EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

GWAS

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000108559 (Gene tree)
Gene ID: 4927
Gene Symbol: NUP88
Alias: MGC8530
Full Name: nucleoporin 88
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Minus strand
Length: 59,198 bases
Position: chr17:5,360,963-5,420,160
Accession: 8067
RBP type: non-canonical RBP
Summary: The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins, a family of 50 to 100 proteins, are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene belongs to the nucleoporin family and is associated with the oncogenic nucleoporin CAN/Nup214 in a dynamic subcomplex. This protein is also overexpressed in a large number of malignant neoplasms and precancerous dysplasias. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]

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
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

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000572019	NUP88-203	580	-	-	- (aa)	-	-
ENST00000572809	NUP88-205	771	-	ENSP00000459370	153 (aa)	-	I3L245
ENST00000574855	NUP88-209	434	-	-	- (aa)	-	-
ENST00000575976	NUP88-211	599	-	-	- (aa)	-	-
ENST00000573584	NUP88-207	2916	XM_017024694	ENSP00000458954	741 (aa)	XP_016880183	Q99567
ENST00000572290	NUP88-204	615	-	ENSP00000459979	128 (aa)	-	I3L2W3
ENST00000573169	NUP88-206	1195	-	-	- (aa)	-	-
ENST00000576862	NUP88-213	788	-	-	- (aa)	-	-
ENST00000570937	NUP88-202	361	-	-	- (aa)	-	-
ENST00000576708	NUP88-212	800	-	ENSP00000461334	110 (aa)	-	I3L4K7
ENST00000574087	NUP88-208	548	-	-	- (aa)	-	-
ENST00000574867	NUP88-210	2081	-	-	- (aa)	-	-
ENST00000225696	NUP88-201	2194	XM_011523893	ENSP00000225696	696 (aa)	XP_011522195	J3KMX1

Gene Model

Click here to download ENSG00000108559's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa03013	RNA transport	KEGG

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000108559	rs72634030	17	5369285	A	Rheumatoid arthritis	24390342	[1.08-1.17]	1.12	EFO_0000685
ENSG00000108559	rs3026101	17	5377145	C	Body mass index	28892062	[0.01-0.018] kg/m2 increase	0.014	EFO_0004340
ENSG00000108559	rs1000940	17	5379957	A	Body mass index	26426971	unit decrease	0.017490005	EFO_0004340
ENSG00000108559	rs3026101	17	5377145	T	Body mass index	30108127	[NR] unit decrease	0.02	EFO_0004340
ENSG00000108559	rs72634030	17	5369285	A	Rheumatoid arthritis	30423114	[0.07-0.15] unit increase	0.110343	EFO_0000685
ENSG00000108559	rs10792	17	5384859	?	Body mass index	30595370			EFO_0004340

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000108559's network

* 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
ENSG00000108559	NUP88	100	89.906	ENSMUSG00000040667	Nup88	100	89.906	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000055	ribosomal large subunit export from nucleus	21873635.	IBA	Process
GO:0000056	ribosomal small subunit export from nucleus	21873635.	IBA	Process
GO:0000278	mitotic cell cycle	-	IEA	Process
GO:0005215	transporter activity	9049309.	TAS	Function
GO:0005643	nuclear pore	21873635.	IBA	Component
GO:0005643	nuclear pore	23777819.	IDA	Component
GO:0005654	nucleoplasm	-	IDA	Component
GO:0005829	cytosol	-	TAS	Component
GO:0006110	regulation of glycolytic process	-	TAS	Process
GO:0006406	mRNA export from nucleus	21873635.	IBA	Process
GO:0006406	mRNA export from nucleus	-	TAS	Process
GO:0006409	tRNA export from nucleus	-	TAS	Process
GO:0006606	protein import into nucleus	21873635.	IBA	Process
GO:0006611	protein export from nucleus	21873635.	IBA	Process
GO:0016032	viral process	-	TAS	Process
GO:0016925	protein sumoylation	-	TAS	Process
GO:0017056	structural constituent of nuclear pore	-	IEA	Function
GO:0019083	viral transcription	-	TAS	Process
GO:0043657	host cell	-	IEA	Component
GO:0060964	regulation of gene silencing by miRNA	-	TAS	Process
GO:0075733	intracellular transport of virus	-	TAS	Process
GO:1900034	regulation of cellular response to heat	-	TAS	Process

