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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: RPS3A (NCBI Gene ID:6189)


Gene Summary

check button Gene Summary
Gene InformationGene Name: RPS3A
Gene ID: 6189
Gene Symbol

RPS3A

Gene ID

6189

Gene Nameribosomal protein S3A
SynonymsFTE1|MFTL|S3A
Cytomap

4q31.3

Type of Geneprotein-coding
Description40S ribosomal protein S3afte-1small ribosomal subunit protein eS1v-fos transformation effector protein 1
Modification date20200320
UniProtAcc

P61247


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0005840Ribosome
GO:0002181Cytoplasmic translation
GO:0006413Translational initiation
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
RPS3A>1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'RPS3A[title] AND translation [title] AND human.'
GeneTitlePMID
RPS3A..


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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
ENST00000274065152022126152022314Frame-shift
ENST00000274065152024022152024231Frame-shift
ENST00000274065152025328152025438Frame-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
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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
CHOLRPS3A-2.955935629267170.00390625
UCECRPS3A-1.593532251869680.03125
BRCARPS3A-2.823523242187641.9558540533629e-14
STADRPS3A1.421816499150459.0546440333128e-05


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue


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)
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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
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Cancer typeGeneCoefficientPvalue
PRADRPS3A0.0570587150.020857063

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with RPS3A (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
DLBCCell metabolism geneRPS3AGFER0.8060057234.80E-12
DLBCCell metabolism geneRPS3ANME20.808761393.56E-12
DLBCCell metabolism geneRPS3AFAU0.8134314422.13E-12
DLBCCell metabolism geneRPS3APFDN50.8192574921.10E-12
DLBCCell metabolism geneRPS3ASNRPD20.8352571841.56E-13
DLBCCGCRPS3ANACA0.8503889052.02E-14
DLBCTFRPS3ANME20.808761393.56E-12
DLBCTSGRPS3AGLTSCR20.821444368.51E-13
DLBCTSGRPS3AGNB2L10.9211061041.80E-20
GBMCell metabolism geneRPS3ALYPLA10.8013442778.81E-40
GBMCell metabolism geneRPS3ATIMM8B0.8057532061.60E-40
GBMCell metabolism geneRPS3APSMB40.8058554131.54E-40
GBMCell metabolism geneRPS3ASUCLG10.8078445217.02E-41
GBMCell metabolism geneRPS3AZNRD10.8080224346.55E-41
GBMCell metabolism geneRPS3ALSM20.8203295384.11E-43
GBMCell metabolism geneRPS3APSMA50.8224126131.68E-43
GBMCell metabolism geneRPS3ASSR20.8269023622.33E-44
GBMCell metabolism geneRPS3AFAU0.8278443191.53E-44
GBMCell metabolism geneRPS3ASNRPG0.8509982752.02E-49
GBMCell metabolism geneRPS3ACCT40.8510477481.97E-49
GBMCell metabolism geneRPS3ASNRPD20.8513606231.67E-49
GBMCell metabolism geneRPS3APFDN50.876435687.71E-56
LAMLCGCRPS3ANACA0.8554547319.65E-51
LGGCGCRPS3ANACA0.8133171462.74E-126
THYMIUPHARRPS3AMFSD2B0.8113495099.33E-30
THYMTSGRPS3AGNB2L10.8025302251.09E-28
UCSIUPHARRPS3AMFSD2B0.8113495099.33E-30
UCSTSGRPS3AGNB2L10.8025302251.09E-28
UVMCell metabolism geneRPS3APMPCB0.8137837674.54E-20
UVMCell metabolism geneRPS3AGLCE0.8143810454.05E-20
UVMCell metabolism geneRPS3ATOMM200.8203674421.27E-20
UVMEpifactorRPS3AMBIP0.8086355371.18E-19
UVMEpifactorRPS3ADDX500.8392842722.43E-22
UVMEpifactorRPS3AFAM175A0.8698030781.21E-25
UVMTFRPS3AZNF354A0.8100807559.07E-20
UVMTFRPS3AZNF5610.810793527.95E-20
UVMTFRPS3AZNF2770.8434522619.49E-23
UVMTSGRPS3ARBMX0.8050791292.26E-19
UVMTSGRPS3ACOPS20.8080667991.31E-19


