EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

Phenotypes

GWAS

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000110801 (Gene tree)
Gene ID: 5715
Gene Symbol: PSMD9
Alias: p27|Rpn4
Full Name: proteasome 26S subunit, non-ATPase 9
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 29,567 bases
Position: chr12:121,888,731-121,918,297
Accession: 9567
RBP type: non-canonical RBP
Summary: The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a non-ATPase subunit of the 19S regulator. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, May 2012]

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 & MCF10A	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
30535233	Inhibition of Skp1-Cullin-F-box complexes during bovine oocyte maturation and preimplantation development leads to delayed development of embryos.	Biol Reprod	2019 Apr 1	Kinterova V	doi: 10.1093/biolre/ioy254.
15568022	Protection of p27(Kip1) mRNA by quaking RNA binding proteins promotes oligodendrocyte differentiation.	Nat Neurosci	2005 Jan	Larocque D	-
22926519	Far upstream element binding protein 1: a commander of transcription, translation and beyond.	Oncogene	2013 Jun 13	Zhang J	doi: 10.1038/onc.2012.350
25009770	Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules.	FEBS Open Bio	2014 Jun 6	Sangith N	doi: 10.1016/j.fob.2014.05.005
30014466	Reduced expression of the RNA-binding protein HuD in pancreatic neuroendocrine tumors correlates with low p27Kip1 levels and poor prognosis.	J Pathol	2018 Oct	Kim C	doi: 10.1002/path.5135

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000537407	PSMD9-204	1195	-	ENSP00000445058	209 (aa)	-	O00233
ENST00000542602	PSMD9-208	516	-	ENSP00000443772	118 (aa)	-	O00233
ENST00000544724	PSMD9-211	3051	-	-	- (aa)	-	-
ENST00000541212	PSMD9-207	2784	-	ENSP00000440485	223 (aa)	-	O00233
ENST00000261817	PSMD9-201	2307	-	ENSP00000261817	222 (aa)	-	J3KN29
ENST00000538613	PSMD9-205	534	-	ENSP00000443081	153 (aa)	-	F5H5V4
ENST00000540962	PSMD9-206	793	-	ENSP00000442210	85 (aa)	-	F5H7X1
ENST00000535293	PSMD9-203	1773	-	ENSP00000443968	128 (aa)	-	F5H169
ENST00000544254	PSMD9-210	1481	-	-	- (aa)	-	-
ENST00000543699	PSMD9-209	1001	-	ENSP00000440500	179 (aa)	-	F5GX23
ENST00000361485	PSMD9-202	2087	-	-	- (aa)	-	-

Gene Model

Click here to download ENSG00000110801's gene model file

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000110801	Urine	4E-16	24586186

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000110801	rs7314056	12	121905058	C	Urinary metabolites (H-NMR features)	24586186	[NR] unit decrease	0.44	EFO_0005116
ENSG00000110801	rs895960	12	121908146	A	Educational attainment (MTAG)	30038396	[0.0058-0.012] unit decrease	0.0089	EFO_0004784
ENSG00000110801	rs1720035	12	121909706	T	Cognitive performance (MTAG)	30038396	[0.011-0.022] unit decrease	0.0162	EFO_0008354

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000110801's network

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

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000165	MAPK cascade	-	TAS	Process
GO:0000209	protein polyubiquitination	-	TAS	Process
GO:0002223	stimulatory C-type lectin receptor signaling pathway	-	TAS	Process
GO:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	-	TAS	Process
GO:0003713	transcription coactivator activity	10567574.	ISS	Function
GO:0005515	protein binding	16189514.19490896.21516116.25009770.25416956.	IPI	Function
GO:0005634	nucleus	21873635.	IBA	Component
GO:0005634	nucleus	10567574.	ISS	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005737	cytoplasm	21873635.	IBA	Component
GO:0005829	cytosol	-	TAS	Component
GO:0005838	proteasome regulatory particle	9653651.	NAS	Component
GO:0006511	ubiquitin-dependent protein catabolic process	9653651.	NAS	Process
GO:0006521	regulation of cellular amino acid metabolic process	-	TAS	Process
GO:0008540	proteasome regulatory particle, base subcomplex	21873635.	IBA	Component
GO:0008540	proteasome regulatory particle, base subcomplex	19490896.	IDA	Component
GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	-	TAS	Process
GO:0016579	protein deubiquitination	-	TAS	Process
GO:0031145	anaphase-promoting complex-dependent catabolic process	-	TAS	Process
GO:0031146	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	-	TAS	Process
GO:0032024	positive regulation of insulin secretion	10567574.	ISS	Process
GO:0033209	tumor necrosis factor-mediated signaling pathway	-	TAS	Process
GO:0038061	NIK/NF-kappaB signaling	-	TAS	Process
GO:0038095	Fc-epsilon receptor signaling pathway	-	TAS	Process
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	-	TAS	Process
GO:0043425	bHLH transcription factor binding	10567574.	ISS	Function
GO:0043488	regulation of mRNA stability	-	TAS	Process
GO:0043687	post-translational protein modification	-	TAS	Process
GO:0045893	positive regulation of transcription, DNA-templated	10567574.16293776.	ISS	Process
GO:0046676	negative regulation of insulin secretion	16099819.	ISS	Process
GO:0050852	T cell receptor signaling pathway	-	TAS	Process
GO:0055085	transmembrane transport	-	TAS	Process
GO:0060071	Wnt signaling pathway, planar cell polarity pathway	-	TAS	Process
GO:0061418	regulation of transcription from RNA polymerase II promoter in response to hypoxia	-	TAS	Process
GO:0070498	interleukin-1-mediated signaling pathway	-	TAS	Process
GO:0070682	proteasome regulatory particle assembly	21873635.	IBA	Process
GO:0070682	proteasome regulatory particle assembly	19490896.	IMP	Process
GO:0090090	negative regulation of canonical Wnt signaling pathway	-	TAS	Process
GO:0090263	positive regulation of canonical Wnt signaling pathway	-	TAS	Process
GO:1901990	regulation of mitotic cell cycle phase transition	-	TAS	Process
GO:1902036	regulation of hematopoietic stem cell differentiation	-	TAS	Process

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
19118035	Cytoplasmic sequestration of p27 via AKT phosphorylation in renal cell carcinoma.	Clin Cancer Res	2009 Jan 1	Kim J	doi: 10.1158/1078-0432.CCR-08-0170.
12778072	Expression of cyclin D1, D3, E, and p27 in human renal cell carcinoma analysed by tissue microarray.	Br J Cancer	2003 May 6	Hedberg Y	-
24673853	PSMD9 expression predicts radiotherapy response in breast cancer.	Mol Cancer	2014 Mar 28	Langlands FE	doi: 10.1186/1476-4598-13-73.
17360176	p53 and p27 as predictors of clinical outcome for rectal-cancer patients receiving neoadjuvant therapy.	Surg Oncol	2006 Dec	Lin LC	-
28650473	Testes-specific protease 50 promotes cell proliferation via inhibiting activin signaling.	Oncogene	2017 Oct 26	Song ZB	doi: 10.1038/onc.2017.198
18694622	Polymorphisms of p21 and p27 jointly contribute to an earlier age at diagnosis of pancreatic cancer.	Cancer Lett	2008 Dec 8	Chen J	doi: 10.1016/j.canlet.2008.06.022

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr12	121915880	Missense_Mutation	rs758694222	R194C	0.24
BLCA	chr12	121915907	Missense_Mutation	novel	L203F	0.16
BLCA	chr12	121894769	Missense_Mutation	rs761768941	V57M	0.19
BLCA	chr12	121916366	3'UTR	novel		0.4
BLCA	chr12	121899800	Silent	rs777738989	F136F	0.09
BRCA	chr12	121888876	Missense_Mutation	NA	R7K	0.31
CESC	chr12	121903024	Missense_Mutation	NA	E158K	0.44
CESC	chr12	121888992	Missense_Mutation	novel	S46R	0.17
CESC	chr12	121888993	Missense_Mutation	novel	S46N	0.17
CESC	chr12	121916406	3'UTR	rs575543796		0.44
CESC	chr12	121888929	Missense_Mutation	NA	E25Q	0.28
CESC	chr12	121915881	Missense_Mutation	rs778204603	R194L	0.1
COAD	chr12	121915880	Missense_Mutation	rs758694222	R194C	0.4
COAD	chr12	121916303	Frame_Shift_Del	novel	*Q222Kfs9**	0.03
COAD	chr12	121915939	Silent	NA	L213L	0.55
COAD	chr12	121888996	Splice_Site	novel	X46_splice	0.36
GBM	chr12	121899702	Missense_Mutation	rs542016320	D104N	0.36
KIRC	chr12	121916358	3'UTR	novel		0.53
KIRP	chr12	121903042	Missense_Mutation	novel	S164T	0.61
LGG	chr12	121899801	Missense_Mutation	rs376571677	A137T	0.25
LUAD	chr12	121916343	3'UTR	novel		0.06
LUAD	chr12	121916362	3'UTR	novel		0.36
LUAD	chr12	121916363	3'UTR	novel		0.34
OV	chr12	121916383	3'UTR	novel		0.23
OV	chr12	121916321	3'UTR	novel		0.32
PAAD	chr12	121899843	Missense_Mutation	rs139208583	A151T	0.14
SARC	chr12	121903043	Missense_Mutation	novel	S164F	0.23
SKCM	chr12	121915879	Silent	NA	I193I	0.33
SKCM	chr12	121915898	Nonsense_Mutation	NA	Q200*	0.17
SKCM	chr12	121915879	Silent	NA	I193I	0.3
SKCM	chr12	121899749	Silent	novel	A119A	0.22
SKCM	chr12	121903053	Silent	novel	T167T	0.38
STAD	chr12	121915870	Silent	novel	V190V	0.16
THYM	chr12	121888920	Missense_Mutation	novel	D22Y	0.17
UCEC	chr12	121899645	Missense_Mutation	NA	D85Y	0.22
UCEC	chr12	121915884	Frame_Shift_Del	NA	*E197Kfs47**	0.47
UCEC	chr12	121915874	Missense_Mutation	novel	V192L	0.33
UCEC	chr12	121894782	Missense_Mutation	novel	G61D	0.12
UCEC	chr12	121916394	3'UTR	novel		0.16
UCEC	chr12	121903074	Silent	novel	H174H	0.33
UCEC	chr12	121903038	Silent	rs756179152	F162F	0.39
UCEC	chr12	121915913	Missense_Mutation	novel	P205T	0.52
UCEC	chr12	121903071	Silent	NA	L173L	0.33
UCEC	chr12	121915884	Missense_Mutation	novel	R195K	0.11
UCEC	chr12	121916383	3'UTR	novel		0.32
UCEC	chr12	121916298	Missense_Mutation	novel	P220H	0.31

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
BRCA	DEL	0.1667	6.3933e-07
CHOL	DEL	0.1944	0.067545
HNSC	DEL	0.0556	0.22646
LUAD	DEL	0.1473	0.0059643
LUSC	DEL	0.1098	0.038823
PAAD	DEL	0.1739	0.0030251
PRAD	AMP	0.0508	0.016187
SKCM	DEL	0.1826	0.00079981
UCEC	DEL	0.0965	0.00053229
UCS	DEL	0.3393	0.033261

Survival Analysis

Cancer	P-value	Q-value
MESO	0.035	Kaplan-Meier Survival Analysis
ACC	0.0039	Kaplan-Meier Survival Analysis
UCS	0.0029	Kaplan-Meier Survival Analysis
SKCM	0.0001	Kaplan-Meier Survival Analysis
CESC	0.0028	Kaplan-Meier Survival Analysis
LIHC	0.00011	Kaplan-Meier Survival Analysis
DLBC	0.031	Kaplan-Meier Survival Analysis
LGG	0.0001	Kaplan-Meier Survival Analysis
LUAD	0.019	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

Phenotypes

GWAS

PPI

Gene Ontology

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Cell lines and drugs in GSE70138 or GSE92742