EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

PRI

Literatures

Expression

Transcripts

Gene Model

Pathways

GWAS

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000004478 (Gene tree)
Gene ID: 2288
Gene Symbol: FKBP4
Alias: FKBP59|FKBP52
Full Name: FKBP prolyl isomerase 4
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 10,482 bases
Position: chr12:2,794,942-2,805,423
Accession: 3720
RBP type: non-canonical RBP
Summary: The protein encoded by this gene is a member of the immunophilin protein family, which play a role in immunoregulation and basic cellular processes involving protein folding and trafficking. This encoded protein is a cis-trans prolyl isomerase that binds to the immunosuppressants FK506 and rapamycin. It has high structural and functional similarity to FK506-binding protein 1A (FKBP1A), but unlike FKBP1A, this protein does not have immunosuppressant activity when complexed with FK506. It interacts with interferon regulatory factor-4 and plays an important role in immunoregulatory gene expression in B and T lymphocytes. This encoded protein is known to associate with phytanoyl-CoA alpha-hydroxylase. It can also associate with two heat shock proteins (hsp90 and hsp70) and thus may play a role in the intracellular trafficking of hetero-oligomeric forms of the steroid hormone receptors. This protein correlates strongly with adeno-associated virus type 2 vectors (AAV) resulting in a significant increase in AAV-mediated transgene expression in human cell lines. Thus this encoded protein is thought to have important implications for the optimal use of AAV vectors in human gene therapy. The human genome contains several non-transcribed pseudogenes similar to this gene. [provided by RefSeq, Sep 2008]

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
29431736	Capturing the interactome of newly transcribed RNA	PolyT-RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
29431736	Capturing the interactome of newly transcribed RNA	RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
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
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
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

Protein-RNA interaction（RNA-Binding Site）

Click here to download all RNA binding sites

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
7893829	Binding of eukaryotic initiation factor-2 and trans-acting factors to the 5' untranslated region of encephalomyocarditis virus RNA.	Biochimie	1994	Scheper GC	-

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000630279	FKBP4-208	156	-	ENSP00000486800	51 (aa)	-	F5H120
ENST00000539181	FKBP4-203	370	-	ENSP00000438491	84 (aa)	-	H0YFG2
ENST00000540260	FKBP4-204	777	-	-	- (aa)	-	-
ENST00000543769	FKBP4-206	425	-	ENSP00000439703	51 (aa)	-	F5H120
ENST00000001008	FKBP4-201	3732	XM_011520929	ENSP00000001008	459 (aa)	XP_011519231	Q02790
ENST00000538622	FKBP4-202	572	-	ENSP00000446368	86 (aa)	-	F5H1U3
ENST00000543037	FKBP4-205	727	-	-	- (aa)	-	-
ENST00000544366	FKBP4-207	287	-	ENSP00000442193	23 (aa)	-	H0YG86

Gene Model

Click here to download ENSG00000004478's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa04915	Estrogen signaling pathway	KEGG

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000004478	rs56196860	12	2799164	?	Heel bone mineral density	30048462	[0.024-0.047] unit decrease	0.0354551	EFO_0009270
ENSG00000004478	rs56196860	12	2799164	?	Lung function (FVC)	30595370			EFO_0004312
ENSG00000004478	rs56196860	12	2799164	?	Waist-hip ratio	30595370			EFO_0004343
ENSG00000004478	rs56196860	12	2799164	A	Lung function (FVC)	30804560	[0.04-0.067] unit decrease	0.0531	EFO_0004312
ENSG00000004478	rs56196860	12	2799164	A	FEV1	30804560	[0.031-0.058] unit decrease	0.0446	EFO_0004314
ENSG00000004478	rs56196860	12	2799164	A	Peak expiratory flow	30804560	[0.02-0.049] unit decrease	0.0345
ENSG00000004478	rs56196860	12	2799164	?	Heel bone mineral density	30595370			EFO_0009270

