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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 COL11A1

check button Gene summary
Gene informationGene symbol

COL11A1

Gene ID

1301

Gene namecollagen type XI alpha 1 chain
SynonymsCO11A1|COLL6|STL2
Cytomap

1p21.1

Type of geneprotein-coding
Descriptioncollagen alpha-1(XI) chaincollagen XI, alpha-1 polypeptidecollagen, type XI, alpha 1
Modification date20180523
UniProtAcc

P12107

ContextPubMed: COL11A1 [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 COL11A1 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 COL11A1

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 COL11A1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_288141103354278:103354314:103354421:103354475:103355010:103355118103354421:103354475ENSG00000060718.14ENST00000512756.1,ENST00000353414.4,ENST00000358392.2,ENST00000370096.3
exon_skip_288151103355010:103355118:103356006:103356060:103363680:103363734103356006:103356060ENSG00000060718.14ENST00000512756.1,ENST00000353414.4,ENST00000358392.2,ENST00000370096.3
exon_skip_288171103364496:103364550:103377714:103377768:103379192:103379246103377714:103377768ENSG00000060718.14ENST00000512756.1,ENST00000353414.4,ENST00000358392.2,ENST00000370096.3
exon_skip_288201103468302:103468347:103468770:103468824:103469999:103470037103468770:103468824ENSG00000060718.14ENST00000512756.1,ENST00000353414.4,ENST00000461720.1,ENST00000358392.2,ENST00000370096.3
exon_skip_288211103471817:103471871:103474018:103474072:103477968:103478025103474018:103474072ENSG00000060718.14ENST00000512756.1,ENST00000353414.4,ENST00000358392.2,ENST00000370096.3
exon_skip_288231103487262:103487325:103488297:103488552:103491076:103491169103488297:103488552ENSG00000060718.14ENST00000353414.4,ENST00000358392.2,ENST00000427239.1,ENST00000370096.3
exon_skip_288261103491076:103491169:103491355:103491508:103496671:103496800103491355:103491508ENSG00000060718.14ENST00000358392.2,ENST00000427239.1
exon_skip_288291103491076:103491169:103491771:103491888:103496671:103496800103491771:103491888ENSG00000060718.14ENST00000370096.3

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

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Exon skipping events with PSIs in GTEx for COL11A1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_288141103354278:103354314:103354421:103354475:103355010:103355118103354421:103354475ENSG00000060718.14ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1
exon_skip_288151103355010:103355118:103356006:103356060:103363680:103363734103356006:103356060ENSG00000060718.14ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1
exon_skip_288171103364496:103364550:103377714:103377768:103379192:103379246103377714:103377768ENSG00000060718.14ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1
exon_skip_288201103468302:103468347:103468770:103468824:103469999:103470037103468770:103468824ENSG00000060718.14ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1,ENST00000461720.1
exon_skip_288211103471817:103471871:103474018:103474072:103477968:103478025103474018:103474072ENSG00000060718.14ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1
exon_skip_288231103487262:103487325:103488297:103488552:103491076:103491169103488297:103488552ENSG00000060718.14ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000427239.1
exon_skip_288261103491076:103491169:103491355:103491508:103496671:103496800103491355:103491508ENSG00000060718.14ENST00000358392.2,ENST00000427239.1
exon_skip_288291103491076:103491169:103491771:103491888:103496671:103496800103491771:103491888ENSG00000060718.14ENST00000370096.3

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 COL11A1

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
ENST00000370096103354421103354475In-frame
ENST00000370096103356006103356060In-frame
ENST00000370096103377714103377768In-frame
ENST00000370096103468770103468824In-frame
ENST00000370096103474018103474072In-frame
ENST00000370096103488297103488552In-frame
ENST00000370096103491771103491888In-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
ENST00000370096103354421103354475In-frame
ENST00000370096103356006103356060In-frame
ENST00000370096103377714103377768In-frame
ENST00000370096103468770103468824In-frame
ENST00000370096103474018103474072In-frame
ENST00000370096103488297103488552In-frame
ENST00000370096103491771103491888In-frame

