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	Gene Summary
	Translation studies in PubMed
	Exon Skipping Events
	Expression
	Expression Regulation
	Associated Genes
	Protein 3D Structure
	Protein-Protein Interaction
	Mutations
	Prognostic Analysis
	Gender Association
	Age Association
	Related Drugs
	Related Diseases

Translation Factor: YBX3 (NCBI Gene ID:8531)

Gene Summary

Gene Summary

Gene Information	Gene Name: YBX3
	Gene ID: 8531
	Gene Symbol	YBX3
	Gene ID	8531
	Gene Name	Y-box binding protein 3
	Synonyms	CSDA\|CSDA1\|DBPA\|ZONAB
	Cytomap	12p13.2
	Type of Gene	protein-coding
	Description	Y-box-binding protein 3DNA-binding protein AZO-1-associated nucleic acid-binding proteincold shock domain-containing protein Acold-shock domain containing A1cold-shock domain protein Asingle-strand DNA-binding protein NF-GMB
	Modification date	20200313
	UniProtAcc	P16989

Child GO biological process term(s) under GO:0006412

GO ID	GO term
GO:0006417	Regulation of translation
GO:0045727	Positive regulation of translation
GO:0002181	Cytoplasmic translation
GO:0006412	Translation

Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Inferred gene age of translation factor.

Gene	Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
YBX3	>1119.25

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Translation Studies in PubMed

We searched PubMed using 'YBX3[title] AND translation [title] AND human.'

Gene	Title	PMID
YBX3	.	.

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Exon Skipping Events

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.

Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	ORF
ENST00000228251	10862506	10862713	In-frame
ENST00000228251	10870686	10870720	Frame-shift

Exon skipping position in the amino acid sequence.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	Len(transcript seq)	Exon skip start (mRNA)	Exon Skip end (mRNA)	Len(amino acid seq)	Exon skip start (AA)	Exon Skip end (AA)
ENST00000228251	10862506	10862713	1813	775	981	372	191	260

Potentially (partially) lost protein functional features of UniProt.

UniProtAcc	Exon skip start (AA)	Exon Skip end (AA)	Function feature start (AA)	Function feature end (AA)	Functional feature type	Functional feature desc.
P16989	191	260	2	372	Chain	ID=PRO_0000100214;Note=Y-box-binding protein 3
P16989	191	260	201	201	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332;Dbxref=PMID:18669648,PMID:19690332
P16989	191	260	203	203	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332;Dbxref=PMID:18669648,PMID:19690332
P16989	191	260	204	204	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231;Dbxref=PMID:18669648,PMID:19690332,PMID:20068231
P16989	191	260	251	251	Modified residue	Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24129315;Dbxref=PMID:24129315
P16989	191	260	192	260	Alternative sequence	ID=VSP_001135;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334

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Expression

Gene expression level across TCGA pancancer

Gene expression level across GTEx pantissue

Expression level of gene isoforms across TCGA pancancer

Expression level of gene isoforms across GTEx pantissue

Cancer(tissue) type-specific expression level of Translation factor using z-score distriution

Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)

Cancer type

Translation factor

adj.pval

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Expression Regulation

Translation factor expression regulation through miRNA binding

Cancer type

Gene

miRNA

TargetScan binding score (Context++ score percentile)

Coefficient

Pvalue

Translation factor expression regulation through methylation in the promoter of Translation factor

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through copy number variation of Translation factor

Cancer type

Gene

Coefficient

Pvalue

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with YBX3 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)

Cancer type

Gene group

Translation factor

Correlated gene

Coefficient

Pvalue

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Protein structure

Protein 3D structure
Visit iCn3D.

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Protein-Protein Interaction

Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

* Edge colors based on TCGA cancer types.

* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))

