EuRBPDB

Description

Ensembl ID: ENSG00000137815 (Gene tree)
Gene ID: 23168
Gene Symbol: RTF1
Alias: KIAA0252
Full Name: RTF1 homolog, Paf1/RNA polymerase II complex component
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 75,156 bases
Position: chr15:41,408,408-41,483,563
Accession: 28996
RBP type: non-canonical RBP
Summary: This locus may represent a gene involved in regulation of transcription elongation and chromatin remodeling, based on studies of similar proteins in other organisms. The encoded protein may bind single-stranded DNA. [provided by RefSeq, Sep 2010]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
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
22658674	Insights into RNA biology from an atlas of mammalian mRNA-binding proteins	RIC & Hela	2012 May 31	Castello A	DOI: 10.1016/j.cell.2012.04.031
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & Hela	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 & 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
18184592	Structure and DNA binding of the human Rtf1 Plus3 domain.	Structure	2008 Jan	de Jong RN	doi: 10.1016/j.str.2007.10.018.

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000560447	RTF1-206	551	-	ENSP00000452973	171 (aa)	-	H0YKX1
ENST00000462276	RTF1-202	485	-	-	- (aa)	-	-
ENST00000558298	RTF1-205	327	-	-	- (aa)	-	-
ENST00000561076	RTF1-207	314	-	-	- (aa)	-	-
ENST00000389629	RTF1-201	5021	-	ENSP00000374280	710 (aa)	-	Q92541
ENST00000473214	RTF1-203	475	-	-	- (aa)	-	-
ENST00000558117	RTF1-204	552	-	-	- (aa)	-	-

Gene Model

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000137815	Cholesterol, LDL	4.6000000E-005	-
ENSG00000137815	Platelet Function Tests	9.7600000E-006	-
ENSG00000137815	Colitis, Ulcerative	8E-8	26192919

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000137815	rs2777491	15	41443512	?	Ulcerative colitis	26192919			EFO_0000729
ENSG00000137815	rs12907526	15	41432863	G	Itch intensity from mosquito bite	28199695	[0.014-0.031] unit decrease	0.0224141	EFO_0008377
ENSG00000137815	rs111371454	15	41468419	G	Allergic rhinitis	30013184	[1.03-1.06]	1.05	EFO_0005854
ENSG00000137815	rs1942	15	41482225	G	Eosinophil percentage of granulocytes	27863252	[0.018-0.032] unit increase	0.02536171	EFO_0007996
ENSG00000137815	rs117643004	15	41472503	?	General cognitive ability	29844566	z-score decrease	4.853	EFO_0004337

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
ENSG00000137815	RTF1	100	97.622	ENSMUSG00000027304	Rtf1	100	97.622	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000122	negative regulation of transcription by RNA polymerase II	-	ISS	Process
GO:0001711	endodermal cell fate commitment	-	ISS	Process
GO:0001832	blastocyst growth	-	IEA	Process
GO:0003697	single-stranded DNA binding	18184592.	IDA	Function
GO:0003723	RNA binding	22658674.	HDA	Function
GO:0005515	protein binding	15923622.16024656.19410543.20178742.	IPI	Function
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005730	nucleolus	-	IEA	Component
GO:0006366	transcription by RNA polymerase II	-	TAS	Process
GO:0006368	transcription elongation from RNA polymerase II promoter	-	TAS	Process
GO:0016055	Wnt signaling pathway	-	IEA	Process
GO:0016567	protein ubiquitination	-	TAS	Process
GO:0016593	Cdc73/Paf1 complex	21873635.	IBA	Component
GO:0016593	Cdc73/Paf1 complex	20178742.	IDA	Component
GO:0019827	stem cell population maintenance	19345177.	IDA	Process
GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	20178742.	IDA	Process
GO:0045944	positive regulation of transcription by RNA polymerase II	20178742.	IDA	Process
GO:0051571	positive regulation of histone H3-K4 methylation	-	IEA	Process
GO:0080182	histone H3-K4 trimethylation	-	IEA	Process
GO:1990269	RNA polymerase II C-terminal domain phosphoserine binding	21873635.	IBA	Function