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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 ITGB1

check button Gene summary
Gene informationGene symbol

ITGB1

Gene ID

3688

Gene nameintegrin subunit beta 1
SynonymsCD29|FNRB|GPIIA|MDF2|MSK12|VLA-BETA|VLAB
Cytomap

10p11.22

Type of geneprotein-coding
Descriptionintegrin beta-1glycoprotein IIaintegrin VLA-4 beta subunitintegrin beta 1integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)very late activation protein, beta polypeptide
Modification date20180523
UniProtAcc

P05556

ContextPubMed: ITGB1 [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
ITGB1

GO:0007159

leukocyte cell-cell adhesion

1715889

ITGB1

GO:0010710

regulation of collagen catabolic process

10455171

ITGB1

GO:0033627

cell adhesion mediated by integrin

12807887|17158881

ITGB1

GO:0051897

positive regulation of protein kinase B signaling

24044949

ITGB1

GO:1903078

positive regulation of protein localization to plasma membrane

10455171

ITGB1

GO:2000273

positive regulation of signaling receptor activity

24044949


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Exon skipping events across known transcript of Ensembl for ITGB1 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 ITGB1

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 ITGB1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_486211033190491:33190563:33195392:33195508:33197295:3319743133195392:33195508ENSG00000150093.14ENST00000374956.4
exon_skip_486221033190491:33190563:33195990:33196071:33197295:3319743133195990:33196071ENSG00000150093.14ENST00000423113.1,ENST00000488427.1
exon_skip_486271033197295:33197462:33199150:33199383:33200375:3320059833199150:33199383ENSG00000150093.14ENST00000423113.1,ENST00000374956.4,ENST00000302278.3,ENST00000396033.2
exon_skip_486291033200454:33200598:33200813:33201052:33208812:3320901233200813:33201052ENSG00000150093.14ENST00000423113.1,ENST00000374956.4,ENST00000302278.3,ENST00000396033.2
exon_skip_486321033200813:33201052:33208812:33209012:33209172:3320931333208812:33209012ENSG00000150093.14ENST00000423113.1,ENST00000374956.4,ENST00000302278.3,ENST00000396033.2
exon_skip_486351033208812:33209012:33209172:33209313:33211184:3321127433209172:33209313ENSG00000150093.14ENST00000423113.1,ENST00000374956.4,ENST00000302278.3,ENST00000396033.2
exon_skip_486391033209172:33209313:33211184:33211274:33211567:3321166333211184:33211274ENSG00000150093.14ENST00000423113.1,ENST00000374956.4,ENST00000302278.3,ENST00000396033.2
exon_skip_486431033211184:33211274:33211567:33211663:33212512:3321266833211567:33211663ENSG00000150093.14ENST00000423113.1,ENST00000374956.4,ENST00000302278.3,ENST00000396033.2
exon_skip_486451033218912:33218972:33221433:33221528:33224419:3322448633221433:33221528ENSG00000150093.14ENST00000488494.1
exon_skip_486471033218912:33218972:33221442:33221528:33224419:3322448633221442:33221528ENSG00000150093.14ENST00000475184.1,ENST00000484088.1,ENST00000423113.1,ENST00000417122.2,ENST00000534049.1,ENST00000480226.1,ENST00000437302.1,ENST00000374956.4,ENST00000302278.3,ENST00000396033.2,ENST00000528877.1
exon_skip_486491033221448:33221528:33222278:33222511:33224419:3322448633222278:33222511ENSG00000150093.14ENST00000472147.1,ENST00000474568.1
exon_skip_486501033221448:33221528:33222409:33222511:33224419:3322448633222409:33222511ENSG00000150093.14ENST00000493758.1
exon_skip_486511033224419:33224486:33224822:33225009:33225144:3322517933224822:33225009ENSG00000150093.14ENST00000472147.1
exon_skip_486631033224419:33224486:33240602:33240686:33242520:3324273733240602:33240686ENSG00000150093.14ENST00000414670.1
exon_skip_486711033224419:33224486:33242520:33242737:33247072:3324712433242520:33242737ENSG00000150093.14ENST00000417122.2
exon_skip_486761033240602:33240686:33242520:33242737:33247072:3324712433242520:33242737ENSG00000150093.14ENST00000414670.1