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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
check button
* 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
KIRPRPS3ARPL18A-1.516513928088850.00016188295558095
KICHRPS3ARPS27A1.753966937859560.000187873840332031
KIRPRPS3ARPS16-1.359570436175170.00019507110118866
STADRPS3ARPS231.850767606645760.000364991836249828
COADRPS3ARPS31.487303751430140.000411599874496461
KIRPRPS3ARPS11-1.018615705651030.00105937570333481
LIHCRPS3ARPL8-4.845882849745580.00110314154326131
PRADRPS3ARPL18A1.406001757484990.00205137828390396
KICHRPS3ARPL191.369011828940890.00250792503356934
KICHRPS3ARPS121.269973817584310.00308787822723389
LUADRPS3ARPL19-1.313980266157250.00993159558412698
THCARPS3ARPS16-6.163227981565770.0115764821363307
LUSCRPS3ARPS231.467511698910470.0174932185880974
BLCARPS3ARPS12-1.478046734404210.0204124450683594
BLCARPS3ARPS27A-1.047474700691880.0258216857910156
HNSCRPS3ARPS3-4.735058190951350.0273726439852453
COADRPS3ARPS111.353075489982040.0312207043170929
LUSCRPS3ARPL19-2.146698895166660.044366810398747
UCECRPS3ARPS23-2.036581598140070.046875
KIRCRPS3ARPL19-2.734852712766761.33980982873695e-10
BRCARPS3ARPS12-4.912393274782441.85340619742495e-09
KIRCRPS3ARPL35-1.064752380593922.72286325678163e-08
KIRCRPS3ARPL8-1.182524599717735.64962994208288e-07
KIRPRPS3ARPL8-1.530036923501196.0301274061203e-05
KIRCRPS3ARPS16-1.661498698893847.8509870430991e-09
BRCARPS3ARPS27A-4.285121482004247.8788217967112e-14
KIRPRPS3ARPL35-1.529811019754969.0546440333128e-05
KIRCRPS3ARPS3-1.295608479263879.05905681935088e-10
KIRCRPS3ARPL18A-4.430793049608439.2516163152192e-11