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000004478's network

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

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000413	protein peptidyl-prolyl isomerization	21873635.	IBA	Process
GO:0003723	RNA binding	22658674.	HDA	Function
GO:0003755	peptidyl-prolyl cis-trans isomerase activity	21873635.	IBA	Function
GO:0003755	peptidyl-prolyl cis-trans isomerase activity	11350175.	IDA	Function
GO:0005515	protein binding	11583998.12604780.14638689.19875381.20188096.21170051.21360678.21730179.23741051.25036637.25277244.	IPI	Function
GO:0005524	ATP binding	-	IEA	Function
GO:0005525	GTP binding	-	IEA	Function
GO:0005528	FK506 binding	1376003.	TAS	Function
GO:0005654	nucleoplasm	-	IDA	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005737	cytoplasm	21873635.	IBA	Component
GO:0005739	mitochondrion	-	IEA	Component
GO:0005829	cytosol	-	IDA	Component
GO:0005829	cytosol	-	ISS	Component
GO:0005829	cytosol	-	TAS	Component
GO:0005874	microtubule	-	IEA	Component
GO:0006457	protein folding	1279700.	TAS	Process
GO:0006463	steroid hormone receptor complex assembly	-	IEA	Process
GO:0006825	copper ion transport	-	IEA	Process
GO:0007566	embryo implantation	-	IEA	Process
GO:0010977	negative regulation of neuron projection development	-	ISS	Process
GO:0030521	androgen receptor signaling pathway	-	IEA	Process
GO:0030674	protein binding, bridging	2378870.	TAS	Function
GO:0030850	prostate gland development	-	IEA	Process
GO:0031072	heat shock protein binding	9660753.	IPI	Function
GO:0031111	negative regulation of microtubule polymerization or depolymerization	-	ISS	Process
GO:0031115	negative regulation of microtubule polymerization	-	IEA	Process
GO:0031503	protein-containing complex localization	-	IEA	Process
GO:0032767	copper-dependent protein binding	-	IEA	Function
GO:0032991	protein-containing complex	-	IEA	Component
GO:0035259	glucocorticoid receptor binding	-	IEA	Function
GO:0043025	neuronal cell body	-	IEA	Component
GO:0044295	axonal growth cone	-	ISS	Component
GO:0046661	male sex differentiation	-	IEA	Process
GO:0048156	tau protein binding	-	IEA	Function
GO:0048471	perinuclear region of cytoplasm	-	IEA	Component
GO:0051219	phosphoprotein binding	-	IEA	Function
GO:0061077	chaperone-mediated protein folding	21873635.	IBA	Process
GO:0061077	chaperone-mediated protein folding	11350175.	IDA	Process
GO:0070062	extracellular exosome	19056867.20458337.	HDA	Component
GO:1900034	regulation of cellular response to heat	-	TAS	Process

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
22074005	Proteomic approach reveals FKBP4 and S100A9 as potential prediction markers of therapeutic response to neoadjuvant chemotherapy in patients with breast cancer.	J Proteome Res	2012 Feb 3	Yang WS	doi: 10.1021/pr2008187
19584157	Identification of a new panel of serum autoantibodies associated with the presence of in situ carcinoma of the breast in younger women.	Clin Cancer Res	2009 Jul 15	Desmetz C	doi: 10.1158/1078-0432.CCR-08-3307

