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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for TARBP1

check button Gene summary
Gene informationGene symbol

TARBP1

Gene ID

6894

Gene nameTAR (HIV-1) RNA binding protein 1
SynonymsTRM3|TRMT3|TRP-185|TRP185
Cytomap

1q42.2

Type of geneprotein-coding
Descriptionprobable methyltransferase TARBP1TAR (HIV) RNA-binding protein 1TAR RNA loop binding proteinTAR RNA-binding protein 1TAR RNA-binding protein of 185 kDatRNA methyltransferase 3 homolog
Modification date20180523
UniProtAcc

Q13395

ContextPubMed: TARBP1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID

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Exon skipping events across known transcript of Ensembl for TARBP1 from UCSC genome browser

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.
all structure

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Gene isoform structures and expression levels for TARBP1

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for TARBP1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_381641234527343:234527491:234528161:234528298:234529107:234529222234528161:234528298ENSG00000059588.5ENST00000462259.1,ENST00000040877.1,ENST00000483404.1
exon_skip_381651234527343:234527491:234528161:234528298:234529391:234529583234528161:234528298ENSG00000059588.5ENST00000496673.1
exon_skip_381711234528161:234528298:234529107:234529222:234529391:234529583234529107:234529222ENSG00000059588.5ENST00000483404.1
exon_skip_381721234528161:234528298:234529107:234529232:234529391:234529583234529107:234529232ENSG00000059588.5ENST00000462259.1,ENST00000040877.1
exon_skip_381741234529391:234529583:234534127:234534299:234536598:234536648234534127:234534299ENSG00000059588.5ENST00000462259.1
exon_skip_381751234529391:234529583:234534127:234534299:234536926:234536962234534127:234534299ENSG00000059588.5ENST00000496673.1,ENST00000040877.1
exon_skip_381771234529391:234529583:234536598:234536694:234536926:234536962234536598:234536694ENSG00000059588.5ENST00000483404.1
exon_skip_381811234534127:234534299:234536598:234536694:234536926:234536962234536598:234536694ENSG00000059588.5ENST00000462259.1
exon_skip_381831234536926:234537008:234541057:234541226:234541648:234541739234541057:234541226ENSG00000059588.5ENST00000468077.1
exon_skip_381881234536926:234537008:234541648:234541845:234546190:234546277234541648:234541845ENSG00000059588.5ENST00000481183.1,ENST00000040877.1
exon_skip_382001234541648:234541845:234546190:234546277:234553829:234553979234546190:234546277ENSG00000059588.5ENST00000040877.1
exon_skip_382041234546190:234546277:234553829:234553979:234556447:234556558234553829:234553979ENSG00000059588.5ENST00000040877.1,ENST00000463793.1
exon_skip_382061234561418:234561539:234563062:234563134:234563321:234563512234563062:234563134ENSG00000059588.5ENST00000040877.1
exon_skip_382071234563321:234563512:234564881:234565070:234565161:234565423234564881:234565070ENSG00000059588.5ENST00000040877.1
exon_skip_382091234565832:234566047:234569155:234569317:234573020:234573118234569155:234569317ENSG00000059588.5ENST00000040877.1
exon_skip_382121234569155:234569317:234573020:234573118:234582548:234582721234573020:234573118ENSG00000059588.5ENST00000040877.1
exon_skip_382151234582548:234582721:234584225:234584325:234586173:234586312234584225:234584325ENSG00000059588.5ENST00000040877.1
exon_skip_382181234586173:234586312:234593412:234593502:234594975:234595072234593412:234593502ENSG00000059588.5ENST00000040877.1
exon_skip_382201234593412:234593502:234594975:234595072:234596006:234596142234594975:234595072ENSG00000059588.5ENST00000040877.1
exon_skip_382221234596006:234596142:234599582:234599680:234601401:234601454234599582:234599680ENSG00000059588.5ENST00000040877.1

