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Center for Computational Systems Medicine
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Gene Summary

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Translation studies in PubMed

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Exon Skipping Events

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Expression

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Expression Regulation

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Associated Genes

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Protein 3D Structure

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Protein-Protein Interaction

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Mutations

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Prognostic Analysis

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Gender Association

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Age Association

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Related Drugs

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Related Diseases

Translation Factor: RBM3 (NCBI Gene ID:5935)


Gene Summary

check button Gene Summary
Gene InformationGene Name: RBM3
Gene ID: 5935
Gene Symbol

RBM3

Gene ID

5935

Gene NameRNA binding motif protein 3
SynonymsIS1-RNPL|RNPL
Cytomap

Xp11.23

Type of Geneprotein-coding
DescriptionRNA-binding protein 3RNA binding motif (RNP1, RRM) protein 3
Modification date20200327
UniProtAcc

P98179


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation of translation
GO:0045727Positive regulation of translation
GO:0006412Translation


check button Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID


check button Inferred gene age of translation factor.
GeneInferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
RBM3(0 - 67.6]


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Translation Studies in PubMed

check button We searched PubMed using 'RBM3[title] AND translation [title] AND human.'
GeneTitlePMID
RBM3Translation regulatory factor RBM3 is a proto-oncogene that prevents mitotic catastrophe18427544


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Exon Skipping Events

check buttonSkipped 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.
all structure

check button 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.
ENSTExon skip start (DNA)Exon Skip end (DNA)ORF
ENST000003767554843394848434055Frame-shift
ENST000003767594843394848434055Frame-shift
ENST000003767554843489548434992Frame-shift
ENST000003767594843489548434992Frame-shift

check button Exon skipping position in the amino acid sequence.
ENSTExon 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)

check button Potentially (partially) lost protein functional features of UniProt.
UniProtAccExon skip start (AA)Exon Skip end (AA)Function feature start (AA)Function feature end (AA)Functional feature typeFunctional feature desc.


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Expression


check buttonGene expression level across TCGA pancancer
all structure

check buttonGene expression level across GTEx pantissue
all structure

check buttonExpression level of gene isoforms across TCGA pancancer
all structure

check buttonExpression level of gene isoforms across GTEx pantissue
all structure

check buttonCancer(tissue) type-specific expression level of Translation factor using z-score distriution
all structure

check buttonDifferential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)
all structure
Cancer typeTranslation factorFCadj.pval
KIRPRBM3-1.209953386157350.00143672106787562
THCARBM3-2.385010424554640.00194539641764689
KICHRBM3-1.955872443154510.0482624173164368
LIHCRBM3-1.389366028538428.97466888721789e-06


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue
DLBCRBM3hsa-miR-410-3p770.3703746530989820.0107926422492362


check buttonTranslation factor expression regulation through methylation in the promoter of Translation factor
all structure
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)
all structure
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through copy number variation of Translation factor
all structure
Cancer typeGeneCoefficientPvalue
THCARBM30.041262650.010867233
LUADRBM30.0628833280.014953106

