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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	29894
Gene name	Cleavage and polyadenylation specific factor 1
Gene symbol	CPSF1
Synonyms (NCBI Gene)	CPSF160HSU37012MYP27P/cl.18
Chromosome	8
Chromosome location	8q24.3
Summary	Cleavage and polyadenylation specificity factor (CPSF) is a multisubunit complex that plays a central role in 3-prime processing of pre-mRNAs. CPSF recognizes the AAUAAA signal in the pre-mRNA and interacts with other proteins to facilitate both RNA cleav

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs782640869	CT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1586620121	G>A	Pathogenic	Stop gained, coding sequence variant

Show/Hide all (51)

miRTarBase ID	miRNA	Experiments	Reference
MIRT004179	hsa-miR-197-3p	Microarray	16822819
MIRT023819	hsa-miR-1-3p	Proteomics	18668040
MIRT028569	hsa-miR-30a-5p	Proteomics	18668040
MIRT032424	hsa-let-7b-5p	Proteomics	18668040
MIRT051016	hsa-miR-17-5p	CLASH	23622248
MIRT440885	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT440885	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT907081	hsa-let-7a	CLIP-seq
MIRT907082	hsa-let-7b	CLIP-seq
MIRT907083	hsa-let-7c	CLIP-seq
MIRT907084	hsa-let-7d	CLIP-seq
MIRT907085	hsa-let-7e	CLIP-seq
MIRT907086	hsa-let-7f	CLIP-seq
MIRT907087	hsa-let-7g	CLIP-seq
MIRT907088	hsa-let-7i	CLIP-seq
MIRT907089	hsa-miR-138	CLIP-seq
MIRT907090	hsa-miR-196a	CLIP-seq
MIRT907091	hsa-miR-196b	CLIP-seq
MIRT907092	hsa-miR-2052	CLIP-seq
MIRT907093	hsa-miR-323-5p	CLIP-seq
MIRT907094	hsa-miR-3689a-3p	CLIP-seq
MIRT907095	hsa-miR-3689c	CLIP-seq
MIRT907096	hsa-miR-4307	CLIP-seq
MIRT907097	hsa-miR-4456	CLIP-seq
MIRT907098	hsa-miR-4458	CLIP-seq
MIRT907099	hsa-miR-4500	CLIP-seq
MIRT907100	hsa-miR-4651	CLIP-seq
MIRT907101	hsa-miR-4728-5p	CLIP-seq
MIRT907102	hsa-miR-502-5p	CLIP-seq
MIRT907103	hsa-miR-581	CLIP-seq
MIRT907104	hsa-miR-608	CLIP-seq
MIRT907105	hsa-miR-876-3p	CLIP-seq
MIRT907106	hsa-miR-98	CLIP-seq
MIRT907081	hsa-let-7a	CLIP-seq
MIRT907082	hsa-let-7b	CLIP-seq
MIRT907083	hsa-let-7c	CLIP-seq
MIRT907084	hsa-let-7d	CLIP-seq
MIRT907085	hsa-let-7e	CLIP-seq
MIRT907086	hsa-let-7f	CLIP-seq
MIRT907087	hsa-let-7g	CLIP-seq
MIRT907088	hsa-let-7i	CLIP-seq
MIRT907090	hsa-miR-196a	CLIP-seq
MIRT907091	hsa-miR-196b	CLIP-seq
MIRT907094	hsa-miR-3689a-3p	CLIP-seq
MIRT907095	hsa-miR-3689c	CLIP-seq
MIRT907098	hsa-miR-4458	CLIP-seq
MIRT907099	hsa-miR-4500	CLIP-seq
MIRT907100	hsa-miR-4651	CLIP-seq
MIRT907101	hsa-miR-4728-5p	CLIP-seq
MIRT907104	hsa-miR-608	CLIP-seq
MIRT907106	hsa-miR-98	CLIP-seq

Show/Hide all (15)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	7590244, 21102410, 21822216, 25416956, 32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005847	Component	MRNA cleavage and polyadenylation specificity factor complex	IBA
GO:0005847	Component	MRNA cleavage and polyadenylation specificity factor complex	IDA	7590244, 21102410
GO:0006397	Process	MRNA processing	IEA
GO:0019899	Function	Enzyme binding	IPI	7590244
GO:0031123	Process	RNA 3'-end processing	IEA
GO:0035925	Function	MRNA 3'-UTR AU-rich region binding	IDA	7590244
GO:0180012	Process	Co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway	IC	7590244

MIM	HGNC	e!Ensembl
606027	2324	ENSG00000071894

Q10570

Protein name

Cleavage and polyadenylation specificity factor subunit 1 (Cleavage and polyadenylation specificity factor 160 kDa subunit) (CPSF 160 kDa subunit)

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

6BLY , 6BM0 , 6DNH , 6F9N , 6FUW , 6URG , 6URO , 8E3I , 8E3Q , 8R8R

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF10433	MMS1_N	92 → 686		Domain
PF03178	CPSF_A	1073 → 1409	CPSF A subunit region	Family

Tissue specificity

TISSUE SPECIFICITY: Widely expressed, with high expression in the retina. {ECO:0000269|PubMed:30689892}.

Sequence

MYAVYKQAHPPTGLEFSMYCNFFNNSERNLVVAGTSQLYVYRLNRDAEALTKNDRSTEGK
AHREKLELAASFSFFGNVMSMASVQLAGAKRDALLLSFKDAKLSVVEYDPGTHDLKTLSL
HYFEEPELRDGFVQNVHTPRVRVDPDGRCAAMLVYGTRLVVLPFRRESLAEEHEGLVGEG
QRSSFLPSYIIDVRALDEKLLNIIDLQFLHGYYEPTLLILFEPNQTWPGRVAVRQDTCSI
VAISLNITQKVHPVIWSLTSLPFDCTQALAVPKPIGGVVVFAVNSLLYLNQSVPPYGVAL
NSLTTGTTAFPLRTQEGVRITLDCAQATFISYDKMVISLKGGEIYVLTLITDGMRSVRAF
HFDKAAASVLTTSMVTMEPGYLFLGSRLGNSLLLKYTEKLQEPPASAVREAADKEEPPSK
KKRVDATAGWSAAGKSVPQDEVDEIEVYGSEAQSGTQLATYSFEVCDSILNIGPCANAAV
GEPAFLSEEFQNSPEPDLEIVVCSGHGKNGALSVLQKSIRPQVVTTFELPGCYDMWTVIA
PVRKEEEDNPKGEGTEQEPSTTPEADDDGRRHGFLILSREDSTMILQTGQEIMELDTSGF
ATQGPTVFAGNIGDNRYIVQVSPLGIRLLEGVNQLHFIPVDLGAPIVQCAVADPYVVIMS
AEGHVTMFLLKSDSYGGRHHRLALHKPPLHHQSKVITLCLYRDLSGMFTTESRLGGARDE
LGGRSGPEAEGLGSETSPTVDDEEEMLYGDSGSLFSPSKEEARRSSQPPADRDPAPFRAE
PTHWCLLVRENGTMEIYQLPDWRLVFLVKNFPVGQRVLVDSSFGQPTTQGEARREEATRQ
GELPLVKEVLLVALGSRQSRPYLLVHVDQELLIYEAFPHDSQLGQGNLKVRFKKVPHNIN
FREKKPKPSKKKAEGGGAEEGAGARGRVARFRYFEDIYGYSGVFICGPSPHWLLVTGRGA
LRLHPMAIDGPVDSFAPFHNVNCPRGFLYFNRQGELRISVLPAYLSYDAPWPVRKIPLRC
TAHYVAYHVESKVYAVATSTNTPCARIPRMTGEEKEFETIERDERYIHPQQEAFSIQLIS
PVSWEAIPNARIELQEWEHVTCMKTVSLRSEETVSGLKGYVAAGTCLMQGEEVTCRGRIL
IMDVIEVVPEPGQPLTKNKFKVLYEKEQKGPVTALCHCNGHLVSAIGQKIFLWSLRASEL
TGMAFIDTQLYIHQMISVKNFILAADVMKSISLLRYQEESKTLSLVSRDAKPLEVYSVDF
MVDNAQLGFLVSDRDRNLMVYMYLPEAKESFGGMRLLRRADFHVGAHVNTFWRTPCRGAT
EGLSKKSVVWENKHITWFATLDGGIGLLLPMQEKTYRRLLMLQNALTTMLPHHAGLNPRA
FRMLHVDRRTLQNAVRNVLDGELLNRYLYLSTMERSELAKKIGTTPDIILDDLLETDRVT
AHF

Sequence length

1443

Interactions

View interactions

	KEGG		Reactome
	mRNA surveillance pathway		Transport of Mature mRNA Derived from an Intronless Transcript tRNA processing in the nucleus 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
Myopia 27	Likely pathogenic; Pathogenic	rs1821166689, rs2537385296, rs782555528, rs1554862601, rs1586620121	RCV003991838 RCV004566414 RCV001029433 RCV001029435 RCV001029437	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (6)

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.
CPSF1-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	-	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOPIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOPIA 27, AUTOSOMAL DOMINANT	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STOMACH NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (16)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alternating hemiplegia of childhood	Alternating hemiplegia of childhood	Pubtator	32929364	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	32929364	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	32929364	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	28634396		★★★★★ ★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	BEFREE	30689892		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary Diffuse Gastric Cancer	Gastric Cancer	CTD_human_DG	21364753		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	28634396	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	28634396		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	CTD_human_DG	21364753		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	35002215, 37191617	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neoplasms	Neoplasms	BEFREE	28634396		★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	37191617	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe myopia	Myopia	BEFREE	30689892		★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	32437477	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach Neoplasms	CTD_human_DG	21364753		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	32929364	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

CPSF1 (cleavage and polyadenylation specific factor 1)