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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: LSM14B (NCBI Gene ID:149986)


Gene Summary

check button Gene Summary
Gene InformationGene Name: LSM14B
Gene ID: 149986
Gene Symbol

LSM14B

Gene ID

149986

Gene NameLSM family member 14B
SynonymsC20orf40|FAM61B|FT005|LSM13|RAP55B|bA11M20.3
Cytomap

20q13.33

Type of Geneprotein-coding
Descriptionprotein LSM14 homolog BLSM14 homolog BLSM14B, SCD6 homolog BRNA-associated protein 55Bfamily with sequence similarity 61, member BhRAP55B
Modification date20200327
UniProtAcc

Q9BX40


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation 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
LSM14B>1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'LSM14B[title] AND translation [title] AND human.'
GeneTitlePMID
LSM14B..


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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
ENST000002790686070135960701495Frame-shift
ENST000002790686070484060705008In-frame
ENST000002790686070527460705352In-frame
ENST0000027906860708345607085313UTR-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)
ENST0000027906860704840607050082565588755385142198
ENST0000027906860705274607053522565756833385198224

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.
Q9BX401421982385ChainID=PRO_0000187093;Note=Protein LSM14 homolog B
Q9BX401982242385ChainID=PRO_0000187093;Note=Protein LSM14 homolog B
Q9BX40142198154154Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231
Q9BX40142198165165Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
Q9BX4014219845142Alternative sequenceID=VSP_014659;Note=In isoform 3. SFGTEDRPTDRPAPPREEIYEYIIFRGSDIKDITVCEPPKAQHTLPQDPAIVQSSLGSASASPFQPHVPYSPFRGMAPYGPLAASSLLSQQYAASLGL->MAPYGPLAASSLLSQQYAASLGLEKLVSPPASAAASSPSSSPSPQPVSELDLSSEPQQLTAKGCLFCFRSLFTYTQSHIVLFRVPTGPGTLEREEMER;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9BX40142198143220Alternative sequenceID=VSP_014660;Note=In isoform 2. GAGFPSIPVGKSPMVEQAVQTGSADNLNAKKLLPGKGTTGTQLNGRQAQPSSKTASDVVQPAAVQAQGQVNDENRRPQ->EKLVSPPASAAASSPSSSPSPQPVSELDLSSEPQQLTAKGNSSLGELHAVLQTILRARGKAADRMTVAVADHLPSPCS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9BX40198224143220Alternative sequenceID=VSP_014660;Note=In isoform 2. GAGFPSIPVGKSPMVEQAVQTGSADNLNAKKLLPGKGTTGTQLNGRQAQPSSKTASDVVQPAAVQAQGQVNDENRRPQ->EKLVSPPASAAASSPSSSPSPQPVSELDLSSEPQQLTAKGNSSLGELHAVLQTILRARGKAADRMTVAVADHLPSPCS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334


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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
CHOLLSM14B-2.257032194797640.00390625
STADLSM14B-1.044979613941630.0139979305677116
KICHLSM14B-1.997748359060461.50799751281738e-05
PRADLSM14B-3.811130212861161.68487044723013e-05
LUADLSM14B-1.996676230049121.92117385607053e-06
KIRPLSM14B-1.039449065437178.74791294336319e-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
READLSM14B-0.0893355270.004724402
LGGLSM14B0.1366485110.019291856

