EuRBPDB

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000110713 (Gene tree)
Gene ID: 4928
Gene Symbol: NUP98
Alias: NUP96
Full Name: nucleoporin 98
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Minus strand
Length: 126,710 bases
Position: chr11:3,671,083-3,797,792
Accession: 8068
RBP type: non-canonical RBP
Summary: Nuclear pore complexes (NPCs) regulate the transport of macromolecules between the nucleus and cytoplasm, and are composed of many polypeptide subunits, many of which belong to the nucleoporin family. This gene belongs to the nucleoporin gene family and encodes a 186 kDa precursor protein that undergoes autoproteolytic cleavage to generate a 98 kDa nucleoporin and 96 kDa nucleoporin. The 98 kDa nucleoporin contains a Gly-Leu-Phe-Gly (GLGF) repeat domain and participates in many cellular processes, including nuclear import, nuclear export, mitotic progression, and regulation of gene expression. The 96 kDa nucleoporin is a scaffold component of the NPC. Proteolytic cleavage is important for targeting of the proteins to the NPC. Translocations between this gene and many other partner genes have been observed in different leukemias. Rearrangements typically result in chimeras with the N-terminal GLGF domain of this gene to the C-terminus of the partner gene. Alternative splicing results in multiple transcript variants encoding different isoforms, at least two of which are proteolytically processed. Some variants lack the region that encodes the 96 kDa nucleoporin. [provided by RefSeq, Feb 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
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
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

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
20339440	Effects of the NUP98-DDX10 oncogene on primary human CD34+ cells: role of a conserved helicase motif.	Leukemia	2010 May	Yassin ER	doi: 10.1038/leu.2010.42
28934014	Nucleoplasmic Nup98 controls gene expression by regulating a DExH/D-box protein.	Nucleus	2018 Jan 1	Capitanio JS	doi: 10.1080/19491034.2017.1364826
10556215	The t(11;20)(p15;q11) chromosomal translocation associated with therapy-related myelodysplastic syndrome results in an NUP98-TOP1 fusion.	Blood	1999 Nov 1	Ahuja HG	-
20639863	Regulation of myeloid leukaemia by the cell-fate determinant Musashi.	Nature	2010 Aug 5	Ito T	doi: 10.1038/nature09171
20498086	Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1.	Proc Natl Acad Sci U S A	2010 Jun 8	Ren Y	doi: 10.1073/pnas.1005389107

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000397013	NUP98-206	939	-	ENSP00000380208	136 (aa)	-	H7BYP8
ENST00000488828	NUP98-212	712	-	-	- (aa)	-	-
ENST00000650171	NUP98-221	6837	-	ENSP00000497709	1348 (aa)	-	-
ENST00000529379	NUP98-216	536	-	ENSP00000432142	179 (aa)	-	H0YCR0
ENST00000483285	NUP98-211	545	-	-	- (aa)	-	-
ENST00000529063	NUP98-215	544	-	ENSP00000433226	75 (aa)	-	H0YDA1
ENST00000482690	NUP98-210	310	-	-	- (aa)	-	-
ENST00000324932	NUP98-201	6973	-	ENSP00000316032	1800 (aa)	-	P52948
ENST00000469881	NUP98-209	687	-	-	- (aa)	-	-
ENST00000355260	NUP98-202	5628	-	ENSP00000347404	1726 (aa)	-	P52948
ENST00000527104	NUP98-214	705	-	ENSP00000436226	235 (aa)	-	H0YEN4
ENST00000530516	NUP98-218	391	-	-	- (aa)	-	-
ENST00000532475	NUP98-219	553	-	ENSP00000434698	124 (aa)	-	E9PNN0
ENST00000429801	NUP98-207	2541	-	ENSP00000413146	753 (aa)	-	H7C3P6
ENST00000359171	NUP98-203	7023	-	ENSP00000352091	1817 (aa)	-	P52948
ENST00000533346	NUP98-220	580	-	ENSP00000432275	93 (aa)	-	H0YCT1
ENST00000397007	NUP98-205	3698	-	ENSP00000380202	937 (aa)	-	P52948
ENST00000397004	NUP98-204	3923	-	ENSP00000380199	920 (aa)	-	P52948
ENST00000530345	NUP98-217	436	-	-	- (aa)	-	-
ENST00000524563	NUP98-213	841	-	ENSP00000433515	232 (aa)	-	H0YDF4
ENST00000461047	NUP98-208	545	-	-	- (aa)	-	-

Gene Model

Click here to download ENSG00000110713's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa03013	RNA transport	KEGG
hsa05164	Influenza A	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000110713	Bilirubin	1.205e-005	-
ENSG00000110713	Bilirubin	1.205e-005	-
ENSG00000110713	Bilirubin	1.205e-005	-
ENSG00000110713	Bilirubin	1.205e-005	-
ENSG00000110713	13,16,19-docosatrienoic acid	7E-6	23934736

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000110713	rs685782	11	3701074	C	Metabolite levels (Dihydroxy docosatrienoic acid)	23934736	[0.05-0.13] unit increase	0.192	EFO_0005275

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000110713'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
ENSG00000110713	NUP98	99	95.289	ENSMUSG00000063550	Nup98	99	94.937	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000776	kinetochore	15146057.	IDA	Component
GO:0000973	posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery	21873635.	IBA	Process
GO:0003713	transcription coactivator activity	28221134.	IMP	Function
GO:0003723	RNA binding	21873635.	IBA	Function
GO:0003729	mRNA binding	28221134.	IMP	Function
GO:0005215	transporter activity	7736573.	TAS	Function
GO:0005515	protein binding	9348540.15146057.17172455.18832153.20498086.28221134.	IPI	Function
GO:0005635	nuclear envelope	15146057.28221134.	IDA	Component
GO:0005635	nuclear envelope	-	TAS	Component
GO:0005643	nuclear pore	9348540.12802065.15229283.	IDA	Component
GO:0005643	nuclear pore	10087256.	NAS	Component
GO:0005654	nucleoplasm	28221134.	IDA	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005829	cytosol	-	TAS	Component
GO:0006110	regulation of glycolytic process	-	TAS	Process
GO:0006260	DNA replication	9348540.	IMP	Process
GO:0006405	RNA export from nucleus	21873635.	IBA	Process
GO:0006406	mRNA export from nucleus	-	TAS	Process
GO:0006409	tRNA export from nucleus	-	TAS	Process
GO:0006508	proteolysis	-	IEA	Process
GO:0006606	protein import into nucleus	21873635.	IBA	Process
GO:0006913	nucleocytoplasmic transport	9348540.	TAS	Process
GO:0006999	nuclear pore organization	9348540.	NAS	Process
GO:0008139	nuclear localization sequence binding	21873635.	IBA	Function
GO:0008236	serine-type peptidase activity	-	IEA	Function
GO:0016032	viral process	-	TAS	Process
GO:0016604	nuclear body	28221134.	IDA	Component
GO:0016925	protein sumoylation	-	TAS	Process
GO:0017056	structural constituent of nuclear pore	21873635.	IBA	Function
GO:0017056	structural constituent of nuclear pore	15229283.	IMP	Function
GO:0017056	structural constituent of nuclear pore	9348540.	NAS	Function
GO:0019083	viral transcription	-	TAS	Process
GO:0031080	nuclear pore outer ring	17360435.	IDA	Component
GO:0031080	nuclear pore outer ring	15146057.	NAS	Component
GO:0031965	nuclear membrane	11839768.12802065.15229283.20407419.	IDA	Component
GO:0034398	telomere tethering at nuclear periphery	21873635.	IBA	Process
GO:0034399	nuclear periphery	11839768.15229283.	IDA	Component
GO:0042405	nuclear inclusion body	11839768.	IDA	Component
GO:0043231	intracellular membrane-bounded organelle	-	IDA	Component
GO:0043657	host cell	-	IEA	Component
GO:0044614	nuclear pore cytoplasmic filaments	21873635.	IBA	Component
GO:0044615	nuclear pore nuclear basket	11839768.	IDA	Component
GO:0048026	positive regulation of mRNA splicing, via spliceosome	28221134.	IMP	Process
GO:0051292	nuclear pore complex assembly	15229283.	IMP	Process
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
GO:1903508	positive regulation of nucleic acid-templated transcription	-	IEA	Process
GO:1990841	promoter-specific chromatin binding	28221134.	IMP	Function
GO:1990904	ribonucleoprotein complex	28221134.	IMP	Component