EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000029993 (Gene tree)
Gene ID: 3149
Gene Symbol: HMGB3
Alias: HMG2A|MGC90319|HMG4
Full Name: high mobility group box 3
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 10,268 bases
Position: chrX:150,980,508-150,990,775
Accession: 5004
RBP type: non-canonical RBP
Summary: This gene encodes a member of a family of proteins containing one or more high mobility group DNA-binding motifs. The encoded protein plays an important role in maintaining stem cell populations, and may be aberrantly expressed in tumor cells. A mutation in this gene was associated with microphthalmia, syndromic 13. There are numerous pseudogenes of this gene on multiple chromosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
22681889	The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts	4SURIC & HEK293	2012 May	Baltz AG	DOI: 10.1016/j.molcel.2012.05.021
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

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
7370264	Characterization of a non-histone chromosomal protein which stimulates RNA polymerase II.	Biochim Biophys Acta	1980 Mar 28	Legraverend M	-

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000325307	HMGB3-201	3560	XM_024452369	ENSP00000359393	200 (aa)	XP_024308137	O15347
ENST00000430118	HMGB3-203	529	-	ENSP00000417027	153 (aa)	-	E9PES6
ENST00000419110	HMGB3-202	707	-	ENSP00000410354	188 (aa)	-	E7ES08
ENST00000448905	HMGB3-204	812	-	ENSP00000442758	200 (aa)	-	O15347
ENST00000455596	HMGB3-205	793	-	ENSP00000405601	193 (aa)	-	E7EQU1

Gene Model

Click here to download ENSG00000029993's gene model file

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000029993'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
ENSG00000029993	HMGB3	100	97.500	ENSMUSG00000015217	Hmgb3	100	97.500	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000400	four-way junction DNA binding	-	ISS	Function
GO:0000790	nuclear chromatin	21873635.	IBA	Component
GO:0003690	double-stranded DNA binding	-	ISS	Function
GO:0003723	RNA binding	22681889.	HDA	Function
GO:0005515	protein binding	21044950.25416956.	IPI	Function
GO:0005737	cytoplasm	21873635.	IBA	Component
GO:0006310	DNA recombination	21873635.	IBA	Process
GO:0006310	DNA recombination	-	ISS	Process
GO:0006338	chromatin remodeling	21873635.	IBA	Process
GO:0006357	regulation of transcription by RNA polymerase II	21873635.	IBA	Process
GO:0007275	multicellular organism development	9598312.	TAS	Process
GO:0008134	transcription factor binding	21873635.	IBA	Function
GO:0008301	DNA binding, bending	21873635.	IBA	Function
GO:0008301	DNA binding, bending	-	ISS	Function
GO:0032392	DNA geometric change	-	ISS	Process
GO:0045087	innate immune response	-	IEA	Process
GO:0045089	positive regulation of innate immune response	21873635.	IBA	Process
GO:0045944	positive regulation of transcription by RNA polymerase II	21873635.	IBA	Process

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
24338397	HMGB3 characterization in gastric cancer.	Genet Mol Res	2013 Dec 2	Gong Y	doi: 10.4238/2013.December.2.1.
25647262	Overexpression of HMGB3 protein promotes cell proliferation, migration and is associated with poor prognosis in urinary bladder cancer patients.	Tumour Biol	2015 Jun	Li M	doi: 10.1007/s13277-015-3130-y
24098490	Tumor suppressive function of mir-205 in breast cancer is linked to HMGB3 regulation.	PLoS One	2013 Oct 2	Elgamal OA	doi: 10.1371/journal.pone.0076402
25095979	Upregulation of miR-513b inhibits cell proliferation, migration, and promotes apoptosis by targeting high mobility group-box 3 protein in gastric cancer.	Tumour Biol	2014 Nov	Chen X	doi: 10.1007/s13277-014-2405-z
23609034	Prognostic value of HMGB3 expression in patients with non-small cell lung cancer.	Tumour Biol	2013 Oct	Song N	doi: 10.1007/s13277-013-0807-y
23326140	High mobility group-box 3 overexpression is associated with poor prognosis of resected gastric adenocarcinoma.	World J Gastroenterol	2012 Dec 28	Tang HR	doi: 10.3748/wjg.v18.i48.7319.
29196733	Regulation of HMGB3 by antitumor miR-205-5p inhibits cancer cell aggressiveness and is involved in prostate cancer pathogenesis.	J Hum Genet	2018 Feb	Yamada Y	doi: 10.1038/s10038-017-0371-1
30166860	Abnormal expression of HMGB-3 is significantly associated with malignant transformation of hepatocytes.	World J Gastroenterol	2018 Aug 28	Zheng WJ	doi: 10.3748/wjg.v24.i32.3650.