Cancer type	Translation factor	Interacting protein coding gene	FC	adj.pval
HNSC	YBX3	TJP1	-1.15535387145194	0.000182808133786239
ESCA	YBX3	CDK4	-1.43377694663384	0.0009765625
COAD	YBX3	RALA	1.23419838406538	0.00144392251968384
KIRP	YBX3	TJP1	-2.27440782036625	0.00337919034063816
CHOL	YBX3	RALA	-2.33863326941556	0.00390625
HNSC	YBX3	ARHGEF2	-1.31133539143434	0.0040605245990264
BLCA	YBX3	TJP2	-1.48414298688371	0.0061798095703125
CHOL	YBX3	ARHGEF2	-2.86920855441846	0.0078125
LUSC	YBX3	RALA	-1.08095321977716	0.00855715492782793
READ	YBX3	SYMPK	-2.3101868669209	0.03125
PRAD	YBX3	RALB	-1.03531976657568	0.0327143182470405
LUAD	YBX3	CDK4	-5.0679847103811	1.10446534121172e-08
KIRP	YBX3	CDK4	-1.87209683895352	1.16415321826935e-08
BRCA	YBX3	TJP1	-4.67254320606445	1.65203581003695e-14
BRCA	YBX3	CDK4	-1.34096999595832	2.82194928272833e-14
LUAD	YBX3	TJP1	-1.96770566983781	2.83612198579349e-08
LUAD	YBX3	ARHGEF2	-1.47169752262487	3.09848396407815e-08
LIHC	YBX3	CDK4	-1.07333331044328	3.4520382341717e-07
LUSC	YBX3	TJP1	-3.26126941857339	3.6218774072117e-09
STAD	YBX3	CDK4	-1.29117226344301	4.05178032672423e-05
KIRC	YBX3	TJP1	-2.01258303787563	4.47117775598177e-07
THCA	YBX3	CDK4	-2.27939796893498	5.37804646473384e-08
KIRC	YBX3	RALA	-1.03492556822076	5.40770022916002e-07
BRCA	YBX3	CCND1	1.69430510513542	5.61905688699845e-07
PRAD	YBX3	TJP1	1.07626720993625	6.13785511132143e-06
KIRC	YBX3	ARHGEF2	-1.69130019909656	7.97979847396234e-08
COAD	YBX3	RALB	-1.76540559963127	8.94069671630861e-08
THCA	YBX3	RALB	-1.06896416526015	9.90028172590343e-06

Protein-protein interactors with this translation factor (BIOGRID-3.4.160)

PPI interactors with YBX3

RRP1B, Rrp1b, MEPCE, TJP1, SRRM1, DOT1L, NPM1, MAPK1, GSK3B, HAUS6, ELAVL1, ARRB2, CUL3, CUL4B, CUL5, CUL2, CUL1, COPS5, DCUN1D1, CAND1, NEDD8, NDUFB10, C1QBP, ESR1, PAXIP1, MAGOH, EIF4A3, IFIT2, IFIT3, IL7R, CBX8, PAN2, IGSF8, ICAM1, HDAC11, SRPK3, TARDBP, PARK2, ABCF1, C14orf166, RTCB, NELFB, CSRP1, DDX1, DHX9, EIF2B2, EIF2B3, EIF5B, MACF1, HNRNPU, IGF2BP3, ILF2, MAP7, MRE11A, NMT1, PTBP1, RFC4, CEP250, CEP76, EZH2, SUZ12, RNF2, BMI1, ARAF, ATR, BLK, CDK2, MAST3, PXK, SRPK1, HNRNPA1, ABCB7, ATP6V0D1, COX5A, NDUFA9, PELO, SKIV2L2, SRPK2, HIST1H3E, USP7, SLAIN2, UBA5, NLRP3, NEDD1, C1qbp, Ruvbl1, Rrbp1, TRIM29, Ksr1, RC3H1, CCDC84, CDK5, CDK4, ZNF746, E4F1, RPL6, ZC3HAV1, RRS1, PPAN, BHLHA15, SART3, H2AFX, CYLD, INO80B, TRIM25, G3BP1, TRIM14, TMPO, UBE2M, PIH1D1, EFTUD2, TNIP2, LARP7, RIOK1, FGF11, ESR2, HEXIM1, AGO2, SNAI1, HRAS, RECQL4, SYMPK, MYC, CDK9, KIAA1429, RC3H2, ACTC1, PHB, USP14, MECOM, DYRK1A, OASL, SNRNP70, Dppa3, FUS, ITFG1, PPP1CA, BIRC3, WWP2, BRD7, TP53, CMTR1, ARIH2, PLEKHA4, HCVgp1, MIRLET7A1, MIRLET7A2, MIRLET7A3, MIRLET7B, MIRLET7C, MIRLET7D, MIRLET7E, MIRLET7F1, MIRLET7F2, MIRLET7G, MIRLET7I, MIR98, MIR1-1, MIR1-2, MIR7-1, MIR7-2, MIR7-3, MIR9-1, MIR9-2, MIR9-3, MIR10B, MIR15A, MIR15B, MIR16-1, MIR16-2, MIR17, MIR18A, MIR18B, MIR19A, MIR19B1, MIR19B2, MIR20A, MIR20B, MIR21, MIR25, MIR29A, MIR29B1, MIR29B2, MIR29C, MIR31, MIR34A, MIR34B, MIR34C, MIR92A1, MIR92A2, MIR93, MIR106A, MIR106B, MIR107, MIR122, MIR128-1, MIR128-2, MIR138-1, MIR138-2, MIR140, MIR141, MIR143, MIR145, MIR155, MIR199A1, MIR199A2, MIR200A, MIR200B, MIR200C, MIR205, MIR206, MIR214, MIR221, MIR222, MIR363, MIR429, MIR451A, ZC3H18, ELK4, RAB5A, PRRC2A, SMG7, YTHDF2, CELF1, MEX3B, PABPC1, NEK4, DUX4, AURKB, ECT2, KIF14, KIF20A, KIF23, PRC1, GRSF1, MKI67, N, LRRC59, HULC, BRD4, NUPR1, Apc2, RBM39, MKRN1, IFI16, LOC100506753, OGT, UFL1, DDRGK1, RPS20, SLC26A4-AS1, UBQLN1, FZR1, DANCR, ZBTB2, KRR1, RPL26, RPL17, HIST1H1B, ADARB1, NEIL1, H1FNT, HIST2H2AC, PABPC5, RPS19, RPS3, AGO1, SRSF5, CNBP, PRR3, RSL1D1, RPS10, YBX1, RBMS2, MRPL30, THAP3, WDR46, UTP23, HIST1H2AM, RBM19, RPL31, YBX2, SURF6, PURG, CBX6, RPS6, SRSF3, RPL23A, RPL10, PRKRA, ZNF346, MRPS27, MRPS17, LIN28A, HIST1H1E, RPLP0, MRPS25, ABT1, RPL7A, FGFBP1, RPS16, SRSF6, SRSF1, MRPL2, RPS3A, APOBEC3D, MRPL12, RPL35, SRSF7, HIST1H2AE, RPS2, NPM3, GSPT2, RPL13, RPSAP58, CHCHD2, RPL19, HIST1H1A, MRPS23, CPEB1, ZEB1, ATRX,