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with RPS3A
MAGEB2, ASF1B, DDX56, CNBP, EIF1B, PINX1, MPDU1, LYAR, FANCC, CHN1, C11orf49, EDEM2, SAP18, SOD2, TOE1, HSP90AA1, DDIT3, PARP1, HGS, SRRM2, HDAC5, STAU1, RICTOR, EBNA-LP, PCK1, VHL, RAD21, ARRB1, ARRB2, SIRT7, NFX1, CUL3, CUL5, CUL2, CDK2, CUL1, COPS5, DCUN1D1, CAND1, NEDD8, RPL10A, RPL21, RPL5, RPL6, RPL7A, RPL7, RPS3, RPS6, RPSA, RPL4, RPS4X, RPLP0, RPS9, RPL12, RPL13, RPL14, RPL15, RPL17, RPL18A, RPL18, RPL19, RPL24, RPL27A, RPL37A, RPL3, RPL8, RPL9, RPS11, RPS13, RPS15A, RPS16, RPS23, RPS24, RPS25, RPS26, RPS5, RPS8, RPL11, RPS2, RPS19, RPLP2, RPL31, RPL23A, RPS20, RPS12, RPLP1, RPL23, RPL22, RPL10, EEF2, RPS17, RPL30, RPS15, RPL27, RPS14, RPS10, RPL35, RPS21, RPS27A, RPL29, RPL32, NCL, EEF1A1, ILF3, SLC25A5, NOP58, HNRNPA1, NAP1L1, EIF3C, RPL10L, RPLP0P6, MAT2A, PPT2, RPS27L, PC, PRKCDBP, SLC25A4, ATP5B, MRPL23, RNPC3, PDRG1, NENF, ESR1, SMURF1, HSP90AB1, FN1, VCAM1, NOS2, UBL4A, ITGA4, PAN2, CD81, IGSF8, ICAM1, TARDBP, NEDD4, EIF3A, EIF3CL, EIF3E, LARP1, RPS27, RPS28, GNB2L1, RPL28, RPS18, RPS29, WIBG, RPS7, SND1, TSR1, rev, RPA3, RPA2, RPA1, AURKA, CEP250, CEP57, CEP76, NEDD1, TP53, TUBG1, TUBGCP4, VCP, HUWE1, CUL7, OBSL1, CCDC8, UBE2I, RNF2, HIST1H1A, NOL12, ZNF22, NIFK, THAP7, ZC3H3, PRR11, RBM4B, ZNF317, RPS6KB2, NTRK1, ABCE1, HNRNPU, RPL13A, RPL38, LOC101929876, DHX37, KRR1, PABPC1, PABPC4, RPL26, RPL34, RPL35A, RPL36, RPL39, SFN, CREB3, XPO1, AHSA1, KIF11, MAD2L1, NPM1, NOP56, CBX8, NOP9, Eif3a, Eif3e, Rpl35, Srp72, Rrbp1, GAN, MCM2, NF2, Ksr1, Mdm2, RC3H1, CRBN, RRS1, WDR46, ZC3HAV1, RBM34, SART3, H2AFX, PPAN, ZCRB1, KNOP1, ZNF324B, ZBTB48, E4F1, ZNF512, U2AF2, HIST1H1T, KIAA0020, BHLHA15, GLTSCR2, HIST1H1E, ZNF2, FGF8, GPATCH4, ZBTB38, CYLD, EIF2AK2, INO80B, TRIM25, BRCA1, LMNA, MTF1, FBXO7, TMPO, WDR77, HDAC4, PCBP1, PPIE, YAF2, API5, BMP4, CTNNB1, GSK3A, JUP, MAP2K3, MED12, MED9, TGFB1, UBE2M, PRPF8, EFTUD2, AAR2, PIH1D1, CHD3, CHD4, RIOK1, HEXIM1, MEPCE, LARP7, SNAI1, RECQL4, REST, ZFP36L2, MYC, CDK9, FBL, AURKAIP1, GRWD1, METTL14, EIF4B, RC3H2, ACTC1, PHB, TGFBR2, FAF1, NR2C2, UBQLN2, PPP1CC, CTCF, ATXN3, VRK1, VRK3, HIST1H4A, PSMD14, SNRNP70, ITFG1, ARAF, HMGB1, BIRC3, WWP2, BRD7, MATR3, SOX2, TRIM28, ARIH2, PINK1, YAP1, TFCP2, FANCD2, NGB, HCVgp1, ORF50, ZC3H18, TXN2, SPTBN1, HIST2H2BF, SNIP1, ANKRD55, nsp13, ORF8, LARP4B, USP10, DUX4, CIT, ANLN, AURKB, CHMP4B, CHMP4C, ECT2, KIF14, KIF20A, MAD2L2, KIF23, PRC1, FASN, LDLR, INS, NMRAL1, NDN, Rnf183, BRD4, CIC, N, Apc2, RBM39, FBP1, LGALS9, IFI16, RIN3, DNAJC2, DNAJC8, OGT, BAG5, SPOP, PARK2, UFL1, DDRGK1, ACTR1A, LRRC59, LYN, SERBP1, SSR1, TUBA1A, TUBA4A, TRIM37, ATG3, LINC01232, UBQLN1, FZR1, PAGE4, NUDCD2, NAA40, YBX2, RPL26L1, RRP8, PRKRA, HERC5, NEIL1, UPF1, RPF2, ZNF689, YBX1, GADD45GIP1, DDX27, GLE1, BMS1, FGF13, DDX31, RRP12, ZNF668, WHSC1, NPM3, ZNF770, RSL1D1, SRSF3, RPL7L1, STAU2, GNL2, NMNAT1, HIST1H2AG, SURF6, RBM19, DHX57, LARP1B, GTPBP4, DDX21, MRPL27, H2AFB2, SRSF6, MRPL52, CCDC86, REXO4, GLYR1, LLPH, AATF, H1FNT, FTSJ3, MRPL2, SRSF5, HIST1H1C, TTF1, IPO4, ZCCHC9, APOBEC3C, SRPK2, ZCCHC3, SMEK2, RBM28, NOC4L, OASL, H2AFB3, ADARB1, PURG, NOP2, HIST1H1B, PRR3, MRPL28, UTP23, CBX6, MAK16, ZKSCAN8, ABT1, RPSAP58, LTV1, RPS4Y2, NOP14, NSA2, NGDN, HIST1H2AM, YBX3, ZNF346, SREK1, NOL10, NAT10, C8orf33, LIN28A, SPRTN, BTF3, TRIM26, FBXW7, NLRP7, FGD5, RCHY1, CCNF, SIRT6, PSMD9, RB1CC1, KLF4, TLX1, ZEB1,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo
RPS3Achr4152021631ATsingle_nucleotide_variantBenignnot_providedSO:0001627|intron_variantSO:0001627|intron_variant


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


check button SNVs and Indels
GeneCancer typeChromosomeStartEndRefSeeqMutSeqMutation typeAAchange# samples
RPS3AGBMchr4152024138152024138ACMissense_Mutation12
RPS3AKIRCchr4152022142152022142GAMissense_Mutationp.G48D4
RPS3ALAMLchr4152243488152243488CTMissense_Mutationp.H124Y2
RPS3APCPGchr4152024138152024138ACMissense_Mutationp.Q157P2
RPS3ALIHCchr4152025347152025347A-Frame_Shift_Delp.G157fs2
RPS3AESCAchr4152020849152020849GASilent2
RPS3AESCAchr4152020849152020849GASilentp.K15K2
RPS3AUCECchr4152022212152022212CAMissense_Mutationp.F84L2
RPS3APAADchr4152021718152021718CASilentp.L48L2
RPS3ABLCAchr4152024203152024203ACMissense_Mutationp.N166H1
RPS3ALIHCchr4152021639152021639TCMissense_Mutationp.V22A1
RPS3ASKCMchr4152025418152025418TCMissense_Mutationp.L218P1
RPS3ACESCchr4152022192152022192GAMissense_Mutation1
RPS3ALIHCchr4152025347152025347A-Frame_Shift_Delp.G194fs1
RPS3ASKCMchr4152024151152024151CTSilentp.V148V1
RPS3ACESCchr4152022192152022192GAMissense_Mutationp.E78K1
RPS3ASKCMchr4152025418152025418TCMissense_Mutationp.L181P1
RPS3AESCAchr4152020849152020849GASilentp.K151
RPS3ALIHCchr4152025410152025410A-Frame_Shift_Delp.V178fs1
RPS3ASTADchr4152024153152024153GAMissense_Mutationp.R162H1
RPS3ALUADchr4152022138152022138GTMissense_Mutationp.D47Y1
RPS3ASTADchr4152024210152024210TCMissense_Mutationp.L181S1
RPS3ALUADchr4152025386152025386CTMissense_Mutationp.P205S1
RPS3AUCECchr4152021688152021688GTMissense_Mutationp.M38I1
RPS3AMESOchr4152021724152021724CASilent1
RPS3AOVchr4152024193152024193GASilentp.E1751
RPS3AKIRPchr4152021725152021725ACSilentp.R51R1
RPS3APAADchr4152021718152021718CASilent1
RPS3ABLCAchr4152024203152024203ACMissense_Mutation1
RPS3AKIRPchr4152024120152024120GTMissense_Mutation1
RPS3ABLCAchr4152020882152020882CTMissense_Mutation1

check buttonCopy number variation (CNV) of RPS3A
* 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 RPS3A
* 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
77889N/AAA747634JMYchr578580355+RPS3Achr4152025789-
77889N/AEC560486RNF103-CHMP3chr286916294-RPS3Achr4152025785-
77891N/AAA523477RPS3Achr4152025767+JMYchr578580137-
77891N/ABG030635RPS3Achr4152025789+JMYchr578579927-
77891N/AAA533662RPS3Achr4152024066+RPS3Achr4152024180-
98645N/AEC500159RPS3Achr4152025783+SH3D19chr4152025921+


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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
COADRPS3A0.02166175798586070.58
KIRCRPS3A5.98210196336778e-050.0017

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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
LGGRPS3A0.01381433253429510.43
BRCARPS3A0.003801940525121630.13
PRADRPS3A0.04969205136675821
THYMRPS3A0.004761789887550910.15

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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