CPSF1 (cleavage and polyadenylation specific factor 1)

Gene

• Entrez ID: 29894
• Gene name: Cleavage and polyadenylation specific factor 1
• Gene symbol: CPSF1
• Synonyms: CPSF160, HSU37012, MYP27, P/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

SNPs

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

miRNA

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000398	Process	MRNA splicing, via spliceosome	TAS
GO:0005515	Function	Protein binding	IPI	7590244, 21102410, 21822216, 25416956, 32296183
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005847	Component	MRNA cleavage and polyadenylation specificity factor complex	IBA	21873635
GO:0005847	Component	MRNA cleavage and polyadenylation specificity factor complex	IDA	7590244, 21102410
GO:0006369	Process	Termination of RNA polymerase II transcription	TAS
GO:0006378	Process	MRNA polyadenylation	IBA	21873635
GO:0006378	Process	MRNA polyadenylation	IMP	7590244
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	TAS
GO:0006406	Process	MRNA export from nucleus	TAS
GO:0019899	Function	Enzyme binding	IPI	7590244
GO:0031124	Process	MRNA 3'-end processing	TAS
GO:0035925	Function	MRNA 3'-UTR AU-rich region binding	IDA	7590244
GO:0098789	Process	Pre-mRNA cleavage required for polyadenylation	IC	7590244

Other IDs

• MIM: 606027
• HGNC: 2324
• e!Ensembl: ENSG00000071894

Protein

• UniProt ID: 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

• 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

Pathways

KEGG:

mRNA surveillance pathway

Reactome:

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

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Gastric cancer	Hereditary Diffuse Gastric Cancer	rs137854571, rs63751108, rs34612342, rs121908383, rs121909144, rs121909775, rs121909219, rs121909223, rs63750871, rs80359530, rs121964873, rs121913530, rs606231203, rs121918505, rs587776802, rs28933369, rs121912469, rs80358011, rs397507262, rs80359439, rs397507333, rs80359543, rs80358831, rs80359596, rs80358920, rs80358972, rs80359659, rs397507404, rs397514661, rs80359516, rs200495564, rs80358419, rs80359274, rs80359283, rs80358427, rs80358428, rs80358435, rs81002805, rs397507660, rs397507663, rs80359391, rs80359443, rs81002797, rs80359466, rs397507752, rs80359484, rs80359603, rs397507954, rs80359058, rs80359071, rs397507981, rs80359121, rs80357086, rs80357064, rs397508936, rs80357695, rs80357661, rs397509035, rs80357544, rs80357577, rs80357881, rs80357296, rs80356923, rs80356866, rs80357504, rs80357390, rs80357239, rs80358099, rs397509284, rs80357258, rs199474738, rs199474747, rs587779204, rs63750439, rs267608076, rs587779246, rs63749999, rs267608078, rs63751327, rs267607719, rs267607734, rs63750706, rs63751711, rs587779047, rs587779075, rs267607949, rs63750633, rs63750803, rs63751618, rs267608154, rs200640585, rs80358018, rs80357857, rs80357882, rs180177103, rs587779815, rs587779865, rs587779872, rs587780059, rs121912666, rs587780088, rs587780104, rs200432447, rs180177100, rs587780226, rs587780784, rs587776416, rs587781276, rs587781629, rs587781694, rs587781727, rs587781730, rs587781807, rs587781894, rs587781948, rs121913344, rs587782292, rs587782350, rs587782558, rs587782719, rs587782885, rs587783057, rs730881833, rs730881411, rs730881336, rs139770721, rs730881869, rs730881633, rs730882007, rs786203115, rs765123255, rs1553333738, rs762083530, rs786202800, rs17174393, rs55996097, rs750621215, rs786203451, rs747604569, rs764389018, rs786204433, rs786204862, rs772821016, rs779582317, rs863225406, rs193922343, rs759965045, rs63749919, rs760228510, rs746481984, rs762307622, rs876659736, rs876660933, rs747727055, rs1450394308, rs876658348, rs876658431, rs876659326, rs876660444, rs730881369, rs878853865, rs753862052, rs587780024, rs138941496, rs886040739, rs886040744, rs886040347, rs878854957, rs886040123, rs398122662, rs886040942, rs1057517104, rs1057516320, rs1057516683, rs879254046, rs1057517253, rs587781927, rs985033810, rs1057519989, rs775464903, rs374230313, rs758304323, rs1060501599, rs758081262, rs1060500126, rs1060502734, rs587776408, rs1060501695, rs1114167816, rs1114167596, rs1114167667, rs1555460315, rs1135402788, rs1554086196, rs730881919, rs773356478, rs769237459, rs1553653158, rs587782087, rs1555107263, rs1555119940, rs1403784434, rs1342519012, rs751710099, rs1553616361, rs1553619721, rs1270783041, rs775036118, rs1555288557, rs1555460548, rs1555461154, rs1298667185, rs1553622218, rs63751101, rs1349928568, rs771936821, rs1021662947, rs1555921011, rs81002831, rs1555124506, rs1555574803, rs1060502716, rs1555605362, rs747057367, rs1565385010, rs1567554500, rs1567516230, rs1558644995, rs1555591308, rs778306619, rs1566231194, rs1603328466, rs1570406302, rs1586108714, rs768362387, rs1597713777, rs1060502926, rs1597867185, rs1591517571, rs1591663236, rs1593903006, rs1555284779, rs1597096243, rs45459799, rs1597360340, rs587781905, rs864622481, rs1601753141, rs1966858562, rs1966967065, rs1967016153, rs1967113484, rs2080473458, rs1591387978, rs1224428422, rs1597747184, rs2082309297, rs2051929740, rs147542208	21364753

Unknown
Disease name	Disease term	dbSNP ID	References
Stomach neoplasms	Malignant neoplasm of stomach, Stomach Neoplasms		21364753