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Infer the effects of exon skipping event on protein functional features for COL11A1

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
ENST000003700967303180610349177110349188810941210260299
ENST000003700967303180610348829710348855213041558330415
ENST000003700967303180610347401810347407219431996543561
ENST000003700967303180610346877010346882422582311648666
ENST00000370096730318061033777141033777684346439913441362
ENST00000370096730318061033560061033560604616466914341452
ENST00000370096730318061033544211033544754778483114881506

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
ENST000003700967303180610349177110349188810941210260299
ENST000003700967303180610348829710348855213041558330415
ENST000003700967303180610347401810347407219431996543561
ENST000003700967303180610346877010346882422582311648666
ENST00000370096730318061033777141033777684346439913441362
ENST00000370096730318061033560061033560604616466914341452
ENST00000370096730318061033544211033544754778483114881506

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 COL11A1

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-G3-A3CJ-01exon_skip_28820
103468771103468824103468777103468777Frame_Shift_DelC-p.G676fs
LUSCTCGA-39-5016-01exon_skip_28820
103468771103468824103468777103468777Frame_Shift_DelC-p.G676fs
LIHCTCGA-G3-A3CJ-01exon_skip_28820
103468771103468824103468796103468796Frame_Shift_DelC-p.G670fs
COADTCGA-G4-6309-01exon_skip_28821
103474019103474072103474067103474067Frame_Shift_DelC-p.P558fs
ESCATCGA-L5-A43J-01exon_skip_28821
103474019103474072103474067103474067Frame_Shift_DelC-p.G557fs
ESCATCGA-L5-A43J-01exon_skip_28821
103474019103474072103474067103474067Frame_Shift_DelC-p.P558fs
ESCATCGA-L5-A4OI-01exon_skip_28821
103474019103474072103474067103474067Frame_Shift_DelC-p.G557fs
ESCATCGA-L5-A4OI-01exon_skip_28821
103474019103474072103474067103474067Frame_Shift_DelC-p.P558fs
LIHCTCGA-DD-A3A0-01exon_skip_28821
103474019103474072103474067103474067Frame_Shift_DelC-p.G557fs
STADTCGA-CD-8536-01exon_skip_28821
103474019103474072103474067103474067Frame_Shift_DelC-p.P558fs
STADTCGA-CG-5723-01exon_skip_28821
103474019103474072103474067103474067Frame_Shift_DelC-p.P558fs
UCECTCGA-D1-A17A-01exon_skip_28821
103474019103474072103474067103474067Frame_Shift_DelC-p.G557fs
LIHCTCGA-DD-A3A0-01exon_skip_28826
103491356103491508103491416103491416Frame_Shift_DelT-p.K291fs
STADTCGA-D7-A4Z0-01exon_skip_28826
103491356103491508103491428103491428Frame_Shift_DelG-p.K288fs
KIRCTCGA-BP-4965-01exon_skip_28821
103474019103474072103474038103474039Frame_Shift_Ins-Tp.W567fs
COADTCGA-AZ-4315-01exon_skip_28821
103474019103474072103474066103474067Frame_Shift_Ins-Cp.P558fs
COADTCGA-G4-6320-01exon_skip_28821
103474019103474072103474066103474067Frame_Shift_Ins-Cp.P558fs
COADTCGA-G4-6628-01exon_skip_28821
103474019103474072103474066103474067Frame_Shift_Ins-Cp.P558fs
STADTCGA-BR-7851-01exon_skip_28821
103474019103474072103474066103474067Frame_Shift_Ins-Cp.P558fs
STADTCGA-HU-A4G8-01exon_skip_28821
103474019103474072103474066103474067Frame_Shift_Ins-Cp.P558fs
STADTCGA-BR-7851-01exon_skip_28821
103474019103474072103474067103474068Frame_Shift_Ins-Cp.G557fs
STADTCGA-HU-A4G8-01exon_skip_28821
103474019103474072103474067103474068Frame_Shift_Ins-Cp.G557fs
LUADTCGA-44-2659-01exon_skip_28826
103491356103491508103491427103491428Frame_Shift_Ins-Gp.I288fs
KIRCTCGA-B0-4810-01exon_skip_28820
103468771103468824103468818103468818Nonsense_MutationGAp.R663X
CESCTCGA-Q1-A73O-01exon_skip_28821
103474019103474072103474021103474021Nonsense_MutationGAp.Q573*
HNSCTCGA-BA-6868-01exon_skip_28821
103474019103474072103474059103474059Nonsense_MutationGTp.S548*
HNSCTCGA-BA-6868-01exon_skip_28821
103474019103474072103474059103474059Nonsense_MutationGTp.S560*
LUSCTCGA-21-5786-01exon_skip_28823
103488298103488552103488510103488510Nonsense_MutationCAp.G357*
COADTCGA-AD-6889-01exon_skip_28823
103488298103488552103488537103488537Nonsense_MutationCAp.E336X
COADTCGA-CA-6717-01exon_skip_28826
103491356103491508103491411103491411Nonsense_MutationGTp.S293X
SKCMTCGA-D3-A3ML-06exon_skip_28815
103356007103356060103356006103356006Splice_SiteCT.
LUADTCGA-49-6767-01exon_skip_28821
103474019103474072103474073103474073Splice_SiteCAp.G544_splice

