PRPF19 (pre-mRNA processing factor 19)

Gene

• Entrez ID: 27339
• Gene name: Pre-mRNA processing factor 19
• Gene symbol: PRPF19
• Synonyms: NMP200, PRP19, PSO4, SNEV, UBOX4, hPSO4
• Chromosome: 11
• Chromosome location: 11q12.2
• Summary: PSO4 is the human homolog of yeast Pso4, a gene essential for cell survival and DNA repair (Beck et al., 2008 [PubMed 18263876]).[supplied by OMIM, Sep 2008]

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT051973	hsa-let-7b-5p	CLASH	23622248
MIRT049927	hsa-miR-30a-5p	CLASH	23622248
MIRT041329	hsa-miR-193b-3p	CLASH	23622248
MIRT1265325	hsa-miR-1273f	CLIP-seq
MIRT1265326	hsa-miR-128	CLIP-seq
MIRT1265327	hsa-miR-143	CLIP-seq
MIRT1265328	hsa-miR-1976	CLIP-seq
MIRT1265329	hsa-miR-203	CLIP-seq
MIRT1265330	hsa-miR-204	CLIP-seq
MIRT1265331	hsa-miR-211	CLIP-seq
MIRT1265332	hsa-miR-24	CLIP-seq
MIRT1265333	hsa-miR-27a	CLIP-seq
MIRT1265334	hsa-miR-27b	CLIP-seq
MIRT1265335	hsa-miR-28-3p	CLIP-seq
MIRT1265336	hsa-miR-3127-3p	CLIP-seq
MIRT1265337	hsa-miR-4284	CLIP-seq
MIRT1265338	hsa-miR-4290	CLIP-seq
MIRT1265339	hsa-miR-4667-3p	CLIP-seq
MIRT1265340	hsa-miR-4687-5p	CLIP-seq
MIRT1265341	hsa-miR-4708-5p	CLIP-seq
MIRT1265342	hsa-miR-4738-3p	CLIP-seq
MIRT1265343	hsa-miR-4755-5p	CLIP-seq
MIRT1265344	hsa-miR-4770	CLIP-seq
MIRT1265345	hsa-miR-4780	CLIP-seq
MIRT1265346	hsa-miR-513a-5p	CLIP-seq
MIRT1265347	hsa-miR-520d-5p	CLIP-seq
MIRT1265348	hsa-miR-524-5p	CLIP-seq
MIRT1265349	hsa-miR-623	CLIP-seq
MIRT1265350	hsa-miR-759	CLIP-seq
MIRT1265326	hsa-miR-128	CLIP-seq
MIRT1265328	hsa-miR-1976	CLIP-seq
MIRT1265330	hsa-miR-204	CLIP-seq
MIRT1265331	hsa-miR-211	CLIP-seq
MIRT1265332	hsa-miR-24	CLIP-seq
MIRT1265333	hsa-miR-27a	CLIP-seq
MIRT1265334	hsa-miR-27b	CLIP-seq
MIRT1265335	hsa-miR-28-3p	CLIP-seq
MIRT1265336	hsa-miR-3127-3p	CLIP-seq
MIRT1265337	hsa-miR-4284	CLIP-seq
MIRT1265338	hsa-miR-4290	CLIP-seq
MIRT2078020	hsa-miR-4641	CLIP-seq
MIRT1265339	hsa-miR-4667-3p	CLIP-seq
MIRT1265340	hsa-miR-4687-5p	CLIP-seq
MIRT2078021	hsa-miR-4722-3p	CLIP-seq
MIRT1265342	hsa-miR-4738-3p	CLIP-seq
MIRT1265343	hsa-miR-4755-5p	CLIP-seq
MIRT1265345	hsa-miR-4780	CLIP-seq
MIRT1265346	hsa-miR-513a-5p	CLIP-seq
MIRT1265347	hsa-miR-520d-5p	CLIP-seq
MIRT1265348	hsa-miR-524-5p	CLIP-seq
MIRT1265349	hsa-miR-623	CLIP-seq
MIRT2304512	hsa-miR-1224-3p	CLIP-seq
MIRT2304513	hsa-miR-1257	CLIP-seq
MIRT2304514	hsa-miR-1260	CLIP-seq
MIRT2304515	hsa-miR-1260b	CLIP-seq
MIRT1265326	hsa-miR-128	CLIP-seq
MIRT2304516	hsa-miR-1280	CLIP-seq
MIRT1265328	hsa-miR-1976	CLIP-seq
MIRT1265330	hsa-miR-204	CLIP-seq
MIRT1265331	hsa-miR-211	CLIP-seq
MIRT2304517	hsa-miR-2115	CLIP-seq
MIRT1265332	hsa-miR-24	CLIP-seq
MIRT1265333	hsa-miR-27a	CLIP-seq
MIRT1265334	hsa-miR-27b	CLIP-seq
MIRT1265336	hsa-miR-3127-3p	CLIP-seq
MIRT2304518	hsa-miR-3154	CLIP-seq
MIRT2304519	hsa-miR-3679-3p	CLIP-seq
MIRT2304520	hsa-miR-3689d	CLIP-seq
MIRT2304521	hsa-miR-4277	CLIP-seq
MIRT1265337	hsa-miR-4284	CLIP-seq
MIRT2304522	hsa-miR-4462	CLIP-seq
MIRT2078020	hsa-miR-4641	CLIP-seq
MIRT2304523	hsa-miR-4645-3p	CLIP-seq
MIRT2078021	hsa-miR-4722-3p	CLIP-seq
MIRT1265343	hsa-miR-4755-5p	CLIP-seq
MIRT1265345	hsa-miR-4780	CLIP-seq
MIRT2304524	hsa-miR-490-5p	CLIP-seq
MIRT1265346	hsa-miR-513a-5p	CLIP-seq
MIRT2304525	hsa-miR-542-3p	CLIP-seq
MIRT2304526	hsa-miR-584	CLIP-seq
MIRT2304527	hsa-miR-602	CLIP-seq
MIRT1265349	hsa-miR-623	CLIP-seq
MIRT2304528	hsa-miR-876-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000209	Process	Protein polyubiquitination	IDA	11435423
GO:0000244	Process	Spliceosomal tri-snRNP complex assembly	IDA	20595234
GO:0000245	Process	Spliceosomal complex assembly	IMP	16332694
GO:0000349	Process	Generation of catalytic spliceosome for first transesterification step	IBA	21873635
GO:0000398	Process	MRNA splicing, via spliceosome	IC	11991638
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	20176811
GO:0000398	Process	MRNA splicing, via spliceosome	TAS
GO:0000974	Component	Prp19 complex	IBA	21873635
GO:0000974	Component	Prp19 complex	IDA	20176811
GO:0001833	Process	Inner cell mass cell proliferation	IEA
GO:0004842	Function	Ubiquitin-protein transferase activity	IBA	21873635
GO:0005515	Function	Protein binding	IPI	19188445, 19633697, 19641227, 20176811, 20467437, 20595234, 21536736, 22365833, 22569250, 22961380, 28514442
GO:0005634	Component	Nucleus	IDA	11435423, 19188445
GO:0005654	Component	Nucleoplasm	TAS
GO:0005662	Component	DNA replication factor A complex	IDA	24332808
GO:0005737	Component	Cytoplasm	IDA	11435423
GO:0005811	Component	Lipid droplet	IEA
GO:0005819	Component	Spindle	IEA
GO:0006283	Process	Transcription-coupled nucleotide-excision repair	TAS
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IMP	18263876
GO:0008610	Process	Lipid biosynthetic process	IEA
GO:0010498	Process	Proteasomal protein catabolic process	IMP	17349974
GO:0016020	Component	Membrane	HDA	19946888
GO:0016607	Component	Nuclear speck	IDA	16332694, 24332808
GO:0034450	Function	Ubiquitin-ubiquitin ligase activity	IDA	11435423
GO:0034613	Process	Cellular protein localization	IMP	18263876
GO:0035861	Component	Site of double-strand break	IDA	18263876
GO:0042802	Function	Identical protein binding	IPI	16332694
GO:0045666	Process	Positive regulation of neuron differentiation	IEA
GO:0048026	Process	Positive regulation of mRNA splicing, via spliceosome	IEA
GO:0048711	Process	Positive regulation of astrocyte differentiation	IEA
GO:0061630	Function	Ubiquitin protein ligase activity	IDA	11435423
GO:0061630	Function	Ubiquitin protein ligase activity	IMP	20595234
GO:0070534	Process	Protein K63-linked ubiquitination	IMP	20595234, 24332808
GO:0071006	Component	U2-type catalytic step 1 spliceosome	IBA	21873635
GO:0071007	Component	U2-type catalytic step 2 spliceosome	IDA	28076346
GO:0071013	Component	Catalytic step 2 spliceosome	IBA	21873635
GO:0071013	Component	Catalytic step 2 spliceosome	IDA	11991638
GO:0072422	Process	Signal transduction involved in DNA damage checkpoint	IMP	24332808

