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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: CNBP (NCBI Gene ID:7555)


Gene Summary

check button Gene Summary
Gene InformationGene Name: CNBP
Gene ID: 7555
Gene Symbol

CNBP

Gene ID

7555

Gene NameCCHC-type zinc finger nucleic acid binding protein
SynonymsCNBP1|DM2|PROMM|RNF163|ZCCHC22|ZNF9
Cytomap

3q21.3

Type of Geneprotein-coding
Descriptioncellular nucleic acid-binding proteinerythroid differentiation-relatedsterol regulatory element-binding proteinzinc finger protein 273zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)
Modification date20200328
UniProtAcc

P62633


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation of translation
GO:0045727Positive regulation of translation
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
HgeneCNBP

GO:0000122

negative regulation of transcription by RNA polymerase II

23774591



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
CNBP>1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'CNBP[title] AND translation [title] AND human.'
GeneTitlePMID
CNBPCNBP regulates wing development in Drosophila melanogaster by promoting IRES-dependent translation of dMyc24275942


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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
ENST000004224531288904761288906143UTR-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)

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
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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
UCECCNBP-3.538197934077210.03125
KIRPCNBP1.288440396214191.42422504723072e-05


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue
UCECCNBPhsa-miR-369-3p980.4407944996180290.00964621172762361


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
OVCNBP0.1365336330.021099076

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with CNBP (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
KICHEpifactorCNBPMBD40.8002762311.79E-21
KICHIUPHARCNBPCRBN0.8021292681.23E-21
KICHTFCNBPMBD40.8002762311.79E-21
KICHTSGCNBPMBD40.8002762311.79E-21
UVMCell metabolism geneCNBPB4GALT40.8019608053.93E-19
UVMCell metabolism geneCNBPDNAJC190.8181689741.96E-20
UVMCell metabolism geneCNBPMETTL60.8328477859.88E-22
UVMCell metabolism geneCNBPPSMD60.8388310572.69E-22
UVMCell metabolism geneCNBPDCP1A0.8497627592.16E-23
UVMCell metabolism geneCNBPTOMM70A0.8956379843.60E-29
UVMCGCCNBPATR0.8115403136.92E-20
UVMCGCCNBPMLF10.8169823092.46E-20
UVMCGCCNBPSETD20.8672910672.43E-25
UVMEpifactorCNBPRNF80.8015211734.25E-19
UVMEpifactorCNBPSETD50.8049493072.31E-19
UVMEpifactorCNBPATR0.8115403136.92E-20
UVMEpifactorCNBPPHC30.8228832647.73E-21
UVMEpifactorCNBPTOP2B0.8263839963.81E-21
UVMEpifactorCNBPHLTF0.8342375797.34E-22
UVMEpifactorCNBPRNF20.8393045522.42E-22
UVMEpifactorCNBPATXN70.8457394845.59E-23
UVMEpifactorCNBPRYBP0.849630522.23E-23
UVMEpifactorCNBPMINA0.8497821952.15E-23
UVMEpifactorCNBPUBE2E10.8538885467.93E-24
UVMEpifactorCNBPACTL6A0.8595081951.92E-24
UVMEpifactorCNBPSETD20.8672910672.43E-25
UVMEpifactorCNBPMSL20.9011257874.88E-30
UVMEpifactorCNBPMBD40.9082771463.00E-31
UVMIUPHARCNBPATR0.8115403136.92E-20
UVMIUPHARCNBPATP2C10.8265001713.72E-21
UVMIUPHARCNBPCRBN0.8349116536.35E-22
UVMIUPHARCNBPSNRK0.8353632655.75E-22
UVMIUPHARCNBPSLC25A360.8353647365.75E-22
UVMIUPHARCNBPRYK0.8362197884.78E-22
UVMIUPHARCNBPPRKCI0.8483772573.01E-23
UVMIUPHARCNBPATP13A30.8619340751.02E-24
UVMIUPHARCNBPOXSR10.8631892947.33E-25
UVMIUPHARCNBPACVR2B0.8644791975.20E-25
UVMIUPHARCNBPSETD20.8672910672.43E-25
UVMIUPHARCNBPSLC35A50.8767918291.61E-26
UVMKinaseCNBPATR0.8115403136.92E-20
UVMKinaseCNBPSNRK0.8353632655.75E-22
UVMKinaseCNBPRYK0.8362197884.78E-22
UVMKinaseCNBPPRKCI0.8483772573.01E-23
UVMKinaseCNBPOXSR10.8631892947.33E-25
UVMKinaseCNBPACVR2B0.8644791975.20E-25
UVMTFCNBPZBTB110.8042394492.62E-19
UVMTFCNBPZNF5250.8051129282.24E-19
UVMTFCNBPZBTB380.8122162446.09E-20
UVMTFCNBPBBX0.8178662562.08E-20
UVMTFCNBPZNF6210.8581793042.70E-24
UVMTFCNBPCGGBP10.8625309988.73E-25
UVMTFCNBPUBP10.8723052695.96E-26
UVMTFCNBPZNF6390.8921268171.22E-28
UVMTFCNBPZNF1970.9056708178.50E-31
UVMTFCNBPMBD40.9082771463.00E-31
UVMTSGCNBPEAF10.800972974.68E-19
UVMTSGCNBPRNF80.8015211734.25E-19
UVMTSGCNBPATR0.8115403136.92E-20
UVMTSGCNBPPHC30.8228832647.73E-21
UVMTSGCNBPHLTF0.8342375797.34E-22
UVMTSGCNBPWDR480.852282411.18E-23
UVMTSGCNBPSETD20.8672910672.43E-25
UVMTSGCNBPMBD40.9082771463.00E-31