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
COL11A1_103491076_103491169_103491355_103491508_103496671_103496800_TCGA-CA-6717-01Sample: TCGA-CA-6717-01
Cancer type: COAD
ESID: exon_skip_28826
Skipped exon start: 103491356
Skipped exon end: 103491508
Mutation start: 103491411
Mutation end: 103491411
Mutation type: Nonsense_Mutation
Reference seq: G
Mutation seq: T
AAchange: p.S293X
exon_skip_107202_COAD_TCGA-CA-6717-01.png
boxplot
exon_skip_135085_COAD_TCGA-CA-6717-01.png
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exon_skip_284772_COAD_TCGA-CA-6717-01.png
boxplot
exon_skip_28826_COAD_TCGA-CA-6717-01.png
boxplot
exon_skip_304901_COAD_TCGA-CA-6717-01.png
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exon_skip_430052_COAD_TCGA-CA-6717-01.png
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exon_skip_430053_COAD_TCGA-CA-6717-01.png
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exon_skip_433462_COAD_TCGA-CA-6717-01.png
boxplot
exon_skip_439050_COAD_TCGA-CA-6717-01.png
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exon_skip_482455_COAD_TCGA-CA-6717-01.png
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exon_skip_503414_COAD_TCGA-CA-6717-01.png
boxplot
COL11A1_103491076_103491169_103491355_103491508_103496671_103496800_TCGA-44-2659-01Sample: TCGA-44-2659-01
Cancer type: LUAD
ESID: exon_skip_28826
Skipped exon start: 103491356
Skipped exon end: 103491508
Mutation start: 103491427
Mutation end: 103491428
Mutation type: Frame_Shift_Ins
Reference seq: -
Mutation seq: G
AAchange: p.I288fs
exon_skip_150665_LUAD_TCGA-44-2659-01.png
boxplot
exon_skip_28826_LUAD_TCGA-44-2659-01.png
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exon_skip_347690_LUAD_TCGA-44-2659-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM103474019103474072103474067103474067Frame_Shift_DelC-p.G545fs
NCIH847_LUNG103491772103491888103491809103491809Frame_Shift_DelC-p.G287fs
YD38_UPPER_AERODIGESTIVE_TRACT103354422103354475103354436103354436Missense_MutationGTp.P1502T
MDAMB157_BREAST103356007103356060103356012103356012Missense_MutationCTp.E1451K
HCC1438_LUNG103356007103356060103356017103356017Missense_MutationTGp.K1449T
ONS76_CENTRAL_NERVOUS_SYSTEM103356007103356060103356024103356024Missense_MutationCTp.G1447S
CAL148_BREAST103356007103356060103356041103356041Missense_MutationCAp.G1441V
MEWO_SKIN103377715103377768103377722103377722Missense_MutationCTp.G1360E
SW872_SOFT_TISSUE103468771103468824103468811103468811Missense_MutationACp.L653W
NCIH810_LUNG103474019103474072103474029103474029Missense_MutationGCp.P558R
BICR18_UPPER_AERODIGESTIVE_TRACT103474019103474072103474057103474057Missense_MutationACp.S549A
M14_SKIN103488298103488552103488336103488336Missense_MutationGAp.P403S