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Mutations

Clinically associated variants from ClinVar.

Gene

Chr

Position

RefSeq

VarSeq

RefSeeq

VarType

Pathogenic

Disease

VarInfo

nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.

SNVs and Indels

Gene	Cancer type	Chromosome	Start	End	RefSeeq	MutSeq	Mutation type	AAchange	# samples
YBX3	CESC	chr12	10854625	10854625	G	A	Silent		5
YBX3	PRAD	chr12	10865863	10865863	G	A	Missense_Mutation	p.R174W	2
YBX3	SKCM	chr12	10856655	10856655	G	A	Silent	p.Y291Y	2
YBX3	CESC	chr12	10862601	10862601	C	T	Missense_Mutation		1
YBX3	STAD	chr12	10868335	10868335	T	C	Silent	p.G136G	1
YBX3	CESC	chr12	10854632	10854632	C	A	Missense_Mutation		1
YBX3	SKCM	chr12	10865878	10865878	G	A	Missense_Mutation	p.R169C	1
YBX3	STAD	chr12	10868309	10868309	A	G	Missense_Mutation	p.V145A	1
YBX3	ESCA	chr12	10852015	10852015	G	A	RNA	NULL	1
YBX3	SKCM	chr12	10862627	10862627	C	T	Silent	p.R220R	1
YBX3	ACC	chr12	10856704	10856704	G	A	Missense_Mutation	p.A275V	1
YBX3	STAD	chr12	10862684	10862684	G	A	Silent	p.S201S	1
YBX3	HNSC	chr12	10862584	10862584	G	C	Missense_Mutation		1
YBX3	SKCM	chr12	10862566	10862566	G	A	Missense_Mutation	p.H241Y	1
YBX3	BLCA	chr12	10854585	10854585	T	C	Missense_Mutation		1
YBX3	THCA	chr12	10862690	10862690	T	C	Silent		1
YBX3	LIHC	chr12	10854616	10854616	G	-	Frame_Shift_Del	p.P332fs	1
YBX3	SKCM	chr12	10856686	10856686	A	G	Missense_Mutation	p.V281A	1
YBX3	BLCA	chr12	10854593	10854593	C	T	Missense_Mutation		1
YBX3	THCA	chr12	10862690	10862690	T	C	Silent	p.E199E	1
YBX3	LIHC	chr12	10856692	10856692	C	-	Frame_Shift_Del	p.G279fs	1
YBX3	SKCM	chr12	10856689	10856689	G	A	Missense_Mutation	p.P280L	1
YBX3	BLCA	chr12	10865866	10865866	C	A	Missense_Mutation		1
YBX3	THYM	chr12	10854710	10854710	G	T	Missense_Mutation		1
YBX3	LIHC	chr12	10871691	10871691	C	-	Frame_Shift_Del	p.G105fs	1
YBX3	BLCA	chr12	10854585	10854585	T	C	Missense_Mutation	p.N343D	1
YBX3	THYM	chr12	10856666	10856666	G	A	Missense_Mutation		1
YBX3	LUAD	chr12	10870707	10870707	C	T	Missense_Mutation	p.E114K	1
YBX3	SKCM	chr12	10856714	10856714	G	A	Missense_Mutation	p.P272S	1
YBX3	BLCA	chr12	10854593	10854593	C	T	Missense_Mutation	p.R340H	1
YBX3	LUAD	chr12	10871718	10871718	T	C	Missense_Mutation	p.K96R	1
YBX3	STAD	chr12	10868335	10868335	T	C	Silent		1
YBX3	BLCA	chr12	10865866	10865866	C	A	Missense_Mutation	p.D173Y	1
YBX3	LUAD	chr12	10865907	10865907	C	T	Missense_Mutation	p.G159D	1
YBX3	STAD	chr12	10862684	10862684	G	A	Silent		1
YBX3	LUAD	chr12	10856658	10856658	C	T	Splice_Site		1
YBX3	STAD	chr12	10868309	10868309	A	G	Missense_Mutation		1