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
ACC	chr12	2803164	Missense_Mutation	rs770611717	A429G	0.27
ACC	chr12	2801232	Missense_Mutation	novel	Y383C	0.6
BLCA	chr12	2798783	Silent	rs776356873	R157R	0.07
BLCA	chr12	2798757	Missense_Mutation	rs772045995	G149R	0.19
BLCA	chr12	2799213	Missense_Mutation	novel	G214R	0.45
BLCA	chr12	2800078	Missense_Mutation	novel	E268K	0.4
BLCA	chr12	2800481	Missense_Mutation	novel	Q312H	0.69
BLCA	chr12	2800577	Missense_Mutation	novel	K344N	0.62
BRCA	chr12	2800520	Silent	novel	L325L	0.38
BRCA	chr12	2799139	Missense_Mutation	rs55672055	R189H	0.11
BRCA	chr12	2801215	Silent	rs753568828	Q377Q	0.33
BRCA	chr12	2801307	Missense_Mutation	novel	K408R	0.1
CESC	chr12	2799236	Silent	rs777530787	L221L	0.22
CESC	chr12	2801192	Missense_Mutation	NA	E370K	0.12
CESC	chr12	2797844	Frame_Shift_Ins	novel	*N125Qfs7**	0.27
CESC	chr12	2800521	Missense_Mutation	novel	A326S	0.15
CESC	chr12	2795165	Missense_Mutation	NA	T9I	0.55
CESC	chr12	2800099	Missense_Mutation	NA	E275Q	0.18
CESC	chr12	2800433	Silent	novel	I296I	0.21
COAD	chr12	2798756	Silent	NA	G148G	0.28
COAD	chr12	2800044	Missense_Mutation	NA	K256N	0.08
COAD	chr12	2801213	Nonsense_Mutation	novel	Q377*	0.15
COAD	chr12	2803221	Missense_Mutation	rs766636474	T448M	0.4
COAD	chr12	2795077	5'UTR	novel		0.43
COAD	chr12	2800102	Missense_Mutation	rs372836178	R276W	0.43
COAD	chr12	2797859	Silent	rs370885732	T127T	0.5
COAD	chr12	2799202	Missense_Mutation	rs766142249	R210H	0.64
ESCA	chr12	2799851	Missense_Mutation	novel	Y225H	0.15
ESCA	chr12	2803496	3'UTR	novel		0.28
GBM	chr12	2799129	Missense_Mutation	rs780740336	R186W	0.5
HNSC	chr12	2800561	Missense_Mutation	rs539277079	I339T	0.2
HNSC	chr12	2798736	Missense_Mutation	novel	L142M	0.25
HNSC	chr12	2797869	Missense_Mutation	novel	E131Q	0.24
KICH	chr12	2798817	Missense_Mutation	rs761447742	I169V	0.47
KIRP	chr12	2799886	Silent	rs201311104	Q236Q	0.58
KIRP	chr12	2801162	Missense_Mutation	NA	G360R	0.23
KIRP	chr12	2800412	Silent	NA	A289A	0.18
KIRP	chr12	2798764	Missense_Mutation	novel	I151T	0.25
KIRP	chr12	2795087	5'UTR	novel		0.26
KIRP	chr12	2801146	Missense_Mutation	NA	K354N	0.28
LGG	chr12	2801153	Missense_Mutation	novel	F357L	0.11
LGG	chr12	2800578	Splice_Site	novel	X344_splice	0.48
LGG	chr12	2801350	Silent	NA	E422E	0.15
LIHC	chr12	2801298	Missense_Mutation	novel	A405V	0.06
LIHC	chr12	2800100	Missense_Mutation	NA	E275G	0.42
LIHC	chr12	2795245	Splice_Site	NA	X35_splice	0.41
LUAD	chr12	2797177	Missense_Mutation	novel	I49V	0.3
LUAD	chr12	2801281	Silent	novel	R399R	0.19
LUAD	chr12	2798787	Missense_Mutation	novel	E159K	0.25
LUSC	chr12	2797805	Silent	NA	P109P	0.11
LUSC	chr12	2798745	Missense_Mutation	novel	E145Q	0.04
OV	chr12	2799218	Missense_Mutation	novel	E215D	0.06
OV	chr12	2797203	Nonsense_Mutation	novel	Y57*	0.1
PAAD	chr12	2798711	Silent	novel	E133E	0.16
PRAD	chr12	2801278	Missense_Mutation	NA	Q398H	0.16
PRAD	chr12	2800390	Splice_Site	novel	X283_splice	0.48
READ	chr12	2803259	3'UTR	novel		0.71
READ	chr12	2801286	Missense_Mutation	rs199923813	R401Q	0.7
READ	chr12	2799090	Missense_Mutation	novel	A173T	0.1
SARC	chr12	2798781	Missense_Mutation	NA	R157C	0.48
SKCM	chr12	2801256	Missense_Mutation	novel	T391I	0.27
SKCM	chr12	2801257	Silent	novel	T391T	0.26
SKCM	chr12	2797266	Silent	NA	S78S	0.36
SKCM	chr12	2800465	Missense_Mutation	NA	S307F	0.35
SKCM	chr12	2799216	Missense_Mutation	NA	E215K	0.52
STAD	chr12	2795214	Silent	rs778270440	I25I	0.33
STAD	chr12	2798782	Missense_Mutation	rs1062478	R157H	0.34
STAD	chr12	2803187	Missense_Mutation	NA	D437N	0.52
STAD	chr12	2795057	5'UTR	novel		0.5
STAD	chr12	2797845	Frame_Shift_Del	novel	*N125Mfs18**	0.11
STAD	chr12	2800558	Missense_Mutation	NA	A338V	0.17
STAD	chr12	2801314	Silent	rs762943432	L410L	0.47
STAD	chr12	2798756	Silent	NA	G148G	0.2
TGCT	chr12	2799167	Silent	novel	L198L	0.18
UCEC	chr12	2799848	Splice_Site	rs755320293	X224_splice	0.43
UCEC	chr12	2803761	3'UTR	novel		0.4
UCEC	chr12	2797167	Missense_Mutation	novel	E45D	0.04
UCEC	chr12	2797159	Missense_Mutation	NA	G43S	0.27
UCEC	chr12	2798766	Missense_Mutation	rs142464168	R152C	0.23
UCEC	chr12	2801143	Missense_Mutation	novel	E353D	0.19
UCEC	chr12	2800050	Silent	NA	S258S	0.31
UCEC	chr12	2799202	Missense_Mutation	rs766142249	R210H	0.39
UCEC	chr12	2803866	3'UTR	novel		0.37
UCEC	chr12	2800102	Frame_Shift_Del	novel	*R276Gfs55**	0.5
UCEC	chr12	2798781	Missense_Mutation	NA	R157C	0.33
UCEC	chr12	2799850	Splice_Region	novel	S224S	0.26
UCEC	chr12	2797860	Missense_Mutation	novel	L128F	0.4
UCEC	chr12	2799129	Missense_Mutation	rs780740336	R186W	0.32
UCEC	chr12	2803723	3'UTR	novel		0.34
UCEC	chr12	2800497	Nonsense_Mutation	novel	R318*	0.28
UCEC	chr12	2797855	Missense_Mutation	novel	A126V	0.38
UCEC	chr12	2800498	Missense_Mutation	novel	R318Q	0.41
UCEC	chr12	2803750	3'UTR	novel		0.47
UCEC	chr12	2800046	Missense_Mutation	NA	E257G	0.27
UCEC	chr12	2800566	Missense_Mutation	novel	S341R	0.41
UCEC	chr12	2803845	3'UTR	rs780392478		0.3
UCEC	chr12	2804060	3'UTR	novel		0.33
UCEC	chr12	2801188	Frame_Shift_Ins	novel	E370*	0.29
UCEC	chr12	2797858	Missense_Mutation	rs749174239	T127M	0.2
UCEC	chr12	2799928	Missense_Mutation	novel	K250N	0.09
UCEC	chr12	2797756	Missense_Mutation	novel	A93V	0.38
UCEC	chr12	2803747	3'UTR	novel		0.41
UCEC	chr12	2803991	3'UTR	novel		0.5
UCEC	chr12	2801118	Missense_Mutation	novel	A345D	0.33
UCEC	chr12	2798756	Silent	NA	G148G	0.21
UCEC	chr12	2797845	Frame_Shift_Del	novel	*N125Mfs18**	0.58
UCEC	chr12	2801179	Silent	rs749685904	A365A	0.37