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with LSM14B (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
COADEpifactorLSM14BTAF40.8897069142.20E-113
DLBCEpifactorLSM14BTAF40.8738350355.23E-16
GBMTFLSM14BZNF512B0.8440722227.05E-48
LUADEpifactorLSM14BTAF40.8024784697.83E-131
LUSCEpifactorLSM14BTAF40.8009342557.77E-125
READCGCLSM14BSS18L10.8108108911.06E-25
READEpifactorLSM14BSS18L10.8108108911.06E-25
READEpifactorLSM14BTAF40.9112900781.75E-41
READTSGLSM14BDIDO10.8069288112.71E-25
THYMCGCLSM14BTOP10.8121006387.52E-30
THYMEpifactorLSM14BYY10.8137512684.67E-30
THYMEpifactorLSM14BTADA10.8151477313.11E-30
THYMIUPHARLSM14BTOP10.8121006387.52E-30
THYMTFLSM14BTOPORS0.8039315987.45E-29
THYMTFLSM14BZNF5670.8076370132.67E-29
THYMTFLSM14BYY10.8137512684.67E-30
THYMTSGLSM14BTOPORS0.8039315987.45E-29
UCSCGCLSM14BTOP10.8121006387.52E-30
UCSEpifactorLSM14BYY10.8137512684.67E-30
UCSEpifactorLSM14BTADA10.8151477313.11E-30
UCSIUPHARLSM14BTOP10.8121006387.52E-30
UCSTFLSM14BTOPORS0.8039315987.45E-29
UCSTFLSM14BZNF5670.8076370132.67E-29
UCSTFLSM14BYY10.8137512684.67E-30
UCSTSGLSM14BTOPORS0.8039315987.45E-29


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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
HNSCLSM14BDCP1B1.145210554861210.000653586169164556
COADLSM14BDCP1A1.371346243749130.00241076946258545
BLCALSM14BDCP1A-4.972620660674380.0033416748046875
THCALSM14BEDC3-1.600720942830680.00403018908583426
STADLSM14BDCP1B-1.134987685460970.00828406633809209
KIRCLSM14BDCP21.264756496825670.0124189994647713
CHOLLSM14BPABPC1L2.783311724942410.01953125
CHOLLSM14BBICC12.982199721652310.02734375
PRADLSM14BBICC11.125045849174670.0350092650357157
STADLSM14BPATL11.641762093111391.11940316855908e-05
LUADLSM14BPABPC1L-2.515830265015241.30692790027182e-05
PRADLSM14BEDC31.415856763637781.51985731338595e-07
LUADLSM14BDCP1A-1.726754262060941.6717782354243e-05
BRCALSM14BDCP1A-1.838306611872611.93681541154994e-23
LUSCLSM14BPABPC1L-2.505381712297143.79466966402315e-05
STADLSM14BPABPC1L-2.432454365419924.02145087718964e-06
LIHCLSM14BPABPC1L-2.775624927144046.17267413816717e-05
LUADLSM14BEDC3-1.967670059473626.36796101058976e-06
BRCALSM14BEIF4ENIF1-1.80000229680017.32601452453987e-06
KICHLSM14BPABPC1L2.225318681877157.49826431274414e-05
THCALSM14BDDX6-4.185937147624168.3083675979354e-06
LIHCLSM14BEDC3-1.350087371117139.26293949573469e-09


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with LSM14B
HECW2, LGR4, DDX6, SEMG2, SEMG1, SIRT3, ICK, LUC7L, NTRK1, DCTN1, XPO1, SMC1A, HUWE1, PHF8, C1qbp, Iffo1, POU5F1, CLEC3A, BHLHA15, GTF3C2, CHCHD10, CASP3, G3BP1, PTCH1, ESR2, HEXIM1, MEPCE, EZH2, RECQL4, SNRNP70, ITFG1, WWP2, HOMER3, WDYHV1, TCEANC, ZC3H18, N, nsp9, ESR1, DAZL, DCP1A, EIF4ENIF1, LSM14A, MEX3B, MOV10, UBAP2L, YTHDF2, YTHDF3, ZC3HAV1, AGO2, CAPRIN1, DDX3X, FAM120C, FXR2, TDRD3, ZFP36, FUBP3, IGF2BP1, IGF2BP2, KIAA0430, HNRNPH1, ZMYND11, OGT, FBL, RPS20, FZR1, PRM2, CHCHD2, PSMD9, RPL37, DDX54, C17orf85, SEPT9, FBXW7, TOP3B, CPEB1,


