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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: JMJD4 (NCBI Gene ID:65094)


Gene Summary

check button Gene Summary
Gene InformationGene Name: JMJD4
Gene ID: 65094
Gene Symbol

JMJD4

Gene ID

65094

Gene Namejumonji domain containing 4
Synonyms-
Cytomap

1q42.13

Type of Geneprotein-coding
Description2-oxoglutarate and iron-dependent oxygenase JMJD42-oxoglutarate- and Fe(II)-dependent oxygenaseC4 lysyl hydroxylasejmjC domain-containing protein 4jumonji domain-containing protein 4lysyl-hydroxylase JMJD4
Modification date20200313
UniProtAcc

Q9H9V9


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation of translation
GO:0006415Translational termination
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
JMJD4>1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'JMJD4[title] AND translation [title] AND human.'
GeneTitlePMID
JMJD4..


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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
ENST00000366758227920581227920728In-frame
ENST00000366758227921114227921382Frame-shift
ENST00000366758227921607227921733In-frame
ENST00000366758227922351227922517Frame-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)
ENST0000036675822792058122792072826129611107463320369
ENST000003667582279216072279217332612567692463189230

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.
Q9H9V91892301463ChainID=PRO_0000291959;Note=JmjC domain-containing protein 4
Q9H9V93203691463ChainID=PRO_0000291959;Note=JmjC domain-containing protein 4
Q9H9V9189230188347DomainNote=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00538
Q9H9V9320369188347DomainNote=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00538
Q9H9V9320369354369Alternative sequenceID=VSP_026324;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039


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Expression


check buttonGene expression level across TCGA pancancer
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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
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check buttonCancer(tissue) type-specific expression level of Translation factor using z-score distriution
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check buttonDifferential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)
all structure
Cancer typeTranslation factorFCadj.pval
KIRPJMJD4-3.25372644851440.000557802151888609
KICHJMJD41.334636231653220.00225526094436645
BLCAJMJD4-1.522636062088230.0180816650390625
HNSCJMJD4-5.927338257314340.049041343804447
COADJMJD4-2.348797857721211.2814998626709e-06
PRADJMJD41.896633098679344.73386230374949e-06


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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)
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
UVMJMJD4-0.1679531560.042001382

