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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: RPS28 (NCBI Gene ID:6234)


Gene Summary

check button Gene Summary
Gene InformationGene Name: RPS28
Gene ID: 6234
Gene Symbol

RPS28

Gene ID

6234

Gene Nameribosomal protein S28
SynonymsDBA15|S28|eS28
Cytomap

19p13.2

Type of Geneprotein-coding
Description40S ribosomal protein S28small ribosomal subunit protein eS28
Modification date20200313
UniProtAcc

P62857


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0005840Ribosome
GO:0002181Cytoplasmic translation
GO:0006412Translation


check button Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneRPS28

GO:0002181

cytoplasmic translation

25957688



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
RPS28>1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'RPS28[title] AND translation [title] AND human.'
GeneTitlePMID
RPS28..


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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
ENST0000060065983865398386587In-frame
ENST00000600659838683683869753UTR-3CDS

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)
ENST0000060065983865398386587134371118691329

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.
P628571329169ChainID=PRO_0000136822;Note=40S ribosomal protein S28


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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


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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
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)
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
Cancer typeGeneCoefficientPvalue
GBMRPS280.041909740.007333052
PRADRPS280.010893390.043371954

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with RPS28 (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 typeGene groupTranslation factorCorrelated geneCoefficientPvalue


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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
KIRPRPS28RPL18A-1.516513928088850.00016188295558095
KICHRPS28RPS27A1.753966937859560.000187873840332031
KIRPRPS28RPS16-1.359570436175170.00019507110118866
COADRPS28RPS31.487303751430140.000411599874496461
KIRPRPS28RPS11-1.018615705651030.00105937570333481
LIHCRPS28RPL8-4.845882849745580.00110314154326131
PRADRPS28RPL18A1.406001757484990.00205137828390396
KICHRPS28RPL191.369011828940890.00250792503356934
KICHRPS28RPS121.269973817584310.00308787822723389
LUADRPS28RPL19-1.313980266157250.00993159558412698
THCARPS28RPS16-6.163227981565770.0115764821363307
BLCARPS28RPS12-1.478046734404210.0204124450683594
BLCARPS28RPS27A-1.047474700691880.0258216857910156
HNSCRPS28RPS3-4.735058190951350.0273726439852453
COADRPS28RPS111.353075489982040.0312207043170929
LUSCRPS28RPL19-2.146698895166660.044366810398747
KIRCRPS28RPL19-2.734852712766761.33980982873695e-10
BRCARPS28RPS12-4.912393274782441.85340619742495e-09
KIRPRPS28RPL37-1.174216219471392.26888805627823e-05
KIRCRPS28RPL35-1.064752380593922.72286325678163e-08
KIRCRPS28RPL8-1.182524599717735.64962994208288e-07
KIRPRPS28RPL8-1.530036923501196.0301274061203e-05
KIRCRPS28RPS16-1.661498698893847.8509870430991e-09
BRCARPS28RPS27A-4.285121482004247.8788217967112e-14
KIRCRPS28RPL37-2.871988220584648.03913394748564e-12
KIRPRPS28RPL35-1.529811019754969.0546440333128e-05
KIRCRPS28RPS3-1.295608479263879.05905681935088e-10
KIRCRPS28RPL18A-4.430793049608439.2516163152192e-11