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with RBM3 (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)
all structure
Cancer typeGene groupTranslation factorCorrelated geneCoefficientPvalue
CHOLCell metabolism geneRBM3SLC44A20.8010482443.90E-11
CHOLCell metabolism geneRBM3INPP5J0.801597663.69E-11
CHOLCell metabolism geneRBM3PLCD30.8020089193.55E-11
CHOLCell metabolism geneRBM3ARF30.8040694012.90E-11
CHOLCell metabolism geneRBM3PAFAH1B30.8080589221.94E-11
CHOLCell metabolism geneRBM3PFKP0.8220159274.45E-12
CHOLCell metabolism geneRBM3ITPR30.8237013983.69E-12
CHOLCell metabolism geneRBM3TEAD40.8382176136.79E-13
CHOLCell metabolism geneRBM3LCMT10.8416182674.46E-13
CHOLCGCRBM3ERCC30.80954441.67E-11
CHOLCGCRBM3ZNF3840.8110268171.43E-11
CHOLCGCRBM3SMARCA40.8132160141.14E-11
CHOLCGCRBM3FLNA0.822355684.29E-12
CHOLCGCRBM3ELF40.8225438324.20E-12
CHOLEpifactorRBM3SMARCA40.8132160141.14E-11
CHOLEpifactorRBM3HCFC10.8168635517.78E-12
CHOLEpifactorRBM3ATN10.8208909995.03E-12
CHOLEpifactorRBM3CTBP20.8224341634.25E-12
CHOLEpifactorRBM3ZNF7110.8284264412.17E-12
CHOLEpifactorRBM3HMGN40.8315143261.51E-12
CHOLEpifactorRBM3HDAC70.8426736093.90E-13
CHOLEpifactorRBM3SRCAP0.8589162614.45E-14
CHOLIUPHARRBM3BACE20.8004225784.14E-11
CHOLIUPHARRBM3LIMK10.8005850994.08E-11
CHOLIUPHARRBM3SLC44A20.8010482443.90E-11
CHOLIUPHARRBM3INPP5J0.801597663.69E-11
CHOLIUPHARRBM3PLCD30.8020089193.55E-11
CHOLIUPHARRBM3DDR10.8034506773.08E-11
CHOLIUPHARRBM3NEK110.803580483.04E-11
CHOLIUPHARRBM3SLC10A30.8039011392.95E-11
CHOLIUPHARRBM3SMARCA40.8132160141.14E-11
CHOLIUPHARRBM3MMP110.8141159551.04E-11
CHOLIUPHARRBM3MFSD50.8142207671.03E-11
CHOLIUPHARRBM3STK390.8157418538.76E-12
CHOLIUPHARRBM3SLC38A10.8214569794.73E-12
CHOLIUPHARRBM3ITPR30.8237013983.69E-12
CHOLIUPHARRBM3IKBKE0.8275977452.38E-12
CHOLIUPHARRBM3S100A110.8339950321.13E-12
CHOLIUPHARRBM3HDAC70.8426736093.90E-13
CHOLIUPHARRBM3ORAI20.8598544383.89E-14
CHOLIUPHARRBM3LPAR20.8676898151.23E-14
CHOLIUPHARRBM3ITGB40.8773001332.68E-15
CHOLKinaseRBM3LIMK10.8005850994.08E-11
CHOLKinaseRBM3DDR10.8034506773.08E-11
CHOLKinaseRBM3NEK110.803580483.04E-11
CHOLKinaseRBM3ABR0.8091276561.74E-11
CHOLKinaseRBM3STK390.8157418538.76E-12
CHOLKinaseRBM3IKBKE0.8275977452.38E-12
CHOLTFRBM3ZBTB450.8009627973.93E-11
CHOLTFRBM3ZNF3840.8110268171.43E-11
CHOLTFRBM3FBXL190.8124878821.23E-11
CHOLTFRBM3ELF40.8225438324.20E-12
CHOLTFRBM3ZNF7110.8284264412.17E-12
CHOLTFRBM3NFE2L30.8302008341.76E-12
CHOLTFRBM3TEAD40.8382176136.79E-13
CHOLTFRBM3SRCAP0.8589162614.45E-14
CHOLTSGRBM3GAS50.801334463.79E-11
CHOLTSGRBM3DOK10.8044537162.79E-11
CHOLTSGRBM3SPINT20.8083831361.88E-11
CHOLTSGRBM3BEX20.8114461641.37E-11
CHOLTSGRBM3SMARCA40.8132160141.14E-11
CHOLTSGRBM3FLNA0.822355684.29E-12
CHOLTSGRBM3PHLDA30.8292846251.96E-12
CHOLTSGRBM3S100A110.8339950321.13E-12


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Protein structure


check button Protein 3D structure
Visit iCn3D.


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Protein-Protein Interaction


check button 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))
all structure

check buttonOverlap 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))
all structure
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* Edge colors based on TCGA cancer types.

check button* 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))
all structure
Cancer typeTranslation factorInteracting protein coding geneFCadj.pval
KIRPRBM3ELAVL1-2.082006572510540.000110303983092308
PRADRBM3ILF3-1.663990022660960.000376184722398862
COADRBM3CELF2-1.575978668521040.000411599874496461
HNSCRBM3KHDRBS31.559035836939050.00106627625814326
BLCARBM3KHDRBS23.424306706919120.00123013955537317
ESCARBM3SNRPA-3.719393078367430.001953125
STADRBM3ELAVL1-2.101410751001840.00222697434946895
KIRPRBM3CELF2-1.405359364072910.00239070039242506
KICHRBM3ILF3-1.086904510870320.00308787822723389
BLCARBM3RBMXL1-1.618104915869080.00714492797851562
THCARBM3HNRNPK-8.734225425633890.00797530353045887
BLCARBM3KHDRBS32.134534439406090.00823211669921875
UCECRBM3RBMXL1-2.722333277537210.015625
PRADRBM3SNRPA-2.992229992911930.0219987445973693
UCECRBM3HNRNPK1.645327445048640.03125
ESCARBM3RBMX-1.332712188582930.0419921875
UCECRBM3ILF31.603150270856840.046875
UCECRBM3SNRPA1.41623669609110.046875
KIRPRBM3RBMXL11.772397484516541.53668224811554e-08
LUADRBM3ELAVL1-1.153273093112371.64690017573449e-06
KIRCRBM3CELF2-2.973758764463572.12552477559147e-07
LIHCRBM3RBM8A-3.060064031113452.58704546629954e-06
LUADRBM3CELF2-1.177032826958792.79010927055879e-10
LUADRBM3RBMXL1-5.246618660172542.91985910758098e-06
KICHRBM3RBM8A2.620559275870152.98023223876953e-07
BRCARBM3ILF3-1.251502403828673.29730506460964e-06
LIHCRBM3ELAVL1-1.114744979291223.60241778081952e-05
LUADRBM3KHDRBS2-1.770122954929853.79251210274868e-11
LIHCRBM3SNRPA-1.488809621625224.13231748257069e-06
LUADRBM3SNRPA-1.363952338351034.39225939988757e-09
LUADRBM3RBMX-3.502611443888934.40678669801292e-06
THCARBM3ELAVL1-1.754469830047425.71717197842929e-07
BRCARBM3RBMXL1-4.00292813813746.48351744106718e-14
KIRPRBM3SNRPA-1.041266361414576.79492950439454e-06
THCARBM3KHDRBS2-1.211538598170197.50861561019654e-11
STADRBM3ILF3-2.090201096796517.8696757555008e-08
HNSCRBM3CELF22.146997098821659.12882633201663e-05


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with RBM3
CHAF1A, UBC, CUL3, CUL4B, CUL5, CUL2, CDK2, CUL1, COPS5, DCUN1D1, CAND1, MRPL12, HNRNPA1, PSMA7, EEF1A1, FN1, IL7R, ITGA4, TP53, HNRNPK, RBMY1A1, SNRPA, RBMX, RBMY1F, KHDRBS2, MOV10, RPL10, MATR3, Rpl35, Taf15, Rrbp1, Srsf1, Fus, MCM2, RC3H1, ELAVL1, YARS2, SUPV3L1, MCAT, PAIP2B, NAGK, NGRN, THUMPD3, NIF3L1, AARS2, PRMT5, UPF1, FAM120A, IGF2BP2, FAP, DNM2, CDV3, MRPS31, TCEB2, SF3A2, PTCD1, ELAVL2, CASC3, CHRNE, YWHAE, CALCA, NCBP2, USP34, CCT4, TROVE2, KLHDC10, ILF3, RPA1, DAP3, WDR74, MRPS9, IGF2BP3, ILF2, UBR3, NFKBIZ, MRPS28, TCEB1, TTN, FLYWCH2, MAGOH, CCT3, FABP5, KIF27, MRPL1, MRPL52, JUP, KIAA0195, PRKRA, DDX60L, RALYL, C3orf70, CHM, RPL39, MRPS18B, AP1G2, CDKN2AIPNL, MRPS6, ZCCHC3, RBP3, RBM8A, EFTUD2, SPDL1, MEPCE, LARP7, REST, KIAA1429, RC3H2, PHB, USP14, HIST1H4A, APEX1, RARA, MAB21L2, SNRNP70, SRSF3, KHDRBS3, CHTOP, RBPMS2, PCBP1, MYPOP, PRR3, RBMY1J, FANCD2, ZC3H18, LCK, RAB5A, ORF8, ESR1, DUX4, CIT, DDX58, DDRGK1, FZR1, MAP4K2, DHX36, PAPSS2, FASTKD2, KLHL24, PRMT6, PRMT8, PRMT1, HNRNPA0, HNRNPR, HNRNPLL, Hnrnpk, Cirbp, Hnrnpu, Ube2i, Srsf3, Pcbp1, Rbm14,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo


check button nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.
all structure


check button SNVs and Indels
GeneCancer typeChromosomeStartEndRefSeeqMutSeqMutation typeAAchange# samples
RBM3COADchrX4843478648434786CTMissense_Mutationp.R99C3
RBM3UCECchrX4843477548434775GAMissense_Mutationp.G95E3
RBM3LIHCchrX4843362748433627ATMissense_Mutation3
RBM3UCECchrX4843395848433958TGMissense_Mutationp.V38G2
RBM3ACCchrX4843357548433575TAMissense_Mutationp.S3T2
RBM3SARCchrX4843497048434970CTMissense_Mutation2
RBM3ESCAchrX4843365648433656GAMissense_Mutationp.G30R2
RBM3UCECchrX4843398048433980GASilentp.R452
RBM3SARCchrX4843497048434970CTMissense_Mutationp.R131C2
RBM3UCECchrX4843551648435516CTMissense_Mutationp.A145V2
RBM3BRCAchrX4843403048434030TAMissense_Mutationp.V62D2
RBM3SKCMchrX4843395348433953CTSilentp.V36V2
RBM3KICHchrX4843480248434802CTMissense_Mutationp.S104F2
RBM3CESCchrX4843477848434778CTMissense_Mutation2
RBM3KIRPchrX4843499448434994TGSplice_Sitep.R138_splice2
RBM3TGCTchrX4843499448434994TGSplice_Site2
RBM3READchrX4843498048434980ATMissense_Mutationp.D134V1
RBM3LIHCchrX4843358448433584GAMissense_Mutation1
RBM3SARCchrX4843397748433977GTMissense_Mutation1
RBM3ESCAchrX4843370948433709GCRNANULL1
RBM3LIHCchrX4843468848434688TCMissense_Mutation1
RBM3ACCchrX4843357548433575TATranslation_Start_Site1
RBM3GBMchrX4843359648433596GCMissense_Mutationp.V10L1
RBM3LIHCchrX4843552848435528CAMissense_Mutation1
RBM3SARCchrX4843447648434476GTRNANULL1
RBM3KICHchrX4843480248434802CTMissense_Mutation1
RBM3LIHCchrX4843404048434040AGSilentp.R65R1
RBM3CESCchrX4843459548434595CTMissense_Mutation1
RBM3LIHCchrX4843362748433627ATMissense_Mutationp.Q20L1
RBM3SKCMchrX4843361148433611TCMissense_Mutationp.F15L1
RBM3KIRCchrX4843499148434992-GFrame_Shift_Insp.R138fs1
RBM3LIHCchrX4843462948434629C-Frame_Shift_Delp.T19fs1
RBM3CESCchrX4843359548433595CTSilent1
RBM3STADchrX4843359648433596GAMissense_Mutationp.V10M1
RBM3LUADchrX4843546848435468CAMissense_Mutationp.D156E1
RBM3CESCchrX4843377548433775CTRNANULL1
RBM3KIRPchrX4843495248434952TGMissense_Mutationp.Y125D1
RBM3LUSCchrX4843359948433599GTNonsense_Mutationp.G11*1
RBM3CESCchrX4843407048434070CTRNANULL1
RBM3THYMchrX4843399348433993GTMissense_Mutation1
RBM3KIRPchrX4843401048434010CASilent1
RBM3PCPGchrX4843396948433969GTMissense_Mutation1
RBM3CESCchrX4843477848434778CTMissense_Mutationp.P69S1
RBM3THYMchrX4843399348433993GTMissense_Mutationp.G50C1
RBM3LGGchrX4843490048434900TCMissense_Mutation1