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with JMJD4 (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)
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Cancer typeGene groupTranslation factorCorrelated geneCoefficientPvalue
DLBCCell metabolism geneJMJD4GFER0.8087204093.58E-12
THYMCell metabolism geneJMJD4CYC10.8010417061.63E-28
THYMCell metabolism geneJMJD4SCO20.805148255.33E-29
THYMCell metabolism geneJMJD4PMPCA0.8060412854.16E-29
THYMCell metabolism geneJMJD4FBXW50.807240322.98E-29
THYMCell metabolism geneJMJD4GEMIN70.8090580571.79E-29
THYMCell metabolism geneJMJD4NME20.8102779361.27E-29
THYMCell metabolism geneJMJD4HMOX20.8183604021.20E-30
THYMCell metabolism geneJMJD4ATP5G10.8242997031.98E-31
THYMCell metabolism geneJMJD4MTX10.8249276751.63E-31
THYMCell metabolism geneJMJD4GSTP10.8285308995.23E-32
THYMCell metabolism geneJMJD4PYCRL0.8285325915.23E-32
THYMCell metabolism geneJMJD4PTGES20.8296122643.71E-32
THYMCell metabolism geneJMJD4DOHH0.853048351.08E-35
THYMCell metabolism geneJMJD4EXOSC40.8646066021.13E-37
THYMCGCJMJD4ASPSCR10.8004376531.92E-28
THYMCGCJMJD4PRCC0.8100694521.34E-29
THYMEpifactorJMJD4PRMT10.817122131.74E-30
THYMEpifactorJMJD4EXOSC40.8646066021.13E-37
THYMIUPHARJMJD4GPR1370.8012073971.56E-28
THYMIUPHARJMJD4PRMT10.817122131.74E-30
THYMIUPHARJMJD4HMOX20.8183604021.20E-30
THYMIUPHARJMJD4PTGES20.8296122643.71E-32
THYMTFJMJD4NME20.8102779361.27E-29
THYMTFJMJD4ZNF5810.8287465874.89E-32
THYMTSGJMJD4PHB0.8063772483.79E-29
THYMTSGJMJD4GSTP10.8285308995.23E-32
THYMTSGJMJD4STUB10.8313564412.11E-32
UCSCell metabolism geneJMJD4CYC10.8010417061.63E-28
UCSCell metabolism geneJMJD4SCO20.805148255.33E-29
UCSCell metabolism geneJMJD4PMPCA0.8060412854.16E-29
UCSCell metabolism geneJMJD4FBXW50.807240322.98E-29
UCSCell metabolism geneJMJD4GEMIN70.8090580571.79E-29
UCSCell metabolism geneJMJD4NME20.8102779361.27E-29
UCSCell metabolism geneJMJD4HMOX20.8183604021.20E-30
UCSCell metabolism geneJMJD4ATP5G10.8242997031.98E-31
UCSCell metabolism geneJMJD4MTX10.8249276751.63E-31
UCSCell metabolism geneJMJD4GSTP10.8285308995.23E-32
UCSCell metabolism geneJMJD4PYCRL0.8285325915.23E-32
UCSCell metabolism geneJMJD4PTGES20.8296122643.71E-32
UCSCell metabolism geneJMJD4DOHH0.853048351.08E-35
UCSCell metabolism geneJMJD4EXOSC40.8646066021.13E-37
UCSCGCJMJD4ASPSCR10.8004376531.92E-28
UCSCGCJMJD4PRCC0.8100694521.34E-29
UCSEpifactorJMJD4PRMT10.817122131.74E-30
UCSEpifactorJMJD4EXOSC40.8646066021.13E-37
UCSIUPHARJMJD4GPR1370.8012073971.56E-28
UCSIUPHARJMJD4PRMT10.817122131.74E-30
UCSIUPHARJMJD4HMOX20.8183604021.20E-30
UCSIUPHARJMJD4PTGES20.8296122643.71E-32
UCSTFJMJD4NME20.8102779361.27E-29
UCSTFJMJD4ZNF5810.8287465874.89E-32
UCSTSGJMJD4PHB0.8063772483.79E-29
UCSTSGJMJD4GSTP10.8285308995.23E-32
UCSTSGJMJD4STUB10.8313564412.11E-32


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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
KIRPJMJD4ALKBH6-1.381370467140330.000121572986245155
STADJMJD4ALKBH7-2.258720421920860.000306400004774332
COADJMJD4ALKBH52.137555521474880.000465095043182374
THCAJMJD4HSPBAP1-1.034043657494560.000691752404911338
CHOLJMJD4ALKBH7-3.139181528943880.00390625
BLCAJMJD4ALKBH4-3.091216214327870.0061798095703125
LUADJMJD4ALKBH71.306882461480350.00627510264512955
HNSCJMJD4ALKBH1-2.395388421096830.00633394569399571
COADJMJD4ALKBH7-1.254283284592230.00793844461441041
KICHJMJD4HSPBAP12.242001934469290.0236499309539795
ESCAJMJD4ALKBH72.560336026747240.0244140625
READJMJD4ALKBH52.444043667148170.03125
KIRPJMJD4HSPBAP1-2.04738618799150.0413399673998356
THCAJMJD4ALKBH5-1.263707420713881.35265985423686e-05
LIHCJMJD4ALKBH4-5.245912435750961.3992718911716e-05
LUSCJMJD4ALKBH2-5.380891252694641.45947399043856e-08
LUADJMJD4ALKBH4-1.401683947991711.61427770148041e-05
LUSCJMJD4ALKBH4-2.279823804581373.67421243367441e-07
KIRCJMJD4ALKBH2-1.237436657223483.85916186028018e-07
HNSCJMJD4ALKBH6-1.707526532554.83197595713137e-06
KIRCJMJD4ALKBH51.220084432699928.228320553924e-07
COADJMJD4HSPBAP1-1.831579535627129.14931297302247e-06


