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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: RPL7 (NCBI Gene ID:6129)


Gene Summary

check button Gene Summary
Gene InformationGene Name: RPL7
Gene ID: 6129
Gene Symbol

RPL7

Gene ID

6129

Gene Nameribosomal protein L7
SynonymsL7|humL7-1
Cytomap

8q21.11

Type of Geneprotein-coding
Description60S ribosomal protein L7large ribosomal subunit protein uL30
Modification date20200313
UniProtAcc

P18124


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


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
RPL7>1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'RPL7[title] AND translation [title] AND human.'
GeneTitlePMID
RPL7..


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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
ENST000003529837420378674203896Frame-shift
ENST000003529837420400774204145In-frame

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)
ENST000003529837420400774204145111857771424897142

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.
P18124971421248ChainID=PRO_0000104633;Note=60S ribosomal protein L7
P1812497142124124Modified residueNote=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861
P1812497142127127Modified residueNote=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P14148
P1812497142139139Modified residueNote=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:15592455;Dbxref=PMID:15592455


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Expression


check buttonGene expression level across TCGA pancancer
all structure

check buttonGene expression level across GTEx pantissue
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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
BLCARPL7-1.694527943620080.0061798095703125
KIRCRPL71.548484560680430.0138655597925316


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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
CESCRPL7320.02204585114448530.748310613026820.5334090909090910.4473067338915470.230288646117491
HNSCRPL7320.02672349329679540.704267503486750.537627668845316-0.02087164296565720.0976681470087173
PCPGRPL7320.02579656942587250.660569547872340.539024596774194-0.261612224288653-0.149214775192296

check buttonTranslation factor expression regulation through copy number variation of Translation factor
Cancer typeGeneCoefficientPvalue
UCECRPL70.1082554550.003031464
MESORPL70.0911476240.003467214
PCPGRPL70.0551365570.037851661
GBMRPL70.2292275620.049181474

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with RPL7 (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
DLBCTFRPL7ZNF5810.8760356273.58E-16
DLBCTSGRPL7GLTSCR20.8249368425.62E-13
DLBCTSGRPL7GNB2L10.8914207242.01E-17
LGGCell metabolism geneRPL7IMPDH20.8172845681.67E-128
LGGCGCRPL7NACA0.8343010471.19E-138
LGGIUPHARRPL7IMPDH20.8172845681.67E-128


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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
KIRPRPL7RPL18A-1.516513928088850.00016188295558095
KICHRPL7RPS27A1.753966937859560.000187873840332031
KIRPRPL7RPS16-1.359570436175170.00019507110118866
STADRPL7RPS231.850767606645760.000364991836249828
COADRPL7RPS31.487303751430140.000411599874496461
KIRPRPL7RPS11-1.018615705651030.00105937570333481
LIHCRPL7RPL8-4.845882849745580.00110314154326131
PRADRPL7RPL18A1.406001757484990.00205137828390396
KICHRPL7RPL191.369011828940890.00250792503356934
KICHRPL7RPS121.269973817584310.00308787822723389
LUADRPL7RPL19-1.313980266157250.00993159558412698
THCARPL7RPS16-6.163227981565770.0115764821363307
LUSCRPL7RPS231.467511698910470.0174932185880974
BLCARPL7RPS12-1.478046734404210.0204124450683594
BLCARPL7RPS27A-1.047474700691880.0258216857910156
HNSCRPL7RPS3-4.735058190951350.0273726439852453
COADRPL7RPS111.353075489982040.0312207043170929
LUSCRPL7RPL19-2.146698895166660.044366810398747
UCECRPL7RPS23-2.036581598140070.046875
KIRCRPL7RPL19-2.734852712766761.33980982873695e-10
BRCARPL7RPS12-4.912393274782441.85340619742495e-09
KIRCRPL7RPL35-1.064752380593922.72286325678163e-08
KIRCRPL7RPL8-1.182524599717735.64962994208288e-07
KIRPRPL7RPL8-1.530036923501196.0301274061203e-05
KIRCRPL7RPS16-1.661498698893847.8509870430991e-09
BRCARPL7RPS27A-4.285121482004247.8788217967112e-14
KIRPRPL7RPL35-1.529811019754969.0546440333128e-05
KIRCRPL7RPS3-1.295608479263879.05905681935088e-10
KIRCRPL7RPL18A-4.430793049608439.2516163152192e-11


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with RPL7
PHC2, ZNF7, USP38, ESR1, SMN1, CD4, HDAC5, NOP56, DYRK2, EBNA-LP, NR4A1, ARRB2, SIRT7, CUL3, CUL4B, CUL5, CUL2, CDK2, COPS5, CAND1, RPL21, RPL5, RPL6, RPL7A, RPS3A, RPS4X, RPS6, RPSA, RPL4, RPS3, RPL10A, RPLP0, RPL11, RPL12, RPL14, RPL15, RPL17, RPL18A, RPL18, RPL19, RPL23A, RPL23, RPL24, RPL27A, RPL30, RPL31, RPL3, RPL9, RPS13, RPS14, RPS15A, RPS15, RPS16, RPS19, RPS23, RPS26, RPS2, RPS7, RPS8, RPS24, RPL8, RPL10, RPS11, RPS5, RPL13, RPL37A, RPS20, RPS12, RPS28, RPS25, RPL22, RPL35, RPL36, EEF2, RPL38, RPL32, RPS21, RPS29, MYBBP1A, NCL, EIF6, SLC25A5, FBL, GNL3, ILF2, ILF3, NOP58, DDX21, HNRNPU, EBNA1BP2, PABPC1, NHP2L1, HNRNPM, TUFM, RPS27L, HSP90AA1, RPL10L, RPLP0P6, NOP2, NIFK, HIST1H2AD, RRS1, TMX1, HSP90AA5P, PPP1CC, MAGOH, EIF4A3, TRAF3IP1, IPO5, RAN, HSP90AB1, FN1, VCAM1, NOS2, IL7R, UBL4A, PHB, PAN2, YWHAQ, TARDBP, PARK2, RPA3, RPA2, RPA1, LGR4, STAU1, CEP250, TP53, TUBG1, TUBGCP4, CUL7, OBSL1, CCDC8, UBE2I, EED, RNF2, THAP7, NTRK1, ABCE1, BRIX1, CAPRIN1, DDX24, EEF1A1, EIF3C, GNB2L1, GNL1, PABPC4, RNPS1, RPL13A, RPL28, RPL35A, RPL3L, ACIN1, HNRNPR, HSPA8, MATR3, MTHFD1, PES1, RPL27, RPL34, RPLP2, RPS10, LOC101929876, RPS9, RPLP1, RPS18, RPS27, TUBB4B, WDR12, BLM, PTEN, NPM1, KIF2C, Eif3a, Rpl35, Srp72, Rrbp1, Brwd3, MCM2, RC3H1, CDC73, ZNF746, EGFR, CBX2, SRSF12, BMI1, RPL26L1, ZNF689, TSPYL2, ZNF22, RPL36AL, NOC4L, VPRBP, GZF1, RRP12, ZBTB11, NGRN, DKC1, RBM19, CNBP, ZBTB24, KRR1, MAGEB10, ZNF771, UTP23, ZC3HAV1, ZNF668, ZNF184, MRPL13, MRPL27, MRPS7, POP1, NSA2, RPL26, ZC3H8, RALY, CYLD, INO80B, TRIM25, BRCA1, MTF1, CFTR, TMPO, API5, BMP4, DIMT1, MAP2K3, MATN2, TRIP4, YAP1, ARNT, HNF1B, KRAS, LARS, MAP2K1, MTCH2, PCBP1, PPIE, PPP6C, TGFB1, PYHIN1, PRPF8, EFTUD2, AAR2, PIH1D1, CHD3, CHD4, TNF, RIOK1, UBE3A, HEXIM1, MEPCE, LARP7, RNF123, PPT1, SNAI1, AGR2, RECQL4, REST, MYC, CDK9, RPS6KB2, GRWD1, METTL14, RC3H2, ZBTB7A, RBX1, TMEM41B, NR2C2, NIN, VRK1, HIST1H4A, SNRNP70, HYPK, ARAF, HMGB1, PPP1CA, BIRC3, NFX1, WWP2, BRD7, Dnajc17, ARIH2, DARS-AS1, PINK1, TFCP2, FANCD2, NGB, HCVgp1, ZC3H18, MAP3K14, PTPN6, EMC4, FGD1, HYOU1, RPL29, SNIP1, E, M, nsp13, nsp14, nsp4, nsp5, nsp6, ORF3a, ORF6, ORF7a, ORF7b, MAP1LC3B, NEK4, DUX4, CIT, ANLN, AURKB, CHMP4B, CHMP4C, ECT2, KIF14, KIF20A, MAD2L2, KIF23, PRC1, GRSF1, INS, NDN, MAFB, BRD4, Apc2, RBM39, FBP1, LGALS9, IFI16, RIN3, DNAJC15, DNAJC16, DNAJC19, DNAJC1, DNAJC25, DNAJC2, DNAJC8, DRG1, SETD8, KDF1, OGT, BAG5, SPOP, TRIM37, UFL1, DDRGK1, POLR2C, FZR1, WDR5, PAGE4, NUDCD2, NAA40, ZFP62, ADARB1, ZNF770, NKRF, YBX1, SPPL3, GLTSCR2, KRI1, H2AFB3, CCDC140, MAGEB2, ZNF346, SRSF6, NEIL1, SURF6, PRKRA, DTX3, BTF3, TRIM26, FBXW7, Nudt21, NLRP7, FGD5, RCHY1, CCNF, N, ZEB1,