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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
LSM14BKIRPchr206070529260705292GAMissense_Mutationp.A205T5
LSM14BBLCAchr206069784260697842CASilent5
LSM14BUCECchr206070567760705677CTSilentp.F2554
LSM14BESCAchr206070137360701373CTMissense_Mutation4
LSM14BESCAchr206070137360701373CTMissense_Mutationp.S102F3
LSM14BBRCAchr206070573760705737GTSilentp.L2753
LSM14BESCAchr206070843460708434CTMissense_Mutationp.R359W3
LSM14BBRCAchr206070843560708435GCMissense_Mutationp.R359P3
LSM14BUCECchr206070559460705594CTNonsense_Mutationp.R228*3
LSM14BHNSCchr206070646860706468GAMissense_Mutationp.E298K3
LSM14BUCECchr206070532960705329GAMissense_Mutationp.R217K3
LSM14BESCAchr206070558460705584AGSplice_Site3
LSM14BPAADchr206070145460701454GAMissense_Mutationp.S129N3
LSM14BSKCMchr206070138560701385CTMissense_Mutationp.S106L3
LSM14BUCECchr206070147960701479CTSilentp.A1372
LSM14BBRCAchr206070130060701300GAMissense_Mutationp.E104K2
LSM14BKIRCchr206070143660701436AGMissense_Mutationp.Y123C2
LSM14BPRADchr206070850760708507GTMissense_Mutationp.G383V2
LSM14BSTADchr206070499760704997AGMissense_Mutationp.K195R2
LSM14BUCECchr206070491060704910CAMissense_Mutationp.A166D2
LSM14BBRCAchr206070641860706418ATMissense_Mutationp.K281M2
LSM14BSTADchr206070652360706523ACMissense_Mutationp.K316T2
LSM14BUCECchr206070500060705000CTMissense_Mutationp.T196M2
LSM14BBLCAchr206070484160704841GASplice_Sitep.G143E2
LSM14BSTADchr206070494960704949GAMissense_Mutationp.G179D2
LSM14BUCECchr206070562560705625GAMissense_Mutationp.R238H2
LSM14BBLCAchr206069774560697745CTMissense_Mutationp.P8L2
LSM14BSTADchr206070486460704864GAMissense_Mutationp.V151I2
LSM14BBLCAchr206070837160708371GCMissense_Mutationp.E338Q2
LSM14BCESCchr206070835460708354GAMissense_Mutation2
LSM14BSKCMchr206070139260701392CTSilentp.F108F2
LSM14BUCECchr206070641560706415AGMissense_Mutationp.D280G2
LSM14BBLCAchr206070647660706476CTSilentp.P300P2
LSM14BCESCchr206070280460702804GCSilent2
LSM14BLGGchr206070137360701373CGMissense_Mutationp.S102C2
LSM14BSKCMchr206070533560705335CTMissense_Mutationp.P219L2
LSM14BPAADchr206070145460701454GAMissense_Mutation2
LSM14BPAADchr206070130560701305CTSilent2
LSM14BUCECchr206070644260706442AGMissense_Mutationp.D289G2
LSM14BESCAchr206070843460708434CTMissense_Mutation2
LSM14BBLCAchr206070654760706547CTMissense_Mutationp.S324F2
LSM14BUCECchr206070844660708446CTNonsense_Mutationp.R363*2
LSM14BSKCMchr206070136460701364CTMissense_Mutationp.S99F2
LSM14BUCECchr206070131060701310GAMissense_Mutationp.R107Q2
LSM14BPCPGchr206070143960701439GTMissense_Mutation2
LSM14BUCECchr206070138660701386GASilentp.S1062
LSM14BBRCAchr206069969960699699CTMissense_Mutationp.P52S2
LSM14BPCPGchr206070143960701439GTMissense_Mutationp.G124V2
LSM14BSTADchr206069974260699742AGMissense_Mutationp.Y66C2
LSM14BLIHCchr206069971760699717C-Frame_Shift_Delp.P59fs2
LSM14BBLCAchr206070647660706476CTSilent1
LSM14BGBMchr206069779060697790GAMissense_Mutationp.R23H1
LSM14BCOADchr206070144360701443GASilentp.P125P1
LSM14BLIHCchr206070642860706428G-Frame_Shift_Delp.K284fs1
LSM14BBLCAchr206070490760704907CTMissense_Mutation1
LSM14BGBMchr206070149560701495GTNonsense_Mutation1
LSM14BKIRPchr206070565260705652TCMissense_Mutationp.I247T1
