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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: RPUSD4 (NCBI Gene ID:84881)


Gene Summary

check button Gene Summary
Gene InformationGene Name: RPUSD4
Gene ID: 84881
Gene Symbol

RPUSD4

Gene ID

84881

Gene NameRNA pseudouridine synthase D4
Synonyms-
Cytomap

11q24.2

Type of Geneprotein-coding
Descriptionmitochondrial RNA pseudouridine synthase RPUSD4RNA pseudouridylate synthase domain containing 4RNA pseudouridylate synthase domain-containing protein 4
Modification date20200313
UniProtAcc

Q96CM3


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation of translation
GO:0032543Mitochondrial 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
RPUSD4>1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'RPUSD4[title] AND translation [title] AND human.'
GeneTitlePMID
RPUSD4..


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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
ENST00000298317126074125126074223Frame-shift
ENST00000298317126079415126079617Frame-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
STADRPUSD4-1.777596280226720.0148032568395138
HNSCRPUSD4-3.648231712562131.42088565553422e-05
KIRCRPUSD4-3.434567489130049.61177113723533e-08


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue
KIRPRPUSD4hsa-miR-136-5p98-0.3091790967626430.00556238747078051


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

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with RPUSD4 (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 geneRPUSD4HMBS0.8009976728.13E-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
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
HNSCRPUSD4PUS72.635278155529090.000182808133786239
KIRCRPUSD4MRM1-1.07529673607360.000369980864421695
BRCARPUSD4RNMTL11.303536404715350.00063395668674051
COADRPUSD4MRM11.239392014167860.000934779644012452
STADRPUSD4NSUN4-1.471621930956990.00256496202200651
LIHCRPUSD4DDX28-1.805569199493780.00268062725366399
COADRPUSD4NSUN4-1.807365284520280.00322914123535157
PRADRPUSD4PUS7L1.555705899559180.00430343371125972
BLCARPUSD4PUS7L-1.936782736366330.00823211669921875
KICHRPUSD4TRUB2-2.061549427115770.00882232189178467
ESCARPUSD4MRM1-1.223443938584780.013671875
ESCARPUSD4TRUB2-1.630554916195490.0185546875
PRADRPUSD4RNMTL11.484183448511040.024485781766368
LIHCRPUSD4FASTKD2-2.174264985089780.0264015241133303
CHOLRPUSD4RNMTL1-2.218311890032510.02734375
CHOLRPUSD4TRUB2-2.30701675175370.02734375
KIRPRPUSD4DDX281.787291563384220.0309218638576567
STADRPUSD4DDX28-1.744733132806930.0309218638576567
READRPUSD4NSUN4-3.483209807646720.03125
HNSCRPUSD4MRM1-1.325652853345560.0341586761198869
BLCARPUSD4NSUN41.357371266361450.040130615234375
HNSCRPUSD4FASTKD2-1.722193451887510.0410440647583528
LUADRPUSD4MRM1-2.803869039759051.0542655358657e-09
PRADRPUSD4PUS7-2.665430669490931.37654470439417e-07
LUADRPUSD4PUS1-2.331498162499261.55042044095848e-09
BRCARPUSD4TRUB2-2.532797560689831.7326162077773e-13
KICHRPUSD4PUS1-1.078309724914591.82986259460449e-05
LUSCRPUSD4TRUB2-3.504733788015461.91629083762368e-08
LIHCRPUSD4PUS7-1.368299946781792.71217975233539e-06
LUSCRPUSD4MRM1-4.212369790580362.79558697199975e-08
PRADRPUSD4NGRN-1.954463306829213.16187259327918e-07
LUADRPUSD4TRUB2-1.929838020306233.47524877088934e-09
KIRPRPUSD4PUS7-1.20385077594783.54335643351078e-05
BRCARPUSD4PUS7L1.855006868843993.75312800430837e-08
BRCARPUSD4FASTKD2-1.956593680899064.12639478109604e-08
KICHRPUSD4DDX282.681666750301714.54187393188476e-05
STADRPUSD4PUS7-5.060743024105984.5965425670147e-06
THCARPUSD4PUS71.247738385190764.88626066707067e-07
KIRCRPUSD4PUS7-2.055345296801495.48040034437071e-11
KIRPRPUSD4PUS1-4.44191193042758.84756445884705e-09