Copy number variation (CNV) of YBX3
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across YBX3
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion genes with this translation factor from FusionGDB2.0.

FusionGDB2 ID	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
92264	N/A	BG168464	CANX	chr5	179147512	+	YBX3	chr12	10851923	-
92264	N/A	AA894477	DDHD2	chr8	38127217	-	YBX3	chr12	10855116	+
92264	Non-Cancer	ERR315469	HIVEP1	chr6	12015901	+	YBX3	chr12	10862713	-
92264	UCEC	TCGA-AP-A1E3-01A	HNRNPA2B1	chr7	26231464	-	YBX3	chr12	10851825	-
92264	ESCA	TCGA-L5-A43C-01A	MAGOHB	chr12	10762430	-	YBX3	chr12	10865932	-
92264	N/A	AF074691	MRC2	chr17	60770479	+	YBX3	chr12	10854691	-
92264	ESCA	TCGA-IG-A3YB	PRR4	chr12	11324021	-	YBX3	chr12	10871742	-
92264	ESCA	TCGA-IG-A3YB	TAS2R14	chr12	11324021	-	YBX3	chr12	10871742	-
92264	PRAD	TCGA-XQ-A8TA	TMEM8A	chr16	434256	-	YBX3	chr12	10856747	-
92264	PRAD	TCGA-XQ-A8TA-01A	TMEM8A	chr16	431701	-	YBX3	chr12	10856747	-
99942	LUSC	TCGA-21-1070-01A	YBX3	chr12	10868293	-	APOLD1	chr12	12982357	+
100506	COAD	TCGA-D5-6929-01A	YBX3	chr12	10865810	-	ATF7IP	chr12	14576843	+
100636	N/A	FN150935	YBX3	chr12	10865934	+	C16orf95	chr16	87242136	-
100959	LUSC	TCGA-21-1070-01A	YBX3	chr12	10868293	-	DDX47	chr12	12982357	+
99942	BRCA	TCGA-EW-A6SC-01A	YBX3	chr12	10865931	+	DGKE	chr17	54920378	+
99942	N/A	BI046011	YBX3	chr12	10854617	+	HIPK2	chr7	139260004	+
99942	PRAD	TCGA-G9-7525	YBX3	chr12	10875449	-	LOH12CR1	chr12	12588562	+
99942	PRAD	TCGA-EJ-7315-01A	YBX3	chr12	10875448	-	MRPL42	chr12	93894951	+
99942	PRAD	TCGA-EJ-7315-01A	YBX3	chr12	10875449	-	MRPL42	chr12	93894952	+
101062	N/A	BE122757	YBX3	chr12	10856655	-	PSMB1	chr6	170844386	+
101120	STAD	TCGA-IN-7808-01A	YBX3	chr12	10865810	-	RPS6KA3	chrX	20252932	-
99942	PRAD	TCGA-XQ-A8TA	YBX3	chr12	10865810	-	TMEM8A	chr16	427585	-
99942	PRAD	TCGA-XQ-A8TA-01A	YBX3	chr12	10862507	-	TMEM8A	chr16	427848	-
99942	N/A	X77777	YBX3	chr12	10875912	+	VIPR1	chr3	42555258	+

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Prognostic Analysis

Kaplan-Meier plots with logrank tests of overall survival (OS)

Cancer type

Translation factor

Coefficent

Hazard ratio

Wald test pval

Likelihool ratio pval

Logrank test pval

# samples

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Translation factor and Gender

Differential gene expression between female and male. (Wilcoxon test, pval<0.05)

Cancer type

Translation factor

pval

adj.p

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Translation factor and Age

Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)

Cancer type

Translation factor

pval

adj.p

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Related Drugs

Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases

Diseases associated with this translation factor.
(DisGeNet 4.0)

Disease ID

Disease Name

# PubMeds

Disease source