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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 TRA2B

check button Gene summary
Gene informationGene symbol

TRA2B

Gene ID

6434

Gene nametransformer 2 beta homolog
SynonymsHtra2-beta|PPP1R156|SFRS10|SRFS10|TRA2-BETA|TRAN2B
Cytomap

3q27.2

Type of geneprotein-coding
Descriptiontransformer-2 protein homolog betaTRA-2 betaprotein phosphatase 1, regulatory subunit 156splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)transformer-2 protein homolog B
Modification date20180523
UniProtAcc

P62995

ContextPubMed: TRA2B [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
TRA2B

GO:0000381

regulation of alternative mRNA splicing, via spliceosome

12165565|12761049

TRA2B

GO:0000398

mRNA splicing, via spliceosome

9546399

TRA2B

GO:0048026

positive regulation of mRNA splicing, via spliceosome

15009664

TRA2B

GO:0051259

protein complex oligomerization

10749975


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Exon skipping events across known transcript of Ensembl for TRA2B 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 TRA2B

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 TRA2B

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3906813185635502:185635513:185636152:185636223:185637224:185637284185636152:185636223ENSG00000136527.13ENST00000414862.1
exon_skip_3906823185635502:185635513:185636152:185636226:185637224:185637284185636152:185636226ENSG00000136527.13ENST00000382191.4,ENST00000487615.1,ENST00000453386.2,ENST00000492417.1,ENST00000466832.1,ENST00000463328.1,ENST00000456380.1
exon_skip_3906833185636152:185636223:185637224:185637284:185638891:185638975185637224:185637284ENSG00000136527.13ENST00000414862.1
exon_skip_3906843185636152:185636226:185637224:185637284:185638891:185638969185637224:185637284ENSG00000136527.13ENST00000382191.4,ENST00000487615.1,ENST00000453386.2,ENST00000492417.1,ENST00000466832.1,ENST00000463328.1,ENST00000456380.1
exon_skip_3906873185637224:185637284:185638891:185638975:185639798:185639895185638891:185638975ENSG00000136527.13ENST00000382191.4,ENST00000487615.1,ENST00000453386.2,ENST00000492417.1,ENST00000414862.1,ENST00000466832.1,ENST00000463328.1,ENST00000456380.1
exon_skip_3906953185639830:185639914:185641583:185641772:185643251:185643414185641583:185641772ENSG00000136527.13ENST00000382191.4,ENST00000487615.1,ENST00000453386.2,ENST00000492417.1,ENST00000456380.1
exon_skip_3906973185639830:185639914:185641583:185641796:185643251:185643414185641583:185641796ENSG00000136527.13ENST00000465245.1
exon_skip_3907013185641583:185641772:185643251:185643414:185655612:185655775185643251:185643414ENSG00000136527.13ENST00000382191.4
exon_skip_3907083185643251:185643414:185644388:185644522:185649364:185649406185644388:185644522ENSG00000136527.13ENST00000487615.1,ENST00000477939.1,ENST00000456380.1
exon_skip_3907093185643251:185643414:185644388:185644522:185655612:185655775185644388:185644522ENSG00000136527.13ENST00000485530.1
exon_skip_3907183185644514:185644522:185649364:185649640:185655612:185655775185649364:185649640ENSG00000136527.13ENST00000456380.1

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

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Exon skipping events with PSIs in GTEx for TRA2B