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

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Exon skipping events with PSIs in GTEx for ITGB1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_486211033190491:33190563:33195392:33195508:33197295:3319743133195392:33195508ENSG00000150093.14ENST00000374956.4
exon_skip_486221033190491:33190563:33195990:33196071:33197295:3319743133195990:33196071ENSG00000150093.14ENST00000423113.1,ENST00000488427.1
exon_skip_486271033197295:33197462:33199150:33199383:33200375:3320059833199150:33199383ENSG00000150093.14ENST00000396033.2,ENST00000423113.1,ENST00000302278.3,ENST00000374956.4
exon_skip_486291033200454:33200598:33200813:33201052:33208812:3320901233200813:33201052ENSG00000150093.14ENST00000396033.2,ENST00000423113.1,ENST00000302278.3,ENST00000374956.4
exon_skip_486321033200813:33201052:33208812:33209012:33209172:3320931333208812:33209012ENSG00000150093.14ENST00000396033.2,ENST00000423113.1,ENST00000302278.3,ENST00000374956.4
exon_skip_486351033208812:33209012:33209172:33209313:33211184:3321127433209172:33209313ENSG00000150093.14ENST00000396033.2,ENST00000423113.1,ENST00000302278.3,ENST00000374956.4
exon_skip_486391033209172:33209313:33211184:33211274:33211567:3321166333211184:33211274ENSG00000150093.14ENST00000396033.2,ENST00000423113.1,ENST00000302278.3,ENST00000374956.4
exon_skip_486431033211184:33211274:33211567:33211663:33212512:3321266833211567:33211663ENSG00000150093.14ENST00000396033.2,ENST00000423113.1,ENST00000302278.3,ENST00000374956.4
exon_skip_486451033218912:33218972:33221433:33221528:33224419:3322448633221433:33221528ENSG00000150093.14ENST00000488494.1
exon_skip_486471033218912:33218972:33221442:33221528:33224419:3322448633221442:33221528ENSG00000150093.14ENST00000396033.2,ENST00000423113.1,ENST00000302278.3,ENST00000374956.4,ENST00000484088.1,ENST00000480226.1,ENST00000534049.1,ENST00000437302.1,ENST00000475184.1,ENST00000528877.1,ENST00000417122.2
exon_skip_486491033221448:33221528:33222278:33222511:33224419:3322448633222278:33222511ENSG00000150093.14ENST00000474568.1,ENST00000472147.1
exon_skip_486501033221448:33221528:33222409:33222511:33224419:3322448633222409:33222511ENSG00000150093.14ENST00000493758.1
exon_skip_486511033224419:33224486:33224822:33225009:33225144:3322517933224822:33225009ENSG00000150093.14ENST00000472147.1
exon_skip_486631033224419:33224486:33240602:33240686:33242520:3324273733240602:33240686ENSG00000150093.14ENST00000414670.1
exon_skip_486711033224419:33224486:33242520:33242737:33247072:3324712433242520:33242737ENSG00000150093.14ENST00000417122.2
exon_skip_486761033240602:33240686:33242520:33242737:33247072:3324712433242520:33242737ENSG00000150093.14ENST00000414670.1