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with JMJD4
SPAG8, MOV10, NXF1, RFPL4B, LIG3, RBFOX2, CHST8, PRG2, CCNJL, KRAS, SNX20, C4orf26, FAM19A3, CCT3, KIAA1683, NCAPH2, HNRNPLL, LYPD4, APOBEC3D, SSH3, CDC16, PTP4A2, ERBB2, CCT2, CCT7, CCT6A, CCT8, CCT4, CCT5, TRABD, SEC61A1, HGSNAT, TCP1, SLC16A1, SRPRB, SLC1A5, SPTLC1, PTPMT1, MRPS15, HSD17B12, ATP2A2, EMD, RPL36A, LAMP2, TUBA1A, VCPIP1, TCEB3B, DUSP16, FBXW5, SNAPC4, C10orf82, SPANXN4, STRIP1, FOSL1, SOCS7, FAM9C, LRRC23, HS3ST6, XRCC6BP1, KANSL3, PDCL3,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo
JMJD4chr1227921253GAsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variant,SO:0001627|intron_variantSO:0001819|synonymous_variant,SO: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
JMJD4ACCchr1227923081227923081GAMissense_Mutationp.A11V9
JMJD4COADchr1227922918227922918ACMissense_Mutationp.D65E9
JMJD4PRADchr1227920349227920349TGMissense_Mutationp.N379T3
JMJD4UCSchr1227922791227922791TCMissense_Mutationp.T108A3
JMJD4CHOLchr1227922428227922428AGMissense_Mutation3
JMJD4CHOLchr1227922428227922428AGMissense_Mutationp.Y164H3
JMJD4LUADchr1227921232227921232GCSilentp.L281L3
JMJD4UCECchr1227920657227920657CGMissense_Mutationp.Q344H3
JMJD4BLCAchr1227921241227921241GASilentp.S278S3
JMJD4SKCMchr1227921164227921164CTMissense_Mutationp.G304D2
JMJD4STADchr1227921267227921267CTMissense_Mutationp.G270S2
JMJD4BLCAchr1227920357227920357CTSilent2
JMJD4UCECchr1227920313227920313GAMissense_Mutationp.A391V2
JMJD4SKCMchr1227921165227921165CTMissense_Mutationp.G304S2
JMJD4STADchr1227920195227920195CTSilentp.A430A2
JMJD4LIHCchr1227922402227922402GASilentp.G172G2
JMJD4UCECchr1227921361227921361GTSilentp.S231Y2
JMJD4HNSCchr1227921284227921284GAMissense_Mutationp.A264V2
JMJD4SKCMchr1227923013227923013CTMissense_Mutationp.E34K2
JMJD4STADchr1227922492227922492GASilentp.N142N2
JMJD4UCECchr1227921626227921626GAMissense_Mutationp.A225V2
JMJD4CESCchr1227920351227920351GCMissense_Mutation2
JMJD4STADchr1227921375227921375AGMissense_Mutationp.F234L2
JMJD4KICHchr1227921193227921193GASilentp.G294G2
JMJD4STADchr1227920624227920624GASilentp.S355S2
JMJD4LIHCchr1227921299227921299G-Frame_Shift_Delp.P259fs2
JMJD4STADchr1227920368227920368TGSilentp.R373R2
JMJD4LUADchr1227922419227922419CANonsense_Mutationp.E167*2
JMJD4STADchr1227921267227921267CTMissense_Mutation2
JMJD4THCAchr1227920103227920103GAMissense_Mutation2
JMJD4STADchr1227920195227920195CTSilent2
JMJD4SKCMchr1227923018227923018GAMissense_Mutationp.P32L2
JMJD4STADchr1227920189227920189GASilent2
JMJD4SKCMchr1227923019227923019GAMissense_Mutationp.P32S2
JMJD4STADchr1227920189227920189GASilentp.P432P2
JMJD4UCECchr1227920302227920302GAMissense_Mutationp.L395F2
JMJD4GBMchr1227922480227922480CAMissense_Mutationp.Q146H1
JMJD4LIHCchr1227922402227922402GASilent1
JMJD4BLCAchr1227920358227920358GAMissense_Mutationp.S376L1
JMJD4MESOchr1227921685227921685GASilentp.S205S1
JMJD4HNSCchr1227921284227921284GAMissense_Mutation1
JMJD4BLCAchr1227922985227922985ATMissense_Mutation1
JMJD4BLCAchr1227921252227921252CTMissense_Mutationp.D275N1
JMJD4BLCAchr1227920190227920190GTMissense_Mutation1
JMJD4LIHCchr1227921212227921212G-Frame_Shift_Delp.P288fs1
JMJD4PRADchr1227920225227920225GASilentp.R420R1
JMJD4KICHchr1227921193227921193GASilent1
JMJD4SKCMchr1227923098227923098CTSilentp.P5P1
JMJD4BLCAchr1227921241227921241GASilent1
JMJD4LIHCchr1227921325227921325C-Frame_Shift_Delp.G250fs1
JMJD4UCSchr1227922791227922791TCMissense_Mutation1
JMJD4CESCchr1227920351227920351GCMissense_Mutationp.I378M1
JMJD4READchr1227920209227920209CTMissense_Mutationp.A426T1
JMJD4SKCMchr1227920604227920604GAMissense_Mutationp.P362L1
JMJD4BLCAchr1227920358227920358GAMissense_Mutation1
JMJD4READchr1227920251227920251CTMissense_Mutationp.E412K1
JMJD4KIRCchr1227921679227921679CTNonsense_Mutationp.W207X1
JMJD4SKCMchr1227920378227920378CTSplice_Site1
JMJD4BLCAchr1227922479227922479CTMissense_Mutation1
JMJD4READchr1227922372227922372GASilentp.L182L1
JMJD4TGCTchr1227922874227922874GCMissense_Mutation1
JMJD4KIRPchr1227921688227921688CGSilentp.S204S1
JMJD4BLCAchr1227921252227921252CTMissense_Mutation1
JMJD4COADchr1227920227227920227GAMissense_Mutationp.R420C1
JMJD4SARCchr1227920186227920186GASilent1
JMJD4KIRPchr1227921240227921240GTMissense_Mutation1
JMJD4BLCAchr1227922985227922985ATMissense_Mutationp.V43E1
JMJD4LUADchr1227920197227920197CTMissense_Mutationp.A430T1
JMJD4COADchr1227920357227920357CTSilentp.S376S1
JMJD4SARCchr1227921610227921610GASilentp.S230S1
JMJD4THCAchr1227922874227922874GCMissense_Mutationp.S80W1
JMJD4LGGchr1227920725227920725CTMissense_Mutationp.D322N1
JMJD4BLCAchr1227922992227922992GANonsense_Mutationp.R41*1
JMJD4LUADchr1227920196227920196GAMissense_Mutationp.A430V1
JMJD4COADchr1227920665227920665AGMissense_Mutationp.F342L1
JMJD4BLCAchr1227922388227922388CAMissense_Mutation1
JMJD4LGGchr1227920211227920211AGMissense_Mutationp.L425P1
JMJD4MESOchr1227921685227921685GASilent1
JMJD4LGGchr1227920126227920126CASilent1
JMJD4BLCAchr1227920269227920269CAMissense_Mutation1
JMJD4BLCAchr1227922981227922981CGSilentp.L44L1
JMJD4MESOchr1227921725227921725GTMissense_Mutation1

check buttonCopy number variation (CNV) of JMJD4
* 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 JMJD4
* 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
40370SKCMTCGA-BF-AAP4-01AITCHchr2033033266+JMJD4chr1227922517-
94381N/ACA488852JMJD4chr1227921129-EFNA2chr191288640+


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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
COADJMJD40.00214342883854410.06
TGCTJMJD40.01357541941515960.37
KIRCJMJD40.01943376008167520.51
ACCJMJD40.02357702024512270.59

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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
STADJMJD40.02419991240349130.73
THCAJMJD40.004499978247624870.15
KIRCJMJD40.0197393744986510.61
LGGJMJD40.007141982638578880.23
OVJMJD40.04680401575958211

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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