EuRBPDB

Description

Ensembl ID: ENSG00000196504 (Gene tree)
Gene ID: 55660
Gene Symbol: PRPF40A
Alias: FLJ20585|FBP11|HYPA|NY-REN-6|HIP10|FBP-11|FLAF1|Prp40|FNBP3
Full Name: pre-mRNA processing factor 40 homolog A
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Minus strand
Length: 66,405 bases
Position: chr2:152,651,593-152,717,997
Accession: 16463
RBP type: non-canonical RBP
Summary: (Pre-MRNA Processing Factor 40 Homolog A) is a Protein Coding gene. Diseases associated with PRPF40A include Rett Syndrome. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include proline-rich region binding. An important paralog of this gene is PRPF40B.

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
22681889	The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts	4SURIC & HEK293	2012 May	Baltz AG	DOI: 10.1016/j.molcel.2012.05.021
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & HEK293	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & HEK293	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
29431736	Capturing the interactome of newly transcribed RNA	PolyT-RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & MCF10A	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & MCF7	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & U2OS	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30352994	Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture	RIC & Jurkat	2018 Oct 23	Perez-Perri JI	DOI:10.1038/s41467-018-06557-8

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
28258342	COL1A1, PRPF40A, and UCP2 correlate with hypoxia markers in non-small cell lung cancer.	J Cancer Res Clin Oncol	2017 Jul	Oleksiewicz U	doi: 10.1007/s00432-017-2381-y
12460579	Solution structure and ligand recognition of the WW domain pair of the yeast splicing factor Prp40.	J Mol Biol	2002 Dec 6	Wiesner S	-
10978320	The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II.	J Biol Chem	2000 Dec 22	Morris DP	-

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000450303	PRPF40A-204	496	-	-	- (aa)	-	-
ENST00000410080	PRPF40A-202	8048	XM_005246676	ENSP00000386458	994 (aa)	XP_005246733	O75400
ENST00000467114	PRPF40A-205	546	-	-	- (aa)	-	-
ENST00000471167	PRPF40A-206	333	-	-	- (aa)	-	-
ENST00000486100	PRPF40A-209	569	-	-	- (aa)	-	-
ENST00000354363	PRPF40A-201	1622	-	ENSP00000346332	109 (aa)	-	H7BXZ7
ENST00000471701	PRPF40A-207	293	-	-	- (aa)	-	-
ENST00000493468	PRPF40A-211	1043	-	ENSP00000441656	346 (aa)	-	H0YG38
ENST00000489741	PRPF40A-210	776	-	-	- (aa)	-	-
ENST00000648940	PRPF40A-213	2815	XM_005246677	ENSP00000497573	930 (aa)	XP_005246734	UPI00015743D9
ENST00000448428	PRPF40A-203	490	-	ENSP00000406924	163 (aa)	-	H7C2N3
ENST00000545856	PRPF40A-212	1358	-	ENSP00000444656	448 (aa)	-	F5H578
ENST00000472760	PRPF40A-208	243	-	-	- (aa)	-	-

Gene Model

Pathways

Pathway ID	Pathway Name	Source
hsa03040	Spliceosome	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000196504	CD40 Ligand	5.54592515222829E-6	17903293
ENSG00000196504	CD40 Ligand	6.98976279678298E-6	17903293
ENSG00000196504	CD40 Ligand	8.42850999482891E-6	17903293
ENSG00000196504	CD40 Ligand	9.07986192633103E-6	17903293
ENSG00000196504	Atrial Natriuretic Factor	1.52231067109773E-6	17903293
ENSG00000196504	Follicle Stimulating Hormone	4.66416696629232E-12	17903292

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000196504	rs13012521	2	152703130	T	Memory dysfunction in frontotemporal lobe dementia	29724592	[2.50-3.48]	2.99	EFO_0001072\|Orphanet_282
ENSG00000196504	rs11392999	2	152697548	?	Heel bone mineral density	30048462	[0.013-0.023] unit decrease	0.0178246	EFO_0009270
ENSG00000196504	rs4664604	2	152716894	C	Heel bone mineral density	30598549	[0.012-0.022] unit decrease	0.0167778	EFO_0009270
ENSG00000196504	rs4664602	2	152686071	?	Menarche (age at onset)	30595370			EFO_0004703

Protein-Protein Interaction (PPI)

* RBP PPI network refers to all genes directly bind to RBP

Orthologs identified by RBPome

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000196504	PRPF40A	87	41.596	FBgn0031492	CG3542	68	43.087	Drosophila_melanogaster
ENSG00000196504	PRPF40A	100	96.344	ENSMUSG00000061136	Prpf40a	100	96.344	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000398	mRNA splicing, via spliceosome	21873635.	IBA	Process
GO:0000398	mRNA splicing, via spliceosome	-	TAS	Process
GO:0003723	RNA binding	22681889.	HDA	Function
GO:0003723	RNA binding	21873635.	IBA	Function
GO:0005515	protein binding	15383276.17161366.17500595.22365833.26420826.	IPI	Function
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005685	U1 snRNP	21873635.	IBA	Component
GO:0005829	cytosol	-	IDA	Component
GO:0007010	cytoskeleton organization	21834987.	IMP	Process
GO:0007049	cell cycle	-	IEA	Process
GO:0008360	regulation of cell shape	21834987.	IMP	Process
GO:0016020	membrane	19946888.	HDA	Component
GO:0016363	nuclear matrix	16391387.	IDA	Component
GO:0016477	cell migration	21834987.	IMP	Process
GO:0016607	nuclear speck	-	IDA	Component
GO:0032465	regulation of cytokinesis	21834987.	IMP	Process
GO:0045292	mRNA cis splicing, via spliceosome	-	IEA	Process
GO:0051301	cell division	-	IEA	Process
GO:0071004	U2-type prespliceosome	21873635.	IBA	Component