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with RPUSD4
HINFP, RNMTL1, SYNCRIP, CYC1, IKBIP, MOV10, NXF1, MRPL4, TP53, XRCC1, RBM45, Cct3, Cul1, Tmed2, Tmed10, Ubr5, Chmp4b, NGRN, WBSCR16, FASTKD2, SSSCA1, MRPL12, DDX28, MRPL39, RBM42, VWCE, ATG16L1, FBXW8, OBSL1, PRKCI, PRKCZ, HIST1H1E, RAB10, HIST1H1C, C12orf65, C6orf203, ICT1, LRPPRC, METTL15, METTL17, MRPL11, MRPS12, MRPS26, MTERF3, AARS2, ABHD10, ACAD9, ACAT1, ACOT1, ACOT2, AFG3L2, ALAS1, ANGEL2, ATP5B, ATP5D, ATP5J2-PTCD1, ATP5F1, ATP5H, ATP5J, ATPAF1, BCS1L, C17orf80, CENPV, CLPX, CS, DAP3, DBT, DHX30, DLAT, DLST, DNAJA3, ECHS1, EIF2AK2, ELAC2, ERAL1, ETFA, ETFB, FASTKD5, FHL3, GADD45GIP1, GLS, GRPEL1, GRSF1, GTPBP10, GUF1, HARS2, HINT2, HNRNPDL, HNRNPL, HSD17B10, HSDL2, HSPA9, HSPD1, IARS2, IMMT, LARS2, LETM1, MDH2, MGME1, MMAB, MRPL1, MRPL13, MRPL15, MRPL17, MRPL19, MRPL2, MRPL20, MRPL21, MRPL22, MRPL23, MRPL24, MRPL28, MRPL3, MRPL37, MRPL38, MRPL40, MRPL41, MRPL42, MRPL43, MRPL44, MRPL45, MRPL46, MRPL47, MRPL48, MRPL49, MRPL50, MRPL53, MRPL55, MRPL9, MRPS10, MRPS14, MRPS16, MRPS17, MRPS18A, MRPS18B, MRPS18C, MRPS2, MRPS22, MRPS23, MRPS24, MRPS25, MRPS27, MRPS28, MRPS30, MRPS31, MRPS33, MRPS34, MRPS35, MRPS36, MRPS5, MRPS6, MRPS7, MRPS9, MTIF2, NDUFA12, NDUFA2, NDUFA5, NDUFA6, NDUFA7, NDUFA9, NDUFAF2, NDUFAF4, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NDUFV3, NFS1, NIPSNAP1, NME4, NNT, NUDT19, OGDH, PAM16, PDE12, PDHA1, PDHB, PDK3, PHB, PNPT1, POLRMT, POTEE, PPIF, PRDX3, PREPL, PTCD3, PYCR1, PYCR2, QRSL1, RBM11, SHMT2, SLIRP, STOML2, SUCLA2, SUPV3L1, TACO1, THEM4, TIMM44, TRMT10C, TRMT61B, TSFM, C10orf2, VARS2, VWA8, TRUB2, COX8A, HNRNPUL2, FTL, HNRNPC, NOTCH2, SRSF3, KCNE3, HNRNPU, CAMK2A, IGF2BP3, PIPSL, CAMK2G, TMED7, PNMA2, PRR3, RNH1, NUPL2, RBMS2, YBX2, MAP7, CCL3, FAM120A, ATE1, TMED4, MRPL51, RPUSD3, YARS2, KBTBD6, KLHL22, UBR1, MALSU1, MCAT, KCTD5, PEX7, PTCD1, C17orf70, KBTBD7, ZRANB1,


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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
RPUSD4BLCAchr11126081403126081403TCMissense_Mutation6
RPUSD4SKCMchr11126074205126074205CTMissense_Mutationp.R272Q5
RPUSD4BRCAchr11126075478126075478GASilentp.D2274
RPUSD4ESCAchr11126073407126073407CTMissense_Mutationp.R347H3
RPUSD4ESCAchr11126080863126080863TCMissense_Mutationp.K93E3
RPUSD4LGGchr11126075477126075477CTMissense_Mutationp.D228N3
RPUSD4UCECchr11126079498126079498CTMissense_Mutationp.V159I3
RPUSD4SKCMchr11126081384126081384GASilentp.L50L3
RPUSD4PAADchr11126079531126079531GASilentp.L148L3
RPUSD4KIRPchr11126075618126075618CANonsense_Mutation2
RPUSD4SKCMchr11126073526126073526CTSilentp.K307K2
RPUSD4LUADchr11126081478126081478CGMissense_Mutationp.G19A2
RPUSD4ESCAchr11126073407126073407CTMissense_Mutation2
RPUSD4SKCMchr11126081442126081442ATMissense_Mutationp.F31Y2
RPUSD4ESCAchr11126080863126080863TCMissense_Mutation2
RPUSD4SKCMchr11126080839126080839GAMissense_Mutationp.H101Y2
RPUSD4SKCMchr11126073509126073509GAMissense_Mutationp.S313L2
RPUSD4BLCAchr11126081382126081382CTMissense_Mutationp.R51Q2
RPUSD4STADchr11126075366126075366TCMissense_Mutationp.T265A2
RPUSD4SKCMchr11126073501126073501GAMissense_Mutationp.R316C2
RPUSD4STADchr11126081486126081486GASilentp.N16N2
RPUSD4BLCAchr11126081508126081508GCMissense_Mutationp.S9W2
RPUSD4LIHCchr11126075494126075494G-Frame_Shift_Delp.P222fs2
RPUSD4STADchr11126073382126073382GASilentp.R355R2
RPUSD4PAADchr11126079531126079531GASilent2
RPUSD4UCECchr11126079614126079614CTMissense_Mutationp.G120D2
RPUSD4STADchr11126075385126075385GASilentp.L258L2
RPUSD4CESCchr11126081456126081456GASilent2
RPUSD4LUADchr11126080928126080928CGMissense_Mutationp.R71P2
RPUSD4UCECchr11126080787126080787TCMissense_Mutationp.H118R2
RPUSD4CESCchr11126075456126075456GAMissense_Mutation2
RPUSD4UCECchr11126081474126081474GASilentp.C202
RPUSD4KIRPchr11126073501126073501GTMissense_Mutation2
RPUSD4CESCchr11126079522126079522GAMissense_Mutation1
RPUSD4LUADchr11126081354126081354CAMissense_Mutationp.K60N1
RPUSD4THCAchr11126081384126081384GCSilent1
RPUSD4PRADchr11126079521126079521CAMissense_Mutationp.R151L1
RPUSD4BLCAchr11126081382126081382CTMissense_Mutation1
RPUSD4CESCchr11126073442126073442CCSilent1
RPUSD4LUADchr11126079500126079500CAMissense_Mutationp.G158V1
RPUSD4THYMchr11126073396126073396GAMissense_Mutation1
RPUSD4SARCchr11126073500126073500CTMissense_Mutation1
RPUSD4BLCAchr11126080938126080938CGMissense_Mutation1
RPUSD4CESCchr11126081456126081456GASilentp.L261
RPUSD4THYMchr11126080920126080920GANonsense_Mutationp.Q74X1
RPUSD4SARCchr11126073430126073430GTSilent1
RPUSD4BLCAchr11126081508126081508GCMissense_Mutation1
RPUSD4LGGchr11126075477126075477CTMissense_Mutation1
RPUSD4CHOLchr11126079517126079517CTSilent1
RPUSD4LUADchr11126081368126081368CANonsense_Mutationp.E56*1
RPUSD4THYMchr11126073396126073396GAMissense_Mutationp.H351Y1
RPUSD4BLCAchr11126081421126081421GCMissense_Mutationp.S38C1
RPUSD4LIHCchr11126079385126079385CASplice_Site1
RPUSD4CHOLchr11126079517126079517CTSilentp.L152L1
RPUSD4LUADchr11126081500126081500ATMissense_Mutationp.W12R1
RPUSD4UCECchr11126081474126081474GASilentp.C20C1
RPUSD4HNSCchr11126081370126081370CAMissense_Mutation1
RPUSD4SKCMchr11126081383126081383GANonsense_Mutationp.R51X1
RPUSD4SKCMchr11126081383126081383GANonsense_Mutationp.R51*1
RPUSD4LIHCchr11126079515126079515TCMissense_Mutation1
RPUSD4COADchr11126073478126073478GASilentp.H323H1
RPUSD4LUSCchr11126075365126075365GAMissense_Mutationp.T265I1
RPUSD4HNSCchr11126081423126081423GASilent1
RPUSD4BLCAchr11126080938126080938CGMissense_Mutationp.A68P1
RPUSD4LIHCchr11126075666126075666CAMissense_Mutationp.V190L1
RPUSD4COADchr11126079437126079437CTMissense_Mutationp.R179H1
RPUSD4LUSCchr11126075379126075379CAMissense_Mutationp.E260D1
RPUSD4UCECchr11126073324126073324CANonsense_Mutationp.G375*1
RPUSD4HNSCchr11126081423126081423GASilentp.A37A1
RPUSD4COADchr11126081469126081469CTMissense_Mutationp.S22N1
RPUSD4OVchr11125578560125578560TAMissense_Mutationp.N366I1
RPUSD4UCECchr11126074127126074128-GFrame_Shift_Insp.Q298_splice1
RPUSD4KIRPchr11126079570126079570CTMissense_Mutationp.A135T1
RPUSD4LIHCchr11126073448126073448C-Frame_Shift_Delp.G333fs1
RPUSD4COADchr11126074167126074167CTMissense_Mutationp.G285S1
RPUSD4KIRPchr11126073438126073438CANonsense_Mutation1
RPUSD4DLBCchr11126075445126075445CTSilentp.R238R1
RPUSD4BLCAchr11126081421126081421GCMissense_Mutation1
RPUSD4KIRPchr11126073516126073516CANonsense_Mutation1
RPUSD4STADchr11126081527126081527CAMissense_Mutationp.A3S1
RPUSD4LUADchr11126073362126073362TCMissense_Mutationp.N362S1
RPUSD4DLBCchr11126081386126081386GAMissense_Mutationp.L50F1
RPUSD4PAADchr11126075456126075456GAMissense_Mutationp.R235W1

check buttonCopy number variation (CNV) of RPUSD4
* 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 RPUSD4
* 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
78252N/ABF370484RPUSD4chr11126072436-RPUSD4chr11126072365+
96342N/ACN414364RPUSD4chr11126076423-TMEM159chr1621187258+


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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
THCARPUSD40.02136305375123190.6
ACCRPUSD40.04472009391841751

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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
BRCARPUSD40.0003674261710653210.012
PRADRPUSD40.008709593297744450.28
PAADRPUSD40.01014117829214990.31
ESCARPUSD40.01147862601141310.34

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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