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with RPS28
KRTAP4-12, PINX1, EEF1G, PFDN1, CUL3, CUL5, CDK2, CUL1, CAND1, RPL10A, RPL11, RPL15, RPL18, RPL21, RPL23, RPL24, RPL37A, RPL5, RPL7A, RPL9, RPS16, RPS19, RPS23, RPS3, RPS4X, RPS6, RPS8, RPSA, RPS25, RPL13, RPL6, RPL19, RPS2, RPS20, RPS17, RPS12, RPL7, RPL14, RPL12, RPL4, RPLP2, RPS13, RPL23A, RPS9, RPL36, RPS15, RPL38, RPL17, RPS21, PABPC1, ILF3, HNRNPM, SLC25A5, RPL10L, RPLP0P6, RPS27L, M6PR, MRPL53, HNRNPD, ELAVL1, CLINT1, PQBP1, RBMX, NDUFA7, MRPS28, HNRNPA3, UBL4A, FN1, VCAM1, ITGA4, CD81, IGSF8, ICAM1, NPM1, CTBP2, HNRNPA2B1, PSMD3, RPS10, RPS14, RPS24, RPS27, EIF3D, EIF3E, EIF3L, FAU, PSMD1, RPS15A, RPS18, RPS26, RPS29, RPS3A, RPS5, RPS7, TSR1, WIBG, CCNDBP1, KRTAP2-4, KRTAP10-7, KRTAP10-8, KRTAP10-3, NOTCH2NL, EED, FBXW11, HIST1H3E, PPP2R2A, UBA5, Eif3a, MCM2, RRS1, H2AFX, SLC9A3R2, FAM208A, RPL35, RPS28, LARS, WDR77, MAP2K3, ADSS, APOE, COPE, CSNK1A1, CTNNB1, HDAC4, KRAS, YAP1, EFTUD2, AAR2, PIH1D1, CHD3, LARP7, ESR2, HEXIM1, MEPCE, RECQL4, KIAA1429, RC3H1, RC3H2, ATG16L1, PHB, NR2C2, PPP1CC, HIST1H4A, SNRNP70, ITFG1, HMGB1, ABCC6, NFX1, WWP2, LRRK2, HSF2BP, KRTAP1-1, ARIH2, TFCP2, nsp13, ORF8, ESR1, CIT, ANLN, CHMP4C, ECT2, KIF14, KIF20A, KIF23, PRC1, INS, MAFB, Apc2, RBM39, LGALS9, RIN3, DNAJA3, TRIM24, CEP78, STMN1, ARHGDIA, MARCKS, MTPN, MDH1, TBCA, DDTL, BASP1, CYCS, CSTB, CALM1, TRIM37, ATG10, FZR1, HMGB2, NUDCD2, NAA40, HIST1H2AM, FGF17, THNSL1, RPL31, HIST1H1B, UTP23, FGF13, EXOSC8, DMRTB1, UNKL, RBFOX2, CCNF, MAP1LC3B, TAX1BP1, CALCOCO2,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo
RPS28chr198386306GAsingle_nucleotide_variantBenignnot_provided
RPS28chr198386367CTsingle_nucleotide_variantBenignnot_provided
RPS28chr198386415AGsingle_nucleotide_variantPathogenicDiamond-Blackfan_anemia_15_with_mandibulofacial_dysostosisSO:0001582|initiatior_codon_variant,SO:0001583|missense_variantSO:0001582|initiatior_codon_variant,SO:0001583|missense_variant
RPS28chr198386593CTsingle_nucleotide_variantLikely_benignnot_providedSO:0001627|intron_variantSO:0001627|intron_variant
RPS28chr198386662TCsingle_nucleotide_variantBenignnot_providedSO:0001627|intron_variantSO:0001627|intron_variant
RPS28chr198386701GAsingle_nucleotide_variantBenignnot_providedSO:0001627|intron_variantSO:0001627|intron_variant
RPS28chr198386998TCsingle_nucleotide_variantBenignDiamond-Blackfan_anemia_15_with_mandibulofacial_dysostosis|not_providedSO:0001627|intron_variantSO:0001627|intron_variant
RPS28chr198387207GAsingle_nucleotide_variantBenignnot_providedSO:0001624|3_prime_UTR_variantSO:0001624|3_prime_UTR_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
RPS28ACCchr1983865548386554GCSilentp.L18L3
RPS28PAADchr1983868718386871CAMissense_Mutationp.S41Y3
RPS28CESCchr1983865548386554GASilent2
RPS28UCECchr1983865568386557-CFrame_Shift_Insp.R20fs2
RPS28BLCAchr1983865428386542CTSilentp.V14V2
RPS28STADchr1983868028386805CTTA-Frame_Shift_Del1
RPS28CESCchr1983864208386420CTSilent1
RPS28CESCchr1983867918386791CAMissense_Mutation1
RPS28UCSchr1983869538386953GCMissense_Mutationp.L68F1
RPS28CESCchr1983864208386420CTSilentp.D21
RPS28CESCchr1983865548386554GASilentp.L181
RPS28CHOLchr1983864288386428GAMissense_Mutationp.R5H1
RPS28COADchr1983868688386868GAMissense_Mutationp.R40Q1
RPS28HNSCchr1983869368386936CGMissense_Mutationp.R63G1
RPS28LUADchr1983869278386927GCMissense_Mutationp.E60Q1
RPS28BLCAchr1983865428386542CTSilent1
RPS28PAADchr1983868718386871CAMissense_Mutation1

check buttonCopy number variation (CNV) of RPS28
* 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 RPS28
* 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
46814N/ABP431664CCDC144Bchr1718476360+RPS28chr198386397+
46814Non-CancerTCGA-IP-7968-11AJSRP1chr192269549-RPS28chr198386392+
92661STADTCGA-BR-7704-01ARPS28chr198387249+CD74chr5149792306-
102833N/ABI860075RPS28chr198387290+KANK3chr198387292+
98938N/AAA641054RPS28chr198387280+LRP1Bchr2142766107-


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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
CHOLRPS280.00900957785037720.25
THCARPS280.04987248495956931

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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
LUADRPS280.04731750540291
LUSCRPS280.005069630819628740.17
UCECRPS280.03775979443025511

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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
C1260899Anemia, Diamond-Blackfan2GENOMICS_ENGLAND;ORPHANET
C2931850Aase Smith syndrome 21ORPHANET
C4225411DIAMOND-BLACKFAN ANEMIA 15 WITH MANDIBULOFACIAL DYSOSTOSIS1CTD_human;GENOMICS_ENGLAND