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
21863385	Increased serum level of Nup88 protein is associated with the development of colorectal cancer.	Med Oncol	2012 Sep	Zhao ZR	doi: 10.1007/s12032-011-0047-1
21896994	Nup88 mRNA overexpression in colorectal cancers and relationship with p53.	Cancer Biomark	2010-2011	Zhao ZR	doi: 10.3233/DMA-2011-0842.
27636375	Multiple biological processes may be associated with tumorigenesis under NUP88-overexpressed condition.	Genes Chromosomes Cancer	2017 Feb	Li J	doi: 10.1002/gcc.22417

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr17	5419545	Missense_Mutation	novel	P36S	0.25
BLCA	chr17	5404192	Missense_Mutation	rs374723055	E367Q	0.14
BLCA	chr17	5386180	3'UTR	novel		0.62
BLCA	chr17	5388772	Intron	novel		0.13
BLCA	chr17	5386232	Missense_Mutation	NA	D734N	0.13
BLCA	chr17	5414091	Silent	novel	L171L	0.19
BLCA	chr17	5386229	Missense_Mutation	NA	I735V	0.93
BLCA	chr17	5419401	Missense_Mutation	rs745395510	R84W	0.33
BLCA	chr17	5394931	Missense_Mutation	novel	F448L	0.69
BRCA	chr17	5386232	Missense_Mutation	NA	D734H	0.23
BRCA	chr17	5419539	Missense_Mutation	NA	E38K	0.22
BRCA	chr17	5387644	Frame_Shift_Del	NA	*K599Rfs4**	0.07
CESC	chr17	5414091	Missense_Mutation	novel	L171V	0.26
CESC	chr17	5387423	Missense_Mutation	NA	E627K	0.3
CESC	chr17	5386739	Nonsense_Mutation	rs764971841	R711*	0.41
CESC	chr17	5405174	Silent	novel	Y309Y	0.27
COAD	chr17	5419516	Silent	NA	S45S	0.82
COAD	chr17	5419415	Nonsense_Mutation	novel	L79*	0.25
COAD	chr17	5416662	Silent	novel	P106P	0.29
COAD	chr17	5387091	Missense_Mutation	novel	S646R	0.29
COAD	chr17	5387873	Missense_Mutation	NA	E559K	0.39
COAD	chr17	5391589	Missense_Mutation	NA	T486A	0.48
COAD	chr17	5419553	Missense_Mutation	novel	N33S	0.18
COAD	chr17	5388782	Intron	novel		0.31
COAD	chr17	5419501	Silent	novel	S50S	0.11
COAD	chr17	5408850	Missense_Mutation	novel	A247V	0.07
COAD	chr17	5419500	Missense_Mutation	NA	P51S	0.3
ESCA	chr17	5391569	Missense_Mutation	novel	W492C	0.41
ESCA	chr17	5386231	Missense_Mutation	novel	D734G	0.36
GBM	chr17	5386174	3'UTR	novel		0.13
GBM	chr17	5414055	Missense_Mutation	novel	I183V	0.05
GBM	chr17	5404188	Frame_Shift_Del	novel	*C368Lfs8**	0.14
GBM	chr17	5394908	Silent	rs138380831	T455T	0.18
GBM	chr17	5388750	Intron	novel		0.26
GBM	chr17	5419523	Missense_Mutation	rs775555017	A43V	0.92
GBM	chr17	5386169	3'UTR	novel		0.13
HNSC	chr17	5408857	Missense_Mutation	novel	P245A	0.3
HNSC	chr17	5387112	Splice_Site	novel	X639_splice	0.27
HNSC	chr17	5408747	Silent	novel	I281I	0.55
HNSC	chr17	5386747	Missense_Mutation	novel	A708V	0.4
HNSC	chr17	5419493	Missense_Mutation	rs551961860	P53L	0.5
HNSC	chr17	5416585	Missense_Mutation	novel	M132K	0.2
KIRC	chr17	5387065	Silent	NA	L654L	0.15
KIRC	chr17	5419410	Missense_Mutation	novel	V81L	0.24
KIRC	chr17	5419405	Silent	NA	R82R	0.18
KIRC	chr17	5386789	Frame_Shift_Ins	novel	*E694Vfs31**	0.04
KIRC	chr17	5419429	Missense_Mutation	NA	E74D	0.17
KIRP	chr17	5408831	Frame_Shift_Ins	novel	*F254Ifs8**	0.24
KIRP	chr17	5410775	Missense_Mutation	rs775368499	R203H	0.36