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 ITGB1

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
ENST000003022783319915033199383Frame-shift
ENST000003960333319915033199383Frame-shift
ENST000003022783320081333201052Frame-shift
ENST000003960333320081333201052Frame-shift
ENST000003022783320881233209012Frame-shift
ENST000003960333320881233209012Frame-shift
ENST000003022783322144233221528Frame-shift
ENST000003960333322144233221528Frame-shift
ENST000003022783320917233209313In-frame
ENST000003960333320917233209313In-frame
ENST000003022783321118433211274In-frame
ENST000003960333321118433211274In-frame
ENST000003022783321156733211663In-frame
ENST000003960333321156733211663In-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
ENST000003022783319915033199383Frame-shift
ENST000003960333319915033199383Frame-shift
ENST000003022783320081333201052Frame-shift
ENST000003960333320081333201052Frame-shift
ENST000003022783320881233209012Frame-shift
ENST000003960333320881233209012Frame-shift
ENST000003022783322144233221528Frame-shift
ENST000003960333322144233221528Frame-shift
ENST000003022783320917233209313In-frame
ENST000003960333320917233209313In-frame
ENST000003022783321118433211274In-frame
ENST000003960333321118433211274In-frame
ENST000003022783321156733211663In-frame
ENST000003960333321156733211663In-frame

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Infer the effects of exon skipping event on protein functional features for ITGB1

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
ENST000003022783657798332115673321166310081103314346
ENST000003960333801798332115673321166310791174314346
ENST000003022783657798332111843321127411041193346376
ENST000003960333801798332111843321127411751264346376
ENST000003022783657798332091723320931311941334376423
ENST000003960333801798332091723320931312651405376423

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
ENST000003022783657798332115673321166310081103314346
ENST000003960333801798332115673321166310791174314346
ENST000003022783657798332111843321127411041193346376
ENST000003960333801798332111843321127411751264346376
ENST000003022783657798332091723320931311941334376423
ENST000003960333801798332091723320931312651405376423

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 ITGB1

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-A1EG-01exon_skip_48629
33200814332010523320082033200820Frame_Shift_DelA-p.C568fs
KIRPTCGA-IZ-8196-01exon_skip_48629
33200814332010523320101333201013Frame_Shift_DelG-p.S503fs
KIRPTCGA-IZ-8196-01exon_skip_48629
33200814332010523320101333201013Frame_Shift_DelG-p.T504fs
LIHCTCGA-DD-A39Y-01exon_skip_48632
33208813332090123320892333208923Frame_Shift_DelT-p.E453fs
HNSCTCGA-QK-A6VB-01exon_skip_48632
33208813332090123320896933208969Frame_Shift_DelT-p.K438fs
READTCGA-EI-6507-01exon_skip_48632
33208813332090123320896933208969Frame_Shift_DelT-p.K438fs
UCECTCGA-B5-A0JZ-01exon_skip_48627
33199151331993833319934433199345Frame_Shift_Ins-Tp.K657fs
HNSCTCGA-CV-6962-01exon_skip_48627
33199151331993833319920933199209Nonsense_MutationACp.Y702*
SKCMTCGA-D3-A8GM-06exon_skip_48632
33208813332090123320890733208907Nonsense_MutationGAp.Q459*