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BRCA	chrX	150988771	3'UTR	novel		0.09
BRCA	chrX	150987846	Nonsense_Mutation	NA	K179*	0.13
BRCA	chrX	150988085	3'UTR	novel		0.11
BRCA	chrX	150987302	Missense_Mutation	NA	K155N	0.24
BRCA	chrX	150987909	Missense_Mutation	NA	E200K	0.14
CESC	chrX	150988872	3'UTR	novel		0.19
CESC	chrX	150987954	3'UTR	novel		0.49
CESC	chrX	150987797	Silent	rs782588935	S162S	0.35
CESC	chrX	150988374	3'UTR	novel		0.58
CESC	chrX	150988451	3'UTR	novel		0.35
CESC	chrX	150987927	3'UTR	novel		0.33
CESC	chrX	150988835	3'UTR	novel		0.1
CHOL	chrX	150988556	3'UTR	novel		0.17
COAD	chrX	150986050	Splice_Site	NA	X51_splice	0.28
ESCA	chrX	150987204	Missense_Mutation	NA	V123M	0.55
GBM	chrX	150986068	Missense_Mutation	novel	E56D	0.23
HNSC	chrX	150987842	Frame_Shift_Ins	novel	*V180Gfs6**	0.73
KIRP	chrX	150987916	3'UTR	novel		1
LGG	chrX	150986134	Silent	novel	Y78Y	0.13
LIHC	chrX	150987251	Missense_Mutation	NA	E138D	0.93
LUAD	chrX	150987829	Missense_Mutation	NA	A173D	0.43
LUAD	chrX	150986135	Nonsense_Mutation	NA	G79*	0.43
LUAD	chrX	150987878	In_Frame_Ins	novel	E198dup	0.12
LUAD	chrX	150987974	3'UTR	novel		0.25
LUAD	chrX	150987230	Missense_Mutation	novel	W131C	0.17
LUSC	chrX	150986168	Missense_Mutation	novel	P90T	0.77
LUSC	chrX	150986165	Missense_Mutation	novel	D89Y	0.24
OV	chrX	150986171	Missense_Mutation	NA	N91Y	0.12
OV	chrX	150987215	Missense_Mutation	NA	K126N	0.69
OV	chrX	150987780	Frame_Shift_Ins	novel	*V157Efs68**	0.04
READ	chrX	150985710	Missense_Mutation	novel	N37K	0.07
READ	chrX	150987153	Missense_Mutation	NA	E106K	0.2
READ	chrX	150987797	Silent	rs782588935	S162S	0.24
SARC	chrX	150987190	Missense_Mutation	novel	I118S	0.49
SKCM	chrX	150988012	3'UTR	novel		0.76
SKCM	chrX	150986117	Missense_Mutation	NA	R73W	0.25
SKCM	chrX	150987943	3'UTR	novel		0.41
SKCM	chrX	150985724	Missense_Mutation	NA	S42F	0.86
SKCM	chrX	150987842	Silent	NA	R177R	0.43
STAD	chrX	150986169	Missense_Mutation	NA	P90H	0.42
STAD	chrX	150987817	Missense_Mutation	NA	A169V	0.21
UCEC	chrX	150986099	Missense_Mutation	NA	D67Y	0.33
UCEC	chrX	150987975	3'UTR	novel		0.3
UCEC	chrX	150988437	3'UTR	novel		0.11
UCEC	chrX	150986169	Missense_Mutation	NA	P90H	0.48
UCEC	chrX	150985677	Silent	novel	E26E	0.47
UCEC	chrX	150988050	3'UTR	novel		0.36
UCEC	chrX	150988703	3'UTR	novel		0.46
UCEC	chrX	150985698	Missense_Mutation	novel	E33D	0.38
UCEC	chrX	150988172	3'UTR	novel		0.52
UCEC	chrX	150988493	3'UTR	novel		0.45
UCEC	chrX	150987797	Silent	rs782588935	S162S	0.35
UCEC	chrX	150987974	3'UTR	rs781834650		0.33
UCEC	chrX	150988597	3'UTR	novel		0.19
UCEC	chrX	150988689	3'UTR	novel		0.38
UCEC	chrX	150988573	3'UTR	novel		0.56
UCEC	chrX	150987908	Silent	rs782545964	D199D	0.56
UCEC	chrX	150985716	Silent	NA	A39A	0.23
UCEC	chrX	150988556	3'UTR	novel		0.52
UCEC	chrX	150987127	Splice_Site	novel	X97_splice	0.24
UCEC	chrX	150987273	Missense_Mutation	NA	A146T	0.51
UCEC	chrX	150987841	Missense_Mutation	rs782427760	R177Q	0.34
UCEC	chrX	150988014	3'UTR	novel		0.12
UCEC	chrX	150988159	3'UTR	novel		0.13
UCEC	chrX	150988812	3'UTR	novel		0.38
UCEC	chrX	150988525	3'UTR	novel		0.38
UCEC	chrX	150988145	3'UTR	novel		0.49
UCEC	chrX	150988429	3'UTR	novel		0.2
UCEC	chrX	150988421	3'UTR	novel		0.51
UCEC	chrX	150988556	3'UTR	novel		0.56
UCEC	chrX	150986068	Missense_Mutation	novel	E56D	0.73
UCEC	chrX	150985620	Silent	novel	K7K	0.21
UCEC	chrX	150987801	Nonsense_Mutation	novel	G164*	0.45
UCEC	chrX	150988034	3'UTR	novel		0.5
UCEC	chrX	150988556	3'UTR	novel		0.92
UCEC	chrX	150985653	Missense_Mutation	novel	F18L	0.47
UCEC	chrX	150986103	Missense_Mutation	novel	K68T	0.18
UCEC	chrX	150988240	3'UTR	novel		0.31
UCEC	chrX	150988959	3'UTR	novel		0.45
UCEC	chrX	150987905	Missense_Mutation	NA	E198D	0.12
UCEC	chrX	150987960	3'UTR	rs782599818		0.29
UCEC	chrX	150986120	Missense_Mutation	novel	E74K	0.42
UCEC	chrX	150988023	3'UTR	novel		0.23
UCEC	chrX	150988856	3'UTR	novel		0.1
UCEC	chrX	150988416	3'UTR	novel		0.38
UCEC	chrX	150988556	3'UTR	novel		0.32
UCEC	chrX	150988573	3'UTR	novel		0.39
UCEC	chrX	150987916	3'UTR	novel		0.29
UCEC	chrX	150985663	Missense_Mutation	NA	T22A	0.42
UCEC	chrX	150987185	Silent	rs782232648	P116P	0.35
UCEC	chrX	150988417	3'UTR	novel		0.29
UCEC	chrX	150987822	Missense_Mutation	NA	G171R	0.08
UCEC	chrX	150988703	3'UTR	novel		0.34
UCEC	chrX	150988556	3'UTR	novel		0.43
UCEC	chrX	150987916	3'UTR	novel		0.39
UCEC	chrX	150988034	3'UTR	novel		0.34
UCEC	chrX	150987797	Silent	rs782588935	S162S	0.44
UCEC	chrX	150985675	Nonsense_Mutation	novel	E26*	0.41
UCEC	chrX	150988368	3'UTR	rs189227474		0.34
UCEC	chrX	150988261	3'UTR	novel		0.29
UCS	chrX	150986158	Silent	novel	K86K	0.29