LAML	chr17	5387782	Missense_Mutation	rs553522883	R589Q	0.05
LGG	chr17	5388646	Intron	novel		0.6
LGG	chr17	5419466	Missense_Mutation	novel	F62S	0.09
LGG	chr17	5408798	Silent	NA	A264A	0.25
LIHC	chr17	5405244	Splice_Site	novel	X286_splice	0.14
LIHC	chr17	5387031	Missense_Mutation	NA	Q666K	0.93
LIHC	chr17	5408766	Missense_Mutation	novel	E275G	0.16
LIHC	chr17	5387928	Intron	novel		0.67
LUAD	chr17	5394955	Missense_Mutation	novel	E440Q	0.08
LUAD	chr17	5394957	Missense_Mutation	novel	Q439L	0.07
LUAD	chr17	5410753	Missense_Mutation	novel	N210K	0.28
LUAD	chr17	5414130	Missense_Mutation	novel	T158S	0.42
LUAD	chr17	5414095	Silent	NA	T169T	0.54
LUSC	chr17	5387063	Missense_Mutation	rs200367094	S655F	0.09
LUSC	chr17	5419382	Missense_Mutation	novel	G90V	0.17
LUSC	chr17	5419770	5'UTR	novel		0.73
LUSC	chr17	5419620	Missense_Mutation	novel	G11C	0.33
MESO	chr17	5414085	Missense_Mutation	rs774993752	L173V	0.17
OV	chr17	5386187	3'UTR	novel		0.04
OV	chr17	5391564	Nonsense_Mutation	novel	L494*	0.07
OV	chr17	5391562	Splice_Region	novel	L495L	0.49
PAAD	chr17	5399561	Missense_Mutation	NA	L428I	0.22
PAAD	chr17	5419703	5'UTR	novel		0.24
PRAD	chr17	5419399	In_Frame_Ins	novel	R82_R84dup	0.3
PRAD	chr17	5419406	Missense_Mutation	novel	R82H	0.23
READ	chr17	5394971	Missense_Mutation	NA	D434E	0.1
READ	chr17	5388763	Intron	novel		0.36
READ	chr17	5399561	Missense_Mutation	NA	L428I	0.43
SKCM	chr17	5386760	Missense_Mutation	NA	I704F	0.41
SKCM	chr17	5386153	3'UTR	novel		0.32
SKCM	chr17	5419773	5'UTR	novel		0.57
SKCM	chr17	5408856	Missense_Mutation	NA	P245L	0.52
SKCM	chr17	5404226	Silent	rs748439940	S355S	0.25
SKCM	chr17	5419527	Missense_Mutation	NA	P42S	0.43
SKCM	chr17	5405123	Silent	rs769510503	I326I	0.38
SKCM	chr17	5419545	Missense_Mutation	novel	P36S	0.34
SKCM	chr17	5419758	5'UTR	novel		1
SKCM	chr17	5394917	Silent	rs574618342	I452I	0.44
SKCM	chr17	5405110	Missense_Mutation	NA	G331R	0.22
STAD	chr17	5408897	Silent	NA	T231T	0.51
STAD	chr17	5408786	Silent	NA	Y268Y	0.26
STAD	chr17	5404144	Missense_Mutation	novel	D383H	0.1
STAD	chr17	5387440	Missense_Mutation	rs774967326	R621H	0.23
STAD	chr17	5386177	3'UTR	rs377606329		0.17
STAD	chr17	5387864	Missense_Mutation	novel	L562F	0.15
STAD	chr17	5410744	Missense_Mutation	NA	I213M	0.08
STAD	chr17	5419387	Silent	NA	G88G	0.08
STAD	chr17	5386804	Missense_Mutation	novel	Q689R	0.06
STAD	chr17	5405189	Missense_Mutation	NA	E304D	0.13
STAD	chr17	5419392	Missense_Mutation	NA	S87G	0.28
STAD	chr17	5388886	Missense_Mutation	rs149123666	R520H	0.16
STAD	chr17	5408904	Missense_Mutation	rs770092360	A229V	0.22
STAD	chr17	5419612	Silent	novel	L13L	0.44
TGCT	chr17	5405164	Missense_Mutation	novel	A313T	0.12
THCA	chr17	5386775	In_Frame_Ins	novel	S698_L699insRRSS	0.02
UCEC	chr17	5419351	Splice_Region	novel		0.08
UCEC	chr17	5386229	Missense_Mutation	NA	I735V	0.45
UCEC	chr17	5391646	Nonsense_Mutation	NA	R467*	0.33
UCEC	chr17	5405169	Missense_Mutation	rs563564141	A311V	0.4
UCEC	chr17	5386723	Missense_Mutation	novel	S716F	0.35
UCEC	chr17	5388830	Missense_Mutation	rs767917093	R539C	0.44