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SNU175_LARGE_INTESTINE33199151331993833319918433199184Missense_MutationTCp.N711D
NCIH1048_LUNG33199151331993833319922433199224Missense_MutationGCp.D697E
MFE319_ENDOMETRIUM33199151331993833319923133199231Missense_MutationTAp.D695V
786O_KIDNEY33199151331993833319923733199237Missense_MutationTAp.E693V
2313287_STOMACH33199151331993833319933333199333Missense_MutationCTp.C661Y
HEC108_ENDOMETRIUM33199151331993833319933933199339Missense_MutationTCp.D659G
KNS62_LUNG33199151331993833319936433199364Missense_MutationCGp.A651P
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE33200814332010523320082833200828Missense_MutationCTp.G565D
HCC1569_BREAST33200814332010523320085133200851Missense_MutationACp.N557K
OVMANA_OVARY33200814332010523320089233200892Missense_MutationTCp.T544A
NCIH854_LUNG33200814332010523320089833200898Missense_MutationCTp.D542N
TCCSUP_URINARY_TRACT33200814332010523320091733200917Missense_MutationCAp.Q535H
COLO684_ENDOMETRIUM33200814332010523320092133200921Missense_MutationCTp.G534E
COLO704_OVARY33200814332010523320092133200921Missense_MutationCTp.G534E
SNU520_STOMACH33208813332090123320883533208835Missense_MutationTAp.T483S
FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE33208813332090123320891533208915Missense_MutationAGp.V456A
OC316_OVARY33208813332090123320892433208924Missense_MutationTCp.E453G
OC314_OVARY33208813332090123320892433208924Missense_MutationTCp.E453G
HEC151_ENDOMETRIUM33209173332093133320922033209220Missense_MutationTGp.T408P
OVCA420_OVARY33211568332116633321157033211570Missense_MutationTCp.K346E
PC9_LUNG33211568332116633321160633211606Missense_MutationTAp.I334F
SNU81_LARGE_INTESTINE33211568332116633321160633211606Missense_MutationTCp.I334V
NCIH1092_LUNG33211568332116633321164933211649Missense_MutationACp.I319M
BV173_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE33211568332116633321159133211591Nonsense_MutationCAp.E339*
MZ7MEL_SKIN33221443332215283322145533221455Nonsense_MutationCTp.W47*
MZ7MEL_SKIN33221434332215283322145533221455Nonsense_MutationCTp.W47*
HEC251_ENDOMETRIUM33221443332215283322148733221487Nonsense_MutationCAp.E37*
HEC251_ENDOMETRIUM33221434332215283322148733221487Nonsense_MutationCAp.E37*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ITGB1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_486391033209172:33209313:33211184:33211274:33211567:3321166333211184:33211274ENST00000423113.1,ENST00000374956.4,ENST00000302278.3,ENST00000396033.2LIHCrs2230395chr10:33211227A/C9.24e-05
exon_skip_486351033208812:33209012:33209172:33209313:33211184:3321127433209172:33209313ENST00000423113.1,ENST00000374956.4,ENST00000302278.3,ENST00000396033.2LIHCrs2230396chr10:33209266G/T2.04e-04
exon_skip_486511033224419:33224486:33224822:33225009:33225144:3322517933224822:33225009ENST00000472147.1BLCArs2504001chr10:33224887A/G1.54e-03
exon_skip_486511033224419:33224486:33224822:33225009:33225144:3322517933224822:33225009ENST00000472147.1BRCArs2504001chr10:33224887A/G3.00e-03
exon_skip_486511033224419:33224486:33224822:33225009:33225144:3322517933224822:33225009ENST00000472147.1BRCArs2504001chr10:33224887A/G4.25e-03
exon_skip_486511033224419:33224486:33224822:33225009:33225144:3322517933224822:33225009ENST00000472147.1LGGrs2504001chr10:33224887A/G2.25e-04
exon_skip_486511033224419:33224486:33224822:33225009:33225144:3322517933224822:33225009ENST00000472147.1KIRCrs2504001chr10:33224887A/G1.70e-07
exon_skip_486511033224419:33224486:33224822:33225009:33225144:3322517933224822:33225009ENST00000472147.1KIRCrs2504001chr10:33224887A/G1.28e-06
exon_skip_486511033224419:33224486:33224822:33225009:33225144:3322517933224822:33225009ENST00000472147.1OVrs2504001chr10:33224887A/G2.28e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ITGB1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ITGB1


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RelatedDrugs for ITGB1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
P05556DB00098Antithymocyte immunoglobulin (rabbit)Integrin beta-1biotechapproved

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RelatedDiseases for ITGB1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
ITGB1C0006663Calcinosis1CTD_human
ITGB1C0007131Non-Small Cell Lung Carcinoma1CTD_human
ITGB1C0007137Squamous cell carcinoma1CTD_human
ITGB1C0007193Cardiomyopathy, Dilated1CTD_human
ITGB1C0014175Endometriosis1CTD_human
ITGB1C0017639Gliosis1CTD_human
ITGB1C0018801Heart failure1CTD_human
ITGB1C0023893Liver Cirrhosis, Experimental1CTD_human
ITGB1C0027626Neoplasm Invasiveness1CTD_human
ITGB1C0027627Neoplasm Metastasis1CTD_human
ITGB1C0878544Cardiomyopathies1CTD_human