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3906813185635502:185635513:185636152:185636223:185637224:185637284185636152:185636223ENSG00000136527.13ENST00000414862.1
exon_skip_3906823185635502:185635513:185636152:185636226:185637224:185637284185636152:185636226ENSG00000136527.13ENST00000453386.2,ENST00000492417.1,ENST00000463328.1,ENST00000466832.1,ENST00000487615.1,ENST00000456380.1,ENST00000382191.4
exon_skip_3906833185636152:185636223:185637224:185637284:185638891:185638975185637224:185637284ENSG00000136527.13ENST00000414862.1
exon_skip_3906843185636152:185636226:185637224:185637284:185638891:185638969185637224:185637284ENSG00000136527.13ENST00000453386.2,ENST00000492417.1,ENST00000463328.1,ENST00000466832.1,ENST00000487615.1,ENST00000456380.1,ENST00000382191.4
exon_skip_3906873185637224:185637284:185638891:185638975:185639798:185639895185638891:185638975ENSG00000136527.13ENST00000453386.2,ENST00000492417.1,ENST00000463328.1,ENST00000414862.1,ENST00000466832.1,ENST00000487615.1,ENST00000456380.1,ENST00000382191.4
exon_skip_3906953185639830:185639914:185641583:185641772:185643251:185643414185641583:185641772ENSG00000136527.13ENST00000453386.2,ENST00000492417.1,ENST00000487615.1,ENST00000456380.1,ENST00000382191.4
exon_skip_3906973185639830:185639914:185641583:185641796:185643251:185643414185641583:185641796ENSG00000136527.13ENST00000465245.1
exon_skip_3907013185641583:185641772:185643251:185643414:185655612:185655775185643251:185643414ENSG00000136527.13ENST00000382191.4
exon_skip_3907083185643251:185643414:185644388:185644522:185649364:185649406185644388:185644522ENSG00000136527.13ENST00000487615.1,ENST00000456380.1,ENST00000477939.1
exon_skip_3907093185643251:185643414:185644388:185644522:185655612:185655775185644388:185644522ENSG00000136527.13ENST00000485530.1
exon_skip_3907183185644514:185644522:185649364:185649640:185655612:185655775185649364:185649640ENSG00000136527.13ENST00000456380.1
exon_skip_3907213185649541:185649640:185652216:185652293:185654025:185654388185652216:185652293ENSG00000136527.13ENST00000471134.1

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 TRA2B

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
ENST00000453386185636152185636226Frame-shift
ENST00000453386185637224185637284In-frame
ENST00000453386185638891185638975In-frame
ENST00000453386185641583185641772In-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
ENST00000453386185636152185636226Frame-shift
ENST00000453386185637224185637284In-frame
ENST00000453386185638891185638975In-frame
ENST00000453386185641583185641772In-frame

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Infer the effects of exon skipping event on protein functional features for TRA2B

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
ENST000004533862969288185641583185641772610798111174
ENST000004533862969288185638891185638975915998213240
ENST0000045338629692881856372241856372849991058241260

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
ENST000004533862969288185641583185641772610798111174
ENST000004533862969288185638891185638975915998213240
ENST0000045338629692881856372241856372849991058241260

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
P6299511117439288Alternative sequenceID=VSP_005899;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9212162;Dbxref=PMID:9212162
P62995111174120124Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P62995111174144151Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P62995111174153168Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P629951111742288ChainID=PRO_0000081983;Note=Transformer-2 protein homolog beta
P6299511117431113Compositional biasNote=Arg/Ser-rich (RS1 domain)
P62995111174118196DomainNote=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176
P62995111174116118HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P62995111174131139HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P62995111174169179HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P6299521324039288Alternative sequenceID=VSP_005899;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9212162;Dbxref=PMID:9212162
P629952132402288ChainID=PRO_0000081983;Note=Transformer-2 protein homolog beta
P62995213240231287Compositional biasNote=Arg/Ser-rich (RS2 domain)
P62995213240215215Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
P62995213240237237Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
P62995213240193230RegionNote=Linker
P6299524126039288Alternative sequenceID=VSP_005899;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9212162;Dbxref=PMID:9212162
P629952412602288ChainID=PRO_0000081983;Note=Transformer-2 protein homolog beta
P62995241260231287Compositional biasNote=Arg/Ser-rich (RS2 domain)
P62995241260241241Modified residueNote=Asymmetric dimethylarginine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315
P62995241260241241Modified residueNote=Dimethylated arginine%3B alternate;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:15782174,ECO:0000269|Ref.7;Dbxref=PMID:15782174
P62995241260241241Modified residueNote=Omega-N-methylarginine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315