UCEC	chr17	5405199	Missense_Mutation	novel	P301L	0.38
UCEC	chr17	5387052	Nonsense_Mutation	rs773202236	R659*	0.42
UCEC	chr17	5399626	Missense_Mutation	novel	H406R	0.39
UCEC	chr17	5399561	Missense_Mutation	NA	L428I	0.26
UCEC	chr17	5394904	Missense_Mutation	novel	P457T	0.04
UCEC	chr17	5404199	Silent	NA	Y364Y	0.12
UCEC	chr17	5399612	Missense_Mutation	NA	A411S	0.13
UCEC	chr17	5391636	Frame_Shift_Ins	novel	*W470Lfs5**	0.39
UCEC	chr17	5391646	Nonsense_Mutation	NA	R467*	0.47
UCEC	chr17	5410732	Silent	novel	A217A	0.1
UCEC	chr17	5416603	Missense_Mutation	rs144721034	I126T	0.41
UCEC	chr17	5387010	Nonsense_Mutation	novel	R673*	0.54
UCEC	chr17	5394898	Missense_Mutation	novel	P459S	0.45
UCEC	chr17	5387065	Silent	novel	L654L	0.58
UCEC	chr17	5404237	Missense_Mutation	novel	S352A	0.49
UCEC	chr17	5416653	Silent	novel	F109F	0.63
UCEC	chr17	5388799	Splice_Region	novel		0.25
UCEC	chr17	5387939	Intron	novel		0.49
UCEC	chr17	5416638	Silent	NA	V114V	0.26
UCEC	chr17	5386731	Silent	novel	C713C	0.39
UCEC	chr17	5405169	Missense_Mutation	rs563564141	A311V	0.33
UCEC	chr17	5416537	Missense_Mutation	novel	G148A	0.07
UCEC	chr17	5388759	Intron	novel		0.35
UCEC	chr17	5386789	Frame_Shift_Ins	novel	*E694Vfs31**	0.07
UCEC	chr17	5386790	Nonsense_Mutation	novel	E694*	0.05
UCEC	chr17	5387441	Missense_Mutation	rs557899492	R621C	0.35
UCEC	chr17	5419468	Silent	novel	V61V	0.13
UCEC	chr17	5387004	Missense_Mutation	novel	L675V	0.24
UCEC	chr17	5394904	Missense_Mutation	NA	P457S	0.15
UCEC	chr17	5410734	Missense_Mutation	novel	A217T	0.06
UCEC	chr17	5387644	Frame_Shift_Del	NA	*K599Rfs4**	0.44
UCEC	chr17	5386239	Silent	novel	Q731Q	0.12
UCEC	chr17	5386812	Frame_Shift_Ins	novel	*D687Gfs37**	0.32
UCEC	chr17	5404096	Splice_Region	novel		0.38
UCEC	chr17	5387605	Missense_Mutation	NA	R612M	0.23
UCEC	chr17	5386107	3'UTR	novel		0.26
UCEC	chr17	5387081	Missense_Mutation	novel	S649Y	0.2
UCEC	chr17	5391567	Missense_Mutation	rs140329092	P493L	0.56
UCEC	chr17	5408864	Silent	novel	D242D	0.16
UCEC	chr17	5410769	Missense_Mutation	rs769974456	P205L	0.43
UCEC	chr17	5419390	Silent	novel	S87S	0.4
UCEC	chr17	5391619	Missense_Mutation	NA	L476M	0.3
UCEC	chr17	5405169	Missense_Mutation	NA	A311E	0.34
UCEC	chr17	5388910	Missense_Mutation	novel	V512A	0.42
UCEC	chr17	5405089	Missense_Mutation	rs779828157	V338M	0.4
UCEC	chr17	5408819	Silent	novel	N257N	0.37

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
DLBC	DEL	0.2083	0.18166
LAML	DEL	0.0733	0.12511
LIHC	DEL	0.5568	3.9592e-10
THCA	DEL	0.016	0.221

Survival Analysis

Cancer	P-value	Q-value
THYM	0.008	Kaplan-Meier Survival Analysis
SARC	0.031	Kaplan-Meier Survival Analysis
ACC	0.00011	Kaplan-Meier Survival Analysis
PRAD	0.017	Kaplan-Meier Survival Analysis
ESCA	0.041	Kaplan-Meier Survival Analysis
PAAD	0.0082	Kaplan-Meier Survival Analysis
CESC	0.016	Kaplan-Meier Survival Analysis
READ	0.019	Kaplan-Meier Survival Analysis
KICH	0.048	Kaplan-Meier Survival Analysis
UVM	0.00017	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

GWAS

PPI

Orthologs

Gene Ontology

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742