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for TARBP1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_381641234527343:234527491:234528161:234528298:234529107:234529222234528161:234528298ENSG00000059588.5ENST00000040877.1,ENST00000483404.1,ENST00000462259.1
exon_skip_381651234527343:234527491:234528161:234528298:234529391:234529583234528161:234528298ENSG00000059588.5ENST00000496673.1
exon_skip_381711234528161:234528298:234529107:234529222:234529391:234529583234529107:234529222ENSG00000059588.5ENST00000483404.1
exon_skip_381721234528161:234528298:234529107:234529232:234529391:234529583234529107:234529232ENSG00000059588.5ENST00000040877.1,ENST00000462259.1
exon_skip_381741234529391:234529583:234534127:234534299:234536598:234536648234534127:234534299ENSG00000059588.5ENST00000462259.1
exon_skip_381751234529391:234529583:234534127:234534299:234536926:234536962234534127:234534299ENSG00000059588.5ENST00000040877.1,ENST00000496673.1
exon_skip_381771234529391:234529583:234536598:234536694:234536926:234536962234536598:234536694ENSG00000059588.5ENST00000483404.1
exon_skip_381811234534127:234534299:234536598:234536694:234536926:234536962234536598:234536694ENSG00000059588.5ENST00000462259.1
exon_skip_381831234536926:234537008:234541057:234541226:234541648:234541739234541057:234541226ENSG00000059588.5ENST00000468077.1
exon_skip_381881234536926:234537008:234541648:234541845:234546190:234546277234541648:234541845ENSG00000059588.5ENST00000040877.1,ENST00000481183.1
exon_skip_382001234541648:234541845:234546190:234546277:234553829:234553979234546190:234546277ENSG00000059588.5ENST00000040877.1
exon_skip_382041234546190:234546277:234553829:234553979:234556447:234556558234553829:234553979ENSG00000059588.5ENST00000040877.1,ENST00000463793.1
exon_skip_382061234561418:234561539:234563062:234563134:234563321:234563512234563062:234563134ENSG00000059588.5ENST00000040877.1
exon_skip_382071234563321:234563512:234564881:234565070:234565161:234565423234564881:234565070ENSG00000059588.5ENST00000040877.1
exon_skip_382091234565832:234566047:234569155:234569317:234573020:234573118234569155:234569317ENSG00000059588.5ENST00000040877.1
exon_skip_382121234569155:234569317:234573020:234573118:234582548:234582721234573020:234573118ENSG00000059588.5ENST00000040877.1
exon_skip_382151234582548:234582721:234584225:234584325:234586173:234586312234584225:234584325ENSG00000059588.5ENST00000040877.1
exon_skip_382181234586173:234586312:234593412:234593502:234594975:234595072234593412:234593502ENSG00000059588.5ENST00000040877.1
exon_skip_382201234593412:234593502:234594975:234595072:234596006:234596142234594975:234595072ENSG00000059588.5ENST00000040877.1
exon_skip_382221234596006:234596142:234599582:234599680:234601401:234601454234599582:234599680ENSG00000059588.5ENST00000040877.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for TARBP1

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000040877234528161234528298Frame-shift
ENST00000040877234529107234529232Frame-shift
ENST00000040877234534127234534299Frame-shift
ENST00000040877234541648234541845Frame-shift
ENST00000040877234573020234573118Frame-shift
ENST00000040877234584225234584325Frame-shift
ENST00000040877234594975234595072Frame-shift
ENST00000040877234599582234599680Frame-shift
ENST00000040877234546190234546277In-frame
ENST00000040877234553829234553979In-frame
ENST00000040877234563062234563134In-frame
ENST00000040877234564881234565070In-frame
ENST00000040877234569155234569317In-frame
ENST00000040877234593412234593502In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000040877234528161234528298Frame-shift
ENST00000040877234529107234529232Frame-shift
ENST00000040877234534127234534299Frame-shift
ENST00000040877234541648234541845Frame-shift
ENST00000040877234573020234573118Frame-shift
ENST00000040877234584225234584325Frame-shift
ENST00000040877234594975234595072Frame-shift
ENST00000040877234599582234599680Frame-shift
ENST00000040877234546190234546277In-frame
ENST00000040877234553829234553979In-frame
ENST00000040877234563062234563134In-frame
ENST00000040877234564881234565070In-frame
ENST00000040877234569155234569317In-frame
ENST00000040877234593412234593502In-frame

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Infer the effects of exon skipping event on protein functional features for TARBP1

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000000408775147162123459341223459350216331722544574
ENST000000408775147162123456915523456931722332394744798
ENST0000004087751471621234564881234565070287230609571020
ENST00000040877514716212345630622345631343252332310841107
ENST00000040877514716212345538292345539793556370511851235
ENST00000040877514716212345461902345462773706379212351264

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000000408775147162123459341223459350216331722544574
ENST000000408775147162123456915523456931722332394744798
ENST0000004087751471621234564881234565070287230609571020
ENST00000040877514716212345630622345631343252332310841107
ENST00000040877514716212345538292345539793556370511851235
ENST00000040877514716212345461902345462773706379212351264

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q1339554457411621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q1339574479811621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q13395957102011621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q133959571020997997Natural variantID=VAR_030106;Note=F->L;Dbxref=dbSNP:rs12135427
Q133951084110711621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q133951185123511621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q133951235126411621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q1339554457411621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q1339574479811621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q13395957102011621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q133959571020997997Natural variantID=VAR_030106;Note=F->L;Dbxref=dbSNP:rs12135427
Q133951084110711621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q133951185123511621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1
Q133951235126411621ChainID=PRO_0000273201;Note=Probable methyltransferase TARBP1


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SNVs in the skipped exons for TARBP1