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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
RPL7BRCAchr87420447974204479GASilentp.I954
RPL7BRCAchr87420493374204933GTSilentp.A383
RPL7BRCAchr87420583774205837ACMissense_Mutationp.V4G3
RPL7LIHCchr87420400774204007C-Splice_Site2
RPL7LIHCchr87420449174204491A-Frame_Shift_Delp.F51fs2
RPL7BLCAchr87420583574205835CTSplice_Sitep.E5K2
RPL7GBMchr87420502074205022CTT-In_Frame_Delp.K9del2
RPL7PRADchr87420500674205006ACMissense_Mutationp.V14G2
RPL7UCECchr87420402474204024GAMissense_Mutationp.P138S2
RPL7UCECchr87420501774205017CTSilentp.E102
RPL7COADchr87420385674203856GAMissense_Mutationp.R157C1
RPL7BLCAchr87420402374204023GAMissense_Mutation1
RPL7SARCchr87420380874203808CTMissense_Mutationp.A133T1
RPL7COADchr87420492974204929TGMissense_Mutationp.K40Q1
RPL7SARCchr87420335874203358TCMissense_Mutationp.K183R1
RPL7DLBCchr87420406174204061GCSilentp.L125L1
RPL7LIHCchr87420584074205840C-Frame_Shift_Delp.G3fs1
RPL7BLCAchr87420456274204562CTMissense_Mutationp.E28K1
RPL7SARCchr87420380874203808CTMissense_Mutationp.A173T1
RPL7LUADchr87420583874205838CAMissense_Mutationp.V4L1
RPL7BLCAchr87420410974204109CTSilentp.L69L1
RPL7SKCMchr87420401274204012ATMissense_Mutationp.W142R1
RPL7HNSCchr87420413374204133CTSilent1
RPL7LUADchr87420386074203860GCNonsense_Mutationp.Y115*1
RPL7BLCAchr87420402374204023GAMissense_Mutationp.P98L1
RPL7SKCMchr87420412074204120GANonsense_Mutationp.R66*1
RPL7HNSCchr87420413374204133CTSilentp.V61V1
RPL7LUADchr87420448574204485GASilentp.I53I1
RPL7SKCMchr87420342874203428GAMissense_Mutationp.R160C1
RPL7KIRCchr87420450074204500TAMissense_Mutationp.K88N1
RPL7LUSCchr87420380374203803CGMissense_Mutationp.L174F1
RPL7SKCMchr87420401274204012ATMissense_Mutationp.W102R1
RPL7KIRCchr87420450074204500TAMissense_Mutationp.K48N1
RPL7PRADchr87420346474203464CGMissense_Mutationp.E148Q1
RPL7STADchr87420389574203895AGMissense_Mutationp.Y144H1
RPL7LGGchr87420458674204586CTMissense_Mutationp.E20K1
RPL7CESCchr87420330674203306GASilent1
RPL7LGGchr87420379574203795CTMissense_Mutationp.R137Q1
RPL7BLCAchr87420583574205835CTMissense_Mutation1
RPL7READchr87420463674204636CTMissense_Mutationp.R43Q1
RPL7CESCchr87420330674203306GASilentp.I2401
RPL7LGGchr87420379574203795CTMissense_Mutation1
RPL7BLCAchr87420410974204109CTSilent1
RPL7SARCchr87420380874203808CTMissense_Mutation1

check buttonCopy number variation (CNV) of RPL7
* 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 RPL7
* 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
87346SARCTCGA-DX-A8BX-01ACCDC92chr12124457076-RPL7chr874205032-
91040N/ADA454229RPL7chr874205458-AP1G2chr1424031083-
98247N/AT12399RPL7chr874202923-CSF1Rchr5149474653-
87350BRCATCGA-D8-A1XZ-01ASTAU2chr874585342-RPL7chr874205032-
87350STADTCGA-BR-A4J5-01ASTAU2chr874659018-RPL7chr874205032-


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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
KIRCRPL71.332568282239330.2871081194517650.01372919847670050.01559477429607040.0140128019626905604
KIRCRPL71.332568282239330.2871081194517650.01372919847670050.01559477429607040.0140128019626905604
UVMRPL70.470162349223557-0.7546772200432170.01747931581857450.01703931660183340.015314027489828880
ACCRPL71.867652488124950.6246822883057910.02174297481464470.02161159287934780.020741134239559179
UCECRPL70.572868772937731-0.5570986060566030.02845019929205090.02874465101500820.0281316230233365188
GBMRPL70.753969389298355-0.2824035095458320.03042901507830890.0254854600110620.0301656536786852165
LGGRPL70.469297627617084-0.7565181113467173.8832677796951e-074.065814265054e-074.62214349803356e-07525


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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
KIRPRPL70.006970470759906980.2
KIRCRPL70.009957843044744160.27

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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
LGGRPL70.00296903438114830.098
BRCARPL70.01523009033337210.47
PRADRPL70.008654871016779930.28
SKCMRPL70.02668046594906960.8

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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