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
P6299511117439288Alternative sequenceID=VSP_005899;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9212162;Dbxref=PMID:9212162
P62995111174120124Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P62995111174144151Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P62995111174153168Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P629951111742288ChainID=PRO_0000081983;Note=Transformer-2 protein homolog beta
P6299511117431113Compositional biasNote=Arg/Ser-rich (RS1 domain)
P62995111174118196DomainNote=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176
P62995111174116118HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P62995111174131139HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P62995111174169179HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CQC
P6299521324039288Alternative sequenceID=VSP_005899;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9212162;Dbxref=PMID:9212162
P629952132402288ChainID=PRO_0000081983;Note=Transformer-2 protein homolog beta
P62995213240231287Compositional biasNote=Arg/Ser-rich (RS2 domain)
P62995213240215215Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
P62995213240237237Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
P62995213240193230RegionNote=Linker
P6299524126039288Alternative sequenceID=VSP_005899;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9212162;Dbxref=PMID:9212162
P629952412602288ChainID=PRO_0000081983;Note=Transformer-2 protein homolog beta
P62995241260231287Compositional biasNote=Arg/Ser-rich (RS2 domain)
P62995241260241241Modified residueNote=Asymmetric dimethylarginine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315
P62995241260241241Modified residueNote=Dimethylated arginine%3B alternate;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:15782174,ECO:0000269|Ref.7;Dbxref=PMID:15782174
P62995241260241241Modified residueNote=Omega-N-methylarginine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315


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SNVs in the skipped exons for TRA2B

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.
TRA2B_BRCA_exon_skip_390695_psi_boxplot.png
boxplot
TRA2B_LIHC_exon_skip_390695_psi_boxplot.png
boxplot
TRA2B_OV_exon_skip_390695_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
OVTCGA-24-1422-01exon_skip_390695
185641584185641772185641608185641608Frame_Shift_DelA-p.F166fs
OVTCGA-24-1422-01exon_skip_390697
185641584185641796185641608185641608Frame_Shift_DelA-p.F166fs
LIHCTCGA-DD-A39Y-01exon_skip_390695
185641584185641772185641759185641759Frame_Shift_DelG-p.P116fs
LIHCTCGA-DD-A39Y-01exon_skip_390697
185641584185641796185641759185641759Frame_Shift_DelG-p.P116fs
LIHCTCGA-DD-A1EG-01exon_skip_390708
exon_skip_390709
185644389185644522185644458185644458Frame_Shift_DelG-p.P34fs
LIHCTCGA-DD-A3A0-01exon_skip_390708
exon_skip_390709
185644389185644522185644475185644475Frame_Shift_DelT-p.K28fs
UCECTCGA-D1-A17B-01exon_skip_390683
exon_skip_390684
185637225185637284185637275185637276Frame_Shift_Ins-Tp.G244fs
BRCATCGA-AO-A03O-01exon_skip_390695
185641584185641772185641773185641773Splice_SiteCGe4-1

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
TRA2B_185639830_185639914_185641583_185641796_185643251_185643414_TCGA-24-1422-01Sample: TCGA-24-1422-01
Cancer type: OV
ESID: exon_skip_390695
Skipped exon start: 185641584
Skipped exon end: 185641772
Mutation start: 185641608
Mutation end: 185641608
Mutation type: Frame_Shift_Del
Reference seq: A
Mutation seq: -
AAchange: p.F166fs
TRA2B_185639830_185639914_185641583_185641796_185643251_185643414_TCGA-24-1422-01Sample: TCGA-24-1422-01
Cancer type: OV
ESID: exon_skip_390697
Skipped exon start: 185641584
Skipped exon end: 185641796
Mutation start: 185641608
Mutation end: 185641608
Mutation type: Frame_Shift_Del
Reference seq: A
Mutation seq: -
AAchange: p.F166fs
exon_skip_390697_OV_TCGA-24-1422-01.png
boxplot
TRA2B_185639830_185639914_185641583_185641772_185643251_185643414_TCGA-AO-A03O-01Sample: TCGA-AO-A03O-01
Cancer type: BRCA
ESID: exon_skip_390695
Skipped exon start: 185641584
Skipped exon end: 185641772
Mutation start: 185641773
Mutation end: 185641773
Mutation type: Splice_Site
Reference seq: C
Mutation seq: G
AAchange: e4-1
exon_skip_361771_BRCA_TCGA-AO-A03O-01.png
boxplot
exon_skip_390695_BRCA_TCGA-AO-A03O-01.png
boxplot
TRA2B_185639830_185639914_185641583_185641772_185643251_185643414_TCGA-24-1422-01Sample: TCGA-24-1422-01
Cancer type: OV
ESID: exon_skip_390695
Skipped exon start: 185641584
Skipped exon end: 185641772
Mutation start: 185641608
Mutation end: 185641608
Mutation type: Frame_Shift_Del
Reference seq: A
Mutation seq: -
AAchange: p.F166fs
TRA2B_185639830_185639914_185641583_185641772_185643251_185643414_TCGA-24-1422-01Sample: TCGA-24-1422-01
Cancer type: OV
ESID: exon_skip_390697
Skipped exon start: 185641584
Skipped exon end: 185641796
Mutation start: 185641608
Mutation end: 185641608
Mutation type: Frame_Shift_Del
Reference seq: A
Mutation seq: -
AAchange: p.F166fs
exon_skip_390697_OV_TCGA-24-1422-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
UMUC3_URINARY_TRACT185638892185638975185638965185638965Frame_Shift_DelG-p.R219fs
CP67MEL_SKIN185643252185643414185643352185643353In_Frame_Ins-GGGAGCp.77_78insRS
SLR26_KIDNEY185643252185643414185643352185643353In_Frame_Ins-GGGAGCp.77_78insRS
KYSE180_OESOPHAGUS185636153185636226185636180185636180Missense_MutationGAp.R277C
KYSE180_OESOPHAGUS185636153185636223185636180185636180Missense_MutationGAp.R277C
NCIH1944_LUNG185636153185636226185636210185636210Missense_MutationGAp.P267S
NCIH1944_LUNG185636153185636223185636210185636210Missense_MutationGAp.P267S
SNU175_LARGE_INTESTINE185636153185636226185636222185636222Missense_MutationGAp.R263W
SNU175_LARGE_INTESTINE185636153185636223185636222185636222Missense_MutationGAp.R263W
HA7EBV_MATCHED_NORMAL_TISSUE185636153185636226185636222185636222Missense_MutationGAp.R263W
HA7EBV_MATCHED_NORMAL_TISSUE185636153185636223185636222185636222Missense_MutationGAp.R263W
HO1N1_UPPER_AERODIGESTIVE_TRACT185637225185637284185637238185637238Missense_MutationCTp.D257N
LU165_LUNG185638892185638975185638901185638901Missense_MutationCAp.R238I
MM415_SKIN185638892185638975185638932185638932Missense_MutationGAp.R228W
PEDS005TPFAD_KIDNEY185638892185638975185638935185638935Missense_MutationCAp.D227Y
ISTMES2_PLEURA185641584185641772185641637185641637Missense_MutationGTp.R157S
ISTMES2_PLEURA185641584185641796185641637185641637Missense_MutationGTp.R157S
SNU1040_LARGE_INTESTINE185641584185641772185641660185641660Missense_MutationAGp.I149T
SNU1040_LARGE_INTESTINE185641584185641796185641660185641660Missense_MutationAGp.I149T
HT115_LARGE_INTESTINE185641584185641772185641670185641670Missense_MutationCTp.D146N
HT115_LARGE_INTESTINE185641584185641796185641670185641670Missense_MutationCTp.D146N
HEC251_ENDOMETRIUM185641584185641772185641692185641692Missense_MutationGTp.F138L
HEC251_ENDOMETRIUM185641584185641796185641692185641692Missense_MutationGTp.F138L
HEC251_ENDOMETRIUM185643252185643414185643359185643359Missense_MutationGAp.R76C
KYSE140_OESOPHAGUS185643252185643414185643394185643394Missense_MutationGAp.S64F
SNU1040_LARGE_INTESTINE185644389185644522185644518185644518Missense_MutationGAp.S14F
CORL279_LUNG185638892185638975185638892185638892Splice_SiteCGp.R241T

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TRA2B

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 TRA2B


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TRA2B


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RelatedDrugs for TRA2B

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 TRA2B

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