	Associate	35121750
Intellectual Disability	Associate	35121750
Microcephaly	Associate	35121750
Muscle Hypertonia	Associate	35121750
Ovarian Neoplasms	Associate	37992178
Seizures	Associate	35121750
Urinary Bladder Neoplasms	Associate	36175880