check buttonCopy number variation (CNV) of RBM3
* Click on the image to open the original image in a new window.
all structure

check buttonFusion gene breakpoints (product of the structural variants (SVs)) across RBM3
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


check button Fusion genes with this translation factor from FusionGDB2.0.
FusionGDB2 IDDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
86748N/AAA564516ARHGAP24chr486497591+RBM3chrX48436388+
86748ESCATCGA-L5-A8NELYZchr1269747259+RBM3chrX48436435+
86748ESCATCGA-L5-A8NELYZchr1269747265+RBM3chrX48436441+
86748N/AAY358132NEGR1chr171872026-RBM3chrX48434920+
86748N/ACB051146NXPH1chr78696157+RBM3chrX48439550-
102857N/AAA177057RBM3chrX48436672+CHMP1Achr1689717175+
102173BRCATCGA-A2-A4S1-01ARBM3chrX48434090+COL1A1chr1748264909-
80868N/ABU676293RBM3chrX48436439-F3chr194995621+
88711N/AAA329557RBM3chrX48434003+ILKchr116630374+
102694N/ACA433037RBM3chrX48436476-NME7chr1169102012+
98486N/AES316009RBM3chrX48436340-NXNchr17811551-
90923N/ABG576987RBM3chrX48436679+OTUD5chrX48788239+
86748N/ABF340733RBM3chrX48436065+RBM3chrX48436050-
86748N/AH20596RBM3chrX48438802+RBM3chrX48436436+
82901N/AAA465493RBM3chrX48436377-SIKE1chr1115313470+
86748N/AAK125614SECISBP2chr991973037+RBM3chrX48434778+
86748STADTCGA-CD-8525-01ASLC25A51chr937880664-RBM3chrX48436377+
86752STADTCGA-FP-8211-01ASSFA2chr2182781154+RBM3chrX48433556+


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Prognostic Analysis


check button Kaplan-Meier plots with logrank tests of overall survival (OS)
all structure
Cancer typeTranslation factorCoefficentHazard ratioWald test pvalLikelihool ratio pvalLogrank test pval# samples


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Translation factor and Gender


check button Differential gene expression between female and male. (Wilcoxon test, pval<0.05)
all structure
Cancer typeTranslation factorpvaladj.p
SARCRBM30.001032369067965220.028
HNSCRBM30.009698476295381530.25
BRCARBM30.0153774188352840.38
TGCTRBM30.02855147274223020.69
GBMRBM30.03741961212870310.86
KIRCRBM32.45915447049639e-050.00069

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Translation factor and Age


check button Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)
all structure
Cancer typeTranslation factorpvaladj.p
THCARBM30.004786501376268680.14
LGGRBM30.0009635271941810930.03
BRCARBM30.0001551053159927420.005
PAADRBM39.76675036790893e-050.0032
SKCMRBM30.003707100327129760.11
THYMRBM30.007648619424209880.21
MESORBM30.04695842013199381

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Related Drugs


check button Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases


check button Diseases associated with this translation factor.
(DisGeNet 4.0)
Disease IDDisease Name# PubMedsDisease source
C0006142Malignant neoplasm of breast1CTD_human
C0023893Liver Cirrhosis, Experimental1CTD_human
C0678222Breast Carcinoma1CTD_human
C1257931Mammary Neoplasms, Human1CTD_human
C4704874Mammary Carcinoma, Human1CTD_human