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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))
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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
THCACNBPHSPA91.43700089254610.000619324585728192
THCACNBPDMPK1.553710022594540.000672964057081266
BRCACNBPPCBP2-1.832220081545830.000732095066837025
STADCNBPMBNL1-1.682958450526220.00166679499670863
COADCNBPPCBP2-3.878781672106650.0021815299987793
KIRPCNBPPCBP2-1.035957748622040.00571200484409928
PRADCNBPPCBP2-1.229157101579170.00712181487955485
CHOLCNBPMBNL3-3.383352953778790.0078125
THCACNBPHNRNPK-8.734225425633890.00797530353045887
PRADCNBPMBNL3-2.692033141695040.0098283424925592
CHOLCNBPHSPA9-2.626990112327530.01171875
KIRPCNBPMBNL1-1.163001954755050.0118026207201183
LIHCCNBPPCBP2-1.547985075911990.0120781615488378
CHOLCNBPMBNL2-3.480651169828080.02734375
UCECCNBPHNRNPK1.645327445048640.03125
READCNBPMBNL3-3.370452858097440.03125
BLCACNBPPCBP2-3.891987584355690.0323410034179688
KIRPCNBPMBNL3-1.241563029609150.0375871751457453
LIHCCNBPMBNL2-3.288264514588991.03660595360911e-06
PRADCNBPDMPK-2.247622106018261.07311825696129e-07
BRCACNBPMBNL1-3.985507277652461.08293518653207e-22
LUSCCNBPMBNL1-1.105223589565291.38150619305268e-08
LUADCNBPHSPA9-2.371665425087732.1660933617938e-09
BRCACNBPEIF4B-2.160327420296962.35556737304054e-22
LUSCCNBPHSPA9-2.243735361253222.51071930113563e-08
BRCACNBPMBNL2-2.615967821312013.64562360701576e-24
KIRCCNBPMBNL3-1.282242970557624.47117775598177e-07
BLCACNBPDMPK-2.764219969364725.340576171875e-05
LUADCNBPMBNL2-1.224707166071016.36796101058976e-06
KIRCCNBPEIF4B1.149971405104747.59366366705366e-09
KICHCNBPHSPA91.925625802608638.34465026855468e-07