LSM14BPRADchr206070143760701437CTSilentp.Y123Y1
LSM14BLIHCchr206070848160708481C-Frame_Shift_Delp.N374fs1
LSM14BGBMchr206070496160704961CTMissense_Mutation1
LSM14BKIRPchr206070497260704972GCMissense_Mutationp.G187R1
LSM14BSARCchr206070130960701309CTMissense_Mutation1
LSM14BLUADchr206070650460706504TAMissense_Mutationp.C310S1
LSM14BHNSCchr206070646860706468GAMissense_Mutation1
LSM14BSARCchr206070408360704083AGMissense_Mutation1
LSM14BESCAchr206070498660704986GASilentp.Q1911
LSM14BLUSCchr206070138160701381GTMissense_Mutationp.A105S1
LSM14BHNSCchr206070570360705703GAMissense_Mutation1
LSM14BKIRPchr206069775360697753GCMissense_Mutationp.G11R1
LSM14BTHYMchr206070838560708385CAMissense_Mutationp.N342K1
LSM14BESCAchr206070558460705584AGSplice_Sitee6-21
LSM14BLUSCchr206069968060699680CTSilentp.S45S1
LSM14BHNSCchr206070570360705703GAMissense_Mutationp.R264Q1
LSM14BBLCAchr206070490760704907CTMissense_Mutationp.S165F1
LSM14BCESCchr206070487260704872GASilentp.K153K1
LSM14BLGGchr206070138060701380CASilent1
LSM14BSKCMchr206070570260705702CTNonsense_Mutationp.R264X1
LSM14BUCECchr206070147960701479CTSilentp.A137A1
LSM14BHNSCchr206069774160697742-CFrame_Shift_Insp.P7fs1
LSM14BPAADchr206070570260705702CASilent1
LSM14BCESCchr206069784260697842CTSilentp.L401
LSM14BLIHCchr206070560360705603AGMissense_Mutation1
LSM14BBLCAchr206070566060705660GCMissense_Mutationp.E250Q1
LSM14BKIRCchr206070844960708449GAMissense_Mutationp.G364R1
LSM14BUCSchr206070144860701448CTMissense_Mutationp.A127V1
LSM14BCESCchr206070280460702804GCSilentp.L1971
LSM14BLIHCchr206070651260706512TCSilent1
LSM14BSKCMchr206070570260705702CTNonsense_Mutationp.R264*1
LSM14BESCAchr206070558460705584AGSplice_Site.1
LSM14BBLCAchr206069776160697761GCMissense_Mutationp.K13N1
LSM14BKIRCchr206070846060708460CASilentp.G367G1
LSM14BCOADchr206069971660699716GASilentp.A57A1
LSM14BLIHCchr206070642260706422TCSilentp.A282A1
LSM14BBLCAchr206070837160708371GCMissense_Mutation1
LSM14BESCAchr206070498660704986GASilentp.Q191Q1
LSM14BKIRCchr206070569260705692CGSilentp.A260A1
LSM14BCOADchr206070140160701401CTSilentp.H111H1

check buttonCopy number variation (CNV) of LSM14B
* 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 LSM14B
* 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
26954N/ABF919146BTNL9chr5180469231+LSM14Bchr2060709217+
26954N/AAW847911CKBchr14103988480+LSM14Bchr2060701377+
26956UCSTCGA-N9-A4PZEPHA2chr116474872-LSM14Bchr2060699672+
26956UCSTCGA-N9-A4PZ-01AEPHA2chr116474873-LSM14Bchr2060699673+
96696N/AAA886089LSM14Bchr2060710430+AGAP1chr2236782167-


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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
THCALSM14B0.0005620778201682220.016
ESCALSM14B0.01600760936962150.43
ACCLSM14B0.02295046815547020.6

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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
LUADLSM14B0.01342101809393070.38
THCALSM14B0.02733284189561310.74
SKCMLSM14B0.0008932000698474710.029
OVLSM14B0.0007740466106659920.026
CESCLSM14B0.001008096792069640.031
ESCALSM14B0.01272923649456640.37
MESOLSM14B0.0358992515642870.93
HNSCLSM14B0.003099925283515340.093

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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