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
DLBC	AMP	0.1458	0.24013
KIRC	AMP	0.0398	0.12739
LUSC	AMP	0.1677	0.08275
PAAD	AMP	0.0761	0.041079
READ	AMP	0.1394	0.14805
STAD	AMP	0.1066	0.0021069
TGCT	DEL	0.0667	0.08422
THCA	DEL	0	0.21991
UCS	DEL	0.2679	0.063955

Survival Analysis

Cancer	P-value	Q-value
THYM	0.017	Kaplan-Meier Survival Analysis
KIRC	0.00011	Kaplan-Meier Survival Analysis
STAD	0.033	Kaplan-Meier Survival Analysis
SARC	0.0001	Kaplan-Meier Survival Analysis
MESO	0.0052	Kaplan-Meier Survival Analysis
SKCM	0.00066	Kaplan-Meier Survival Analysis
LUSC	0.034	Kaplan-Meier Survival Analysis
BRCA	0.0058	Kaplan-Meier Survival Analysis
ESCA	0.0069	Kaplan-Meier Survival Analysis
KIRP	0.033	Kaplan-Meier Survival Analysis
PCPG	0.03	Kaplan-Meier Survival Analysis
CESC	0.028	Kaplan-Meier Survival Analysis
LAML	0.028	Kaplan-Meier Survival Analysis
UCEC	0.0074	Kaplan-Meier Survival Analysis
LIHC	0.0072	Kaplan-Meier Survival Analysis
LGG	0.023	Kaplan-Meier Survival Analysis
OV	0.00013	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

PPI

Orthologs

Gene Ontology

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742