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with CNBP
IGF2BP1, RPL3, HNRNPC, PURA, RPS3A, DHX9, HNRNPAB, RPL34, IGF2BP3, BRIX1, RPL23A, RBMX, HNRNPR, RPL31, RPL35A, RPS16, APOBEC3C, RPA3, RPL36, RPS19, ERH, EBNA1BP2, HNRNPUL1, SYNCRIP, HNRNPA3, RSL1D1, DAP3, FKTN, MYH4, ZWINT, Cnbp, Mis12, KCND3, VCAM1, ITGA4, PAN2, MAPK14, BZW2, DFFA, EIF6, FERMT2, HSPA9, PFAS, EZH2, SUZ12, RNF2, BMI1, CDK2, MARK3, WEE1, CADM1, HK2, NMD3, PABPC3, PABPC4, CASP8, HIST1H3E, EGFR, TRIM56, HIST1H1A, NLE1, ZNF275, ITGB3BP, RPL18, RPF2, RPL26L1, DDX31, RPLP0, RPL27, GTPBP4, RPLP2, GNL2, ZC3HAV1, RPF1, RPL4, RPL10A, RPL18A, KIAA0020, ZNF689, STAU1, RPL32, RPS8, CENPN, RPL37A, PAK1IP1, RPL13, RPL14, RRS1, RPL15, CENPU, ZNF184, WHSC1, ZNF800, RPL12, GLYR1, RPS6, RSL24D1, RRP8, RPL6, TTF1, ZFP62, ZNF512, DDX27, REPIN1, RPLP1, ZNF48, RPL30, RPL7, RPS13, RPL8, C8orf33, NSA2, RBM34, ZSCAN25, DDX24, SURF6, FTSJ3, NIP7, RPL11, DKC1, RPL5, PPAN-P2RY11, NOL12, NOP56, POP1, NOP2, DHX30, DDX21, FCF1, RPL7A, MAK16, RPL13A, RBM28, RPL7L1, LLPH, PAPD5, ABT1, ZNF771, GLTSCR2, CCDC137, NR3C1, AR, ARNT, EFTUD2, RNF31, ESR2, HEXIM1, MEPCE, LARP7, VCP, RAB11A, BET1, CDK7, DYRK1A, LRRK2, PLEKHA4, NGB, NHLRC2, HCVgp1, RAB5A, ESR1, HRH1, KIF23, Arhgap1, DOCK9, CDC42, PTEN, Apc2, FBP1, nsp14, BRD1, KDM4C, ING4, ING5, MEAF6, KDM4D, SMCHD1, KAT7, ERP44, KAT6B, IDH2, HOMER1, DDX58, TRIM37, WDR5, NIFK, RPL26, RPL17, ZNF22, CCDC86, HIST1H2AG, YBX3, NKRF, C7orf50, FYTTD1, HP1BP3, RPS9, BTF3, ORF10, ORF8, NRP1, TMPRSS2, TOP3B, CTSL, FURIN, IFITM1, DPP4, IFITM3, TMPRSS11B, CLEC4D, ACE2, CLEC4E, E, nsp2, nsp4, ORF3a, ORF6, S, CCNF, KLF10, KLF3, KLF6, KLF9,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo
CNBPchr3128890350GAsingle_nucleotide_variantBenignMyotonic_dystrophy_type_2|not_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
CNBPchr3128890540TCsingle_nucleotide_variantUncertain_significanceMyotonic_dystrophy_type_2SO:0001583|missense_variantSO:0001583|missense_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
CNBPKIRCchr3128890023128890023GASilentp.G105G4
CNBPPAADchr3128890615128890615CASplice_Site3
CNBPPAADchr3128889940128889940GAMissense_Mutationp.T133I2
CNBPPAADchr3128890570128890570GANonsense_Mutationp.R11*2
CNBPUCECchr3128889344128889344GASilentp.G1642
CNBPUCECchr3128889962128889962CTMissense_Mutationp.G128R2
CNBPPAADchr3128889940128889940GAMissense_Mutation2
CNBPLGGchr3128889325128889325GAMissense_Mutationp.R169W2
CNBPUCECchr3128890058128890058GANonsense_Mutationp.R96*2
CNBPUCECchr3128890121128890121CASplice_Sitee3-12
CNBPLGGchr3128890339128890339CTMissense_Mutation1
CNBPPAADchr3128889940128889940GAMissense_Mutationp.T135I1
CNBPCESCchr3128902672128902672ACMissense_Mutation1
CNBPSTADchr3128890519128890519CANonsense_Mutationp.G28X1
CNBPLIHCchr3128889330128889330AGMissense_Mutation1
CNBPCOADchr3128890099128890099CTMissense_Mutationp.G81D1
CNBPSTADchr3128890519128890519CANonsense_Mutationp.G28*1
CNBPLIHCchr3128889414128889414CTSplice_Site.1
CNBPESCAchr3128889387128889387AGMissense_Mutationp.I150T1
CNBPTGCTchr3128889947128889948--Frame_Shift_Ins1
CNBPLIHCchr3128890513128890513TANonsense_Mutationp.R30X1
CNBPPAADchr3128890570128890570GANonsense_Mutation1
CNBPESCAchr3128890058128890058GANonsense_Mutationp.R96X1
CNBPTGCTchr3128889947128889948-TFrame_Shift_Insp.D133fs1
CNBPLIHCchr3128890513128890513TANonsense_Mutationp.R30*1
CNBPPRADchr3128890476128890476CASplice_Site1
CNBPESCAchr3128890490128890490A-Frame_Shift_Delp.F37fs1
CNBPTGCTchr3128889947128889948-TFrame_Shift_Insp.L131fs1
CNBPLIHCchr3128890513128890513TAMissense_Mutation1
CNBPREADchr3128890005128890005GASilentp.C112C1
CNBPHNSCchr3128889324128889324CAMissense_Mutation1
CNBPUCECchr3128889318128889318CAMissense_Mutationp.C173F1
CNBPLUADchr3128889925128889925TCMissense_Mutationp.Y138C1
CNBPSKCMchr3128889945128889945GASilentp.D132D1
CNBPKIRCchr3128890023128890023GASilentp.G107G1
CNBPLUSCchr3128890383128890383TCSplice_Sitep.G42_splice1
CNBPACCchr3128889366128889366TCMissense_Mutationp.E157G1
CNBPSKCMchr3128889945128889945GASilentp.D131D1
CNBPACCchr3128889366128889366TCMissense_Mutationp.E156G1
CNBPSKCMchr3128890366128890366GAMissense_Mutationp.S47F1
CNBPBLCAchr3128889334128889334GTMissense_Mutation1
CNBPSKCMchr3128890001128890001GAMissense_Mutationp.H113Y1
CNBPLGGchr3128890339128890339CTMissense_Mutationp.R56H1
CNBPPAADchr3128890615128890615CASplice_Site.1
CNBPBLCAchr3128889334128889334GTMissense_Mutationp.H166N1
CNBPSTADchr3128890121128890121CTMissense_Mutationp.A75T1