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A3A0-01exon_skip_38164
exon_skip_38165
234528162234528298234528214234528214Frame_Shift_DelT-p.S1549fs
LIHCTCGA-G3-A3CJ-01exon_skip_38204
234553830234553979234553860234553860Frame_Shift_DelA-p.F1225fs
LIHCTCGA-G3-A3CJ-01exon_skip_38209
234569156234569317234569292234569292Frame_Shift_DelA-p.L753fs
KIRPTCGA-WN-A9G9-01exon_skip_38188
234541649234541845234541785234541786Frame_Shift_Ins-AAp.S1285fs
LUADTCGA-55-6712-01exon_skip_38171
234529108234529222234529176234529176Nonsense_MutationGAp.Q1498*
LUADTCGA-55-6712-01exon_skip_38172
234529108234529232234529176234529176Nonsense_MutationGAp.Q1498*
STADTCGA-BR-4368-01exon_skip_38188
234541649234541845234541716234541716Nonsense_MutationCAp.E1308*
LUADTCGA-MP-A4TH-01exon_skip_38188
234541649234541845234541755234541755Nonsense_MutationTAp.K1295*
BLCATCGA-4Z-AA83-01exon_skip_38188
234541649234541845234541779234541779Nonsense_MutationGAp.R1287*
SKCMTCGA-FS-A1ZB-06exon_skip_38188
234541649234541845234541779234541779Nonsense_MutationGAp.R1287*
SKCMTCGA-FS-A1ZB-06exon_skip_38188
234541649234541845234541779234541779Nonsense_MutationGAp.R1287X
HNSCTCGA-CR-6472-01exon_skip_38200
234546191234546277234546228234546228Nonsense_MutationGCp.S1252*
SKCMTCGA-FS-A4F0-06exon_skip_38207
234564882234565070234564992234564992Nonsense_MutationGAp.Q984*
SKCMTCGA-FS-A4F0-06exon_skip_38207
234564882234565070234564992234564992Nonsense_MutationGAp.Q984X
CHOLTCGA-3X-AAV9-01exon_skip_38209
234569156234569317234569297234569297Nonsense_MutationGTp.C751X
SKCMTCGA-D3-A3MR-06exon_skip_38174
exon_skip_38175
234534128234534299234534127234534127Splice_SiteCT.
BRCATCGA-B6-A0RT-01exon_skip_38207
234564882234565070234565071234565071Splice_SiteCAe17-1

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
TARBP1_234529391_234529583_234534127_234534299_234536926_234536962_TCGA-D3-A3MR-06Sample: TCGA-D3-A3MR-06
Cancer type: SKCM
ESID: exon_skip_38175
Skipped exon start: 234534128
Skipped exon end: 234534299
Mutation start: 234534127
Mutation end: 234534127
Mutation type: Splice_Site
Reference seq: C
Mutation seq: T
AAchange: .
exon_skip_13419_SKCM_TCGA-D3-A3MR-06.png
boxplot
exon_skip_346500_SKCM_TCGA-D3-A3MR-06.png
boxplot
exon_skip_352716_SKCM_TCGA-D3-A3MR-06.png
boxplot
exon_skip_38175_SKCM_TCGA-D3-A3MR-06.png
boxplot
exon_skip_477214_SKCM_TCGA-D3-A3MR-06.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
CFPAC1_PANCREAS234541649234541845234541677234541678In_Frame_Ins-GAGGCTp.1319_1320insLS
OC316_OVARY234529108234529232234529143234529143Missense_MutationTCp.S1509G
OC316_OVARY234529108234529222234529143234529143Missense_MutationTCp.S1509G
OC314_OVARY234529108234529232234529143234529143Missense_MutationTCp.S1509G
OC314_OVARY234529108234529222234529143234529143Missense_MutationTCp.S1509G
MELJUSO_SKIN234529108234529232234529152234529152Missense_MutationGTp.Q1506K
MELJUSO_SKIN234529108234529222234529152234529152Missense_MutationGTp.Q1506K
SNUC2A_LARGE_INTESTINE234534128234534299234534170234534170Missense_MutationGAp.L1401F
LU139_LUNG234534128234534299234534170234534170Missense_MutationGAp.L1401F
SNUC2B_LARGE_INTESTINE234534128234534299234534170234534170Missense_MutationGAp.L1401F
RERFLCFM_LUNG234534128234534299234534296234534296Missense_MutationTCp.I1359V
H4_CENTRAL_NERVOUS_SYSTEM234564882234565070234564915234564915Missense_MutationTGp.K1009N
HCC1937_MATCHED_NORMAL_TISSUE234569156234569317234569230234569230Missense_MutationTGp.N774H
MCAS_OVARY234573021234573118234573024234573024Missense_MutationACp.N743K
SNU175_LARGE_INTESTINE234573021234573118234573070234573070Missense_MutationCAp.S728I
NCIH2172_LUNG234593413234593502234593456234593456Missense_MutationCTp.R560K
MFE319_ENDOMETRIUM234594976234595072234595014234595014Missense_MutationAGp.C532R
CALU6_LUNG234541649234541845234541779234541779Nonsense_MutationGAp.R1287*
SNU81_LARGE_INTESTINE234599583234599680234599592234599592Nonsense_MutationCAp.E464*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TARBP1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TARBP1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TARBP1


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RelatedDrugs for TARBP1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for TARBP1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource