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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 MR1

check button Gene summary
Gene informationGene symbol

MR1

Gene ID

3140

Gene namemajor histocompatibility complex, class I-related
SynonymsHLALS
Cytomap

1q25.3

Type of geneprotein-coding
Descriptionmajor histocompatibility complex class I-related gene proteinMHC class I-like antigen MR-1MHC class-I related-gene proteinmajor histocompatibility complex, class I-like sequence
Modification date20180523
UniProtAcc

Q95460

ContextPubMed: MR1 [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 MR1 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 MR1

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 MR1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_145561181003157:181003210:181006132:181006248:181018187:181018368181006132:181006248ENSG00000153029.10ENST00000438435.2
exon_skip_145581181003157:181003210:181018187:181018448:181019146:181019422181018187:181018448ENSG00000153029.10ENST00000367578.1,ENST00000282990.6,ENST00000367580.5
exon_skip_145641181019281:181019422:181021370:181021646:181022708:181022813181021370:181021646ENSG00000153029.10ENST00000367579.3,ENST00000367580.5
exon_skip_145661181019281:181019422:181022708:181022813:181024360:181024420181022708:181022813ENSG00000153029.10ENST00000438435.2,ENST00000282990.6

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

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Exon skipping events with PSIs in GTEx for MR1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_145561181003157:181003210:181006132:181006248:181018187:181018368181006132:181006248ENSG00000153029.10ENST00000438435.2
exon_skip_145581181003157:181003210:181018187:181018448:181019146:181019422181018187:181018448ENSG00000153029.10ENST00000282990.6,ENST00000367580.5,ENST00000367578.1
exon_skip_145641181019281:181019422:181021370:181021646:181022708:181022813181021370:181021646ENSG00000153029.10ENST00000367579.3,ENST00000367580.5
exon_skip_145661181019281:181019422:181022708:181022813:181024360:181024420181022708:181022813ENSG00000153029.10ENST00000282990.6,ENST00000438435.2

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 MR1

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
ENST00000367580181018187181018448In-frame
ENST00000367580181021370181021646In-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
ENST00000367580181018187181018448In-frame
ENST00000367580181021370181021646In-frame

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Infer the effects of exon skipping event on protein functional features for MR1

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
ENST0000036758077213411810181871810184487333322109
ENST000003675807721341181021370181021646610885201293

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
ENST0000036758077213411810181871810184487333322109
ENST000003675807721341181021370181021646610885201293

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


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


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SNVs in the skipped exons for MR1

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.
MR1_BRCA_exon_skip_14564_psi_boxplot.png
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MR1_HNSC_exon_skip_14564_psi_boxplot.png
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MR1_LIHC_exon_skip_14564_psi_boxplot.png
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check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-G3-A3CJ-01exon_skip_14564
181021371181021646181021373181021373Frame_Shift_DelC-p.P204fs
LIHCTCGA-DD-A3A0-01exon_skip_14564
181021371181021646181021412181021412Frame_Shift_DelG-p.G216fs
HNSCTCGA-CR-7390-01exon_skip_14564
181021371181021646181021478181021478Frame_Shift_DelA-p.K238fs
BRCATCGA-A2-A0EO-01exon_skip_14564
181021371181021646181021547181021547Nonsense_MutationCTp.Q261*
SKCMTCGA-FS-A1ZA-06exon_skip_14566
181022709181022813181022797181022797Nonsense_MutationGAp.W323*
SKCMTCGA-FS-A1ZA-06exon_skip_14566
181022709181022813181022797181022797Nonsense_MutationGAp.W323X

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
MR1_181019281_181019422_181021370_181021646_181022708_181022813_TCGA-A2-A0EO-01Sample: TCGA-A2-A0EO-01
Cancer type: BRCA
ESID: exon_skip_14564
Skipped exon start: 181021371
Skipped exon end: 181021646
Mutation start: 181021547
Mutation end: 181021547
Mutation type: Nonsense_Mutation
Reference seq: C
Mutation seq: T
AAchange: p.Q261*
exon_skip_14564_BRCA_TCGA-A2-A0EO-01.png
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MR1_181019281_181019422_181021370_181021646_181022708_181022813_TCGA-CR-7390-01Sample: TCGA-CR-7390-01
Cancer type: HNSC
ESID: exon_skip_14564
Skipped exon start: 181021371
Skipped exon end: 181021646
Mutation start: 181021478
Mutation end: 181021478
Mutation type: Frame_Shift_Del
Reference seq: A
Mutation seq: -
AAchange: p.K238fs
exon_skip_11029_HNSC_TCGA-CR-7390-01.png
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exon_skip_14564_HNSC_TCGA-CR-7390-01.png
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exon_skip_434739_HNSC_TCGA-CR-7390-01.png
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MR1_181019281_181019422_181021370_181021646_181022708_181022813_TCGA-G3-A3CJ-01Sample: TCGA-G3-A3CJ-01
Cancer type: LIHC
ESID: exon_skip_14564
Skipped exon start: 181021371
Skipped exon end: 181021646
Mutation start: 181021373
Mutation end: 181021373
Mutation type: Frame_Shift_Del
Reference seq: C
Mutation seq: -
AAchange: p.P204fs
exon_skip_101516_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_106378_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_106524_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_109529_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_109778_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_11286_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_11289_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_11349_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_113894_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_113898_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_11611_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_11638_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_1274_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_129795_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_129799_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_131401_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_135545_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_13626_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_138676_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_141657_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_143515_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_143728_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_14564_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_149490_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_153354_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_1873_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_1874_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_24442_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_284510_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_289275_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_291218_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_293221_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_300058_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_300676_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_302253_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_309404_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_309486_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_309505_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_309539_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_311823_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_313290_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_315285_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_315286_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_316122_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_325693_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_329666_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_329933_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_331517_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_354387_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_354396_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_356468_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_365019_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_365023_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_371589_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_375393_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_380574_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_382000_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_382738_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_385031_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_387684_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_421130_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_421134_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_426528_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_427391_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_433655_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_436327_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_436618_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_444593_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_445559_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_447600_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_452739_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_4535_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_464169_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_470485_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_478117_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_483618_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_483622_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_492152_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_499409_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_59476_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_67293_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_67402_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_69019_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_71100_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_73796_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_84528_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_86050_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_86051_LIHC_TCGA-G3-A3CJ-01.png
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exon_skip_86135_LIHC_TCGA-G3-A3CJ-01.png
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check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
DMS273_LUNG181018188181018448181018190181018190Missense_MutationATp.T24S
M1203273_SKIN181018188181018448181018211181018211Missense_MutationCTp.R31C
HT115_LARGE_INTESTINE181018188181018448181018224181018224Missense_MutationCTp.S35L
CAL148_BREAST181018188181018448181018229181018229Missense_MutationCTp.P37S
CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE181018188181018448181018235181018235Missense_MutationCAp.H39N
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE181018188181018448181018268181018268Missense_MutationGAp.V50M
KP2_PANCREAS181018188181018448181018275181018275Missense_MutationCTp.S52L
LNCAPCLONEFGC_PROSTATE181018188181018448181018293181018293Missense_MutationAGp.Y58C
TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE181018188181018448181018318181018318Missense_MutationGTp.E66D
DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE181018188181018448181018322181018322Missense_MutationCTp.R68W
8MGBA_CENTRAL_NERVOUS_SYSTEM181018188181018448181018440181018440Missense_MutationAGp.N107S
FTC238_THYROID181021371181021646181021395181021395Missense_MutationGAp.R210H
NB14_AUTONOMIC_GANGLIA181021371181021646181021419181021419Missense_MutationCTp.T218I
RERFLCFM_LUNG181021371181021646181021474181021474Missense_MutationGCp.W236C
HOP62_LUNG181021371181021646181021554181021554Missense_MutationGTp.W263L
BT474_BREAST181021371181021646181021579181021579Missense_MutationGCp.Q271H
HEC251_ENDOMETRIUM181022709181022813181022716181022716Missense_MutationACp.E296D
HMC18_BREAST181022709181022813181022811181022811Missense_MutationGAp.R328Q
HEC251_ENDOMETRIUM181021371181021646181021490181021490Nonsense_MutationGTp.E242*
DOV13_OVARY181022709181022813181022813181022813Splice_SiteGTp.E329*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MR1

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 MR1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MR1


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RelatedDrugs for MR1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
Q95460DB00098Antithymocyte immunoglobulin (rabbit)Major histocompatibility complex class I-related gene proteinbiotechapproved

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RelatedDiseases for MR1

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