check buttonCopy number variation (CNV) of CNBP
* 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 CNBP
* 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
102978STADTCGA-FP-8209-01AABRchr17982570-CNBPchr3128890614-
102978N/AAV733123ATP1A3chr1942474365+CNBPchr3128889023-
91364LGGTCGA-HT-7858-01ACNBPchr3128902619-ALDH1L1chr3125831723-
101911N/ABG149780CNBPchr3128887013+CSNK2A1chr20523424+
82238N/ABI856841CNBPchr3128888451-LACE1chr6108785808+
99955Non-CancerTCGA-HU-A4GP-11ACNBPchr3128902619-LRCH3chr3197574280+
90724STADTCGA-EQ-A4SO-01ACNBPchr3128902619-RPN1chr3128341252-
102785STADTCGA-BR-A4PDCNBPchr3128902618-SMARCB1chr2224175758+
102785STADTCGA-BR-A4PD-01ACNBPchr3128902619-SMARCB1chr2224175759+
17624ESCATCGA-LN-A49RCNBPchr3128902619-UNC93B6chr1171318338+
17624ESCATCGA-LN-A49R-01ACNBPchr3128902619-UNC93B6chr1171316395+
90735aneurysmal bone cystAY624556CNBPchr3128902727USP6chr175033660
90735..CNBPchr3128902618-USP6chr175031686+
90735..CNBPchr3128902618-USP6chr175033661+
90735N/AAY624556CNBPchr3128902618-USP6chr175033660+
90735N/AAY624557CNBPchr3128902618-USP6chr175033229+
102978BLCATCGA-DK-A2I1-01AFBLN1chr2245898944+CNBPchr3128890614-
102978N/AAW796677NAP1L4chr113003185-CNBPchr3128888575-
102978STADTCGA-HU-A4GYTBL1XR1chr3176914908-CNBPchr3128890614-
102978N/ABM150482ZBTB38chr3141106446-CNBPchr3128888420+
102982STADTCGA-BR-A4PDZNF7chr8146054989+CNBPchr3128890614-


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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
TGCTCNBP0.0003785714925987780.011

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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
TGCTCNBP0.001994254294522730.064
KIRPCNBP0.04873129971251381
ESCACNBP6.03042097766637e-062e-04
THYMCNBP0.01721513827782250.53

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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
C2931689Dystrophia myotonica 21CTD_human;GENOMICS_ENGLAND