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
COAD	AMP	0.2195	2.8622e-08
DLBC	DEL	0.0833	0.11856
LUSC	AMP	0.4092	0.0059474
OV	AMP	0.532	1.6751e-06
PAAD	AMP	0.1467	0.0041088
READ	AMP	0.2061	0.027505
TGCT	AMP	0.9333	3.5918e-21
THYM	AMP	0.0325	0.24554

Survival Analysis

Cancer	P-value	Q-value
KIRC	0.033	Kaplan-Meier Survival Analysis
SARC	0.0026	Kaplan-Meier Survival Analysis
MESO	0.00092	Kaplan-Meier Survival Analysis
ACC	0.043	Kaplan-Meier Survival Analysis
SKCM	0.00028	Kaplan-Meier Survival Analysis
LUSC	0.038	Kaplan-Meier Survival Analysis
ESCA	0.046	Kaplan-Meier Survival Analysis
KIRP	0.0054	Kaplan-Meier Survival Analysis
COAD	0.013	Kaplan-Meier Survival Analysis
PAAD	0.021	Kaplan-Meier Survival Analysis
PCPG	0.021	Kaplan-Meier Survival Analysis
KICH	0.044	Kaplan-Meier Survival Analysis
UCEC	0.0011	Kaplan-Meier Survival Analysis
LIHC	0.0001	Kaplan-Meier Survival Analysis
LGG	0.016	Kaplan-Meier Survival Analysis
LUAD	0.0001	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

PRI

Literatures

Expression

Transcripts

Gene Model

Pathways

GWAS

PPI

Gene Ontology

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742