LS411N_LARGE_INTESTINE103488298103488552103488346103488346Missense_MutationTGp.E399D
BFTC905_URINARY_TRACT103488298103488552103488354103488354Missense_MutationGCp.P397A
HLE_LIVER103488298103488552103488388103488388Missense_MutationTAp.E385D
HLF_LIVER103488298103488552103488388103488388Missense_MutationTAp.E385D
HCC2998_LARGE_INTESTINE103488298103488552103488396103488396Missense_MutationACp.F383V
CHLA258_BONE103488298103488552103488405103488405Missense_MutationCTp.E380K
HEC251_ENDOMETRIUM103488298103488552103488405103488405Missense_MutationCTp.E380K
NCIH1648_LUNG103488298103488552103488423103488423Missense_MutationCAp.V374L
HUCCT1_BILIARY_TRACT103488298103488552103488444103488444Missense_MutationCTp.G367S
YD38_UPPER_AERODIGESTIVE_TRACT103488298103488552103488455103488455Missense_MutationTCp.K363R
KHYG_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE103488298103488552103488473103488473Missense_MutationTAp.D357V
SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE103488298103488552103488489103488489Missense_MutationTAp.R352W
MZ7MEL_SKIN103488298103488552103488522103488522Missense_MutationCTp.E341K
JHOS2_OVARY103491772103491888103491860103491860Missense_MutationTCp.D270G
NCIH2066_LUNG103488298103488552103488391103488391Nonsense_MutationATp.Y384*
A101D_SKIN103488298103488552103488540103488540Nonsense_MutationCAp.E335*
HS294T_SKIN103488298103488552103488540103488540Nonsense_MutationCAp.E335*
NCIH630_LARGE_INTESTINE103356007103356060103356059103356059Splice_SiteCTp.G1435E
CROAP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE103377715103377768103377716103377716Splice_SiteCTp.R1362Q
HEC1_ENDOMETRIUM103474019103474072103474019103474019Splice_SiteCAp.Q561H
CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE103488298103488552103488298103488298Splice_SiteGAp.S415S
CORL24_LUNG103488298103488552103488552103488552Splice_SiteGTp.P331T
NCIH838_LUNG103491772103491888103491772103491772Splice_SiteCAp.E299D

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COL11A1

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 COL11A1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for COL11A1


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RelatedDrugs for COL11A1

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 COL11A1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
COL11A1C1858084STICKLER SYNDROME, TYPE II (disorder)3CTD_human;ORPHANET;UNIPROT
COL11A1C0017605Angle Closure Glaucoma2CTD_human
COL11A1C0021818Intervertebral Disk Displacement1CTD_human
COL11A1C0029422Osteochondrodysplasias1CTD_human
COL11A1C0029927Ovarian Cysts1CTD_human
COL11A1C0265235Marshall syndrome1CTD_human;ORPHANET
COL11A1C0376634Craniofacial Abnormalities1CTD_human
COL11A1C3278138FIBROCHONDROGENESIS 11UNIPROT