Other IDs

• MIM: 608330
• HGNC: 17896
• e!Ensembl: ENSG00000110107

Protein

• UniProt ID: Q9UMS4
• Protein name: Pre-mRNA-processing factor 19 (EC 2.3.2.27) (Nuclear matrix protein 200) (PRP19/PSO4 homolog) (hPso4) (RING-type E3 ubiquitin transferase PRP19) (Senescence evasion factor)
• Protein function: Ubiquitin-protein ligase which is a core component of several complexes mainly involved pre-mRNA splicing and DNA repair. Required for pre-mRNA splicing as component of the spliceosome (PubMed:28076346, PubMed:28502770, PubMed:29301961, PubMed:2
• PDB: 4LG8, 5MQF, 5XJC, 5YZG, 5Z56, 5Z57, 6FF7, 6ICZ, 6ID0, 6ID1, 6QDV, 7A5P, 7W59, 7W5A, 7W5B, 8C6J, 8CH6, 8I0T, 8I0U, 8I0V, 8I0W, 8RO2, 9FMD
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04564	U-box	2 → 57	U-box domain	Domain
  PF08606	Prp19	67 → 134	Prp19/Pso4-like	Domain
  PF00400	WD40	254 → 292	WD domain, G-beta repeat	Repeat
  PF00400	WD40	296 → 329	WD domain, G-beta repeat	Repeat
  PF00400	WD40	338 → 378	WD domain, G-beta repeat	Repeat
  PF00400	WD40	382 → 420	WD domain, G-beta repeat	Repeat
  PF00400	WD40	465 → 503	WD domain, G-beta repeat	Repeat

• Sequence:

  MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP
  IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL
  TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA
  TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG
  GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ
  VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP
  DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD
  LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG
  VAFGHHAKFIASTGMDRSLKFYSL

• Sequence length: 504

Pathways

KEGG:

Spliceosome
Ubiquitin mediated proteolysis

Reactome:

Formation of TC-NER Pre-Incision Complex
Transcription-Coupled Nucleotide Excision Repair (TC-NER)
Dual incision in TC-NER
Gap-filling DNA repair synthesis and ligation in TC-NER
mRNA Splicing - Major Pathway

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