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![]() | Open reading frame (ORF) annotation in the exon skipping event |
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![]() | Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
![]() | Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for COL11A1 |
Gene summary |
| Gene information | Gene symbol | COL11A1 | Gene ID | 1301 |
| Gene name | collagen type XI alpha 1 chain | |
| Synonyms | CO11A1|COLL6|STL2 | |
| Cytomap | 1p21.1 | |
| Type of gene | protein-coding | |
| Description | collagen alpha-1(XI) chaincollagen XI, alpha-1 polypeptidecollagen, type XI, alpha 1 | |
| Modification date | 20180523 | |
| UniProtAcc | P12107 | |
| Context | PubMed: COL11A1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Exon skipping events across known transcript of Ensembl for COL11A1 from UCSC genome browser |
Skipped 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. |
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Gene isoform structures and expression levels for COL11A1 |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for COL11A1 |
Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_28814 | 1 | 103354278:103354314:103354421:103354475:103355010:103355118 | 103354421:103354475 | ENSG00000060718.14 | ENST00000512756.1,ENST00000353414.4,ENST00000358392.2,ENST00000370096.3 |
| exon_skip_28815 | 1 | 103355010:103355118:103356006:103356060:103363680:103363734 | 103356006:103356060 | ENSG00000060718.14 | ENST00000512756.1,ENST00000353414.4,ENST00000358392.2,ENST00000370096.3 |
| exon_skip_28817 | 1 | 103364496:103364550:103377714:103377768:103379192:103379246 | 103377714:103377768 | ENSG00000060718.14 | ENST00000512756.1,ENST00000353414.4,ENST00000358392.2,ENST00000370096.3 |
| exon_skip_28820 | 1 | 103468302:103468347:103468770:103468824:103469999:103470037 | 103468770:103468824 | ENSG00000060718.14 | ENST00000512756.1,ENST00000353414.4,ENST00000461720.1,ENST00000358392.2,ENST00000370096.3 |
| exon_skip_28821 | 1 | 103471817:103471871:103474018:103474072:103477968:103478025 | 103474018:103474072 | ENSG00000060718.14 | ENST00000512756.1,ENST00000353414.4,ENST00000358392.2,ENST00000370096.3 |
| exon_skip_28823 | 1 | 103487262:103487325:103488297:103488552:103491076:103491169 | 103488297:103488552 | ENSG00000060718.14 | ENST00000353414.4,ENST00000358392.2,ENST00000427239.1,ENST00000370096.3 |
| exon_skip_28826 | 1 | 103491076:103491169:103491355:103491508:103496671:103496800 | 103491355:103491508 | ENSG00000060718.14 | ENST00000358392.2,ENST00000427239.1 |
| exon_skip_28829 | 1 | 103491076:103491169:103491771:103491888:103496671:103496800 | 103491771:103491888 | ENSG00000060718.14 | ENST00000370096.3 |
PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for COL11A1 |
Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_28814 | 1 | 103354278:103354314:103354421:103354475:103355010:103355118 | 103354421:103354475 | ENSG00000060718.14 | ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1 |
| exon_skip_28815 | 1 | 103355010:103355118:103356006:103356060:103363680:103363734 | 103356006:103356060 | ENSG00000060718.14 | ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1 |
| exon_skip_28817 | 1 | 103364496:103364550:103377714:103377768:103379192:103379246 | 103377714:103377768 | ENSG00000060718.14 | ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1 |
| exon_skip_28820 | 1 | 103468302:103468347:103468770:103468824:103469999:103470037 | 103468770:103468824 | ENSG00000060718.14 | ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1,ENST00000461720.1 |
| exon_skip_28821 | 1 | 103471817:103471871:103474018:103474072:103477968:103478025 | 103474018:103474072 | ENSG00000060718.14 | ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000512756.1 |
| exon_skip_28823 | 1 | 103487262:103487325:103488297:103488552:103491076:103491169 | 103488297:103488552 | ENSG00000060718.14 | ENST00000370096.3,ENST00000358392.2,ENST00000353414.4,ENST00000427239.1 |
| exon_skip_28826 | 1 | 103491076:103491169:103491355:103491508:103496671:103496800 | 103491355:103491508 | ENSG00000060718.14 | ENST00000358392.2,ENST00000427239.1 |
| exon_skip_28829 | 1 | 103491076:103491169:103491771:103491888:103496671:103496800 | 103491771:103491888 | ENSG00000060718.14 | ENST00000370096.3 |
PSI values of skipped exons in GTEx. |
| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for COL11A1 |
Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000370096 | 103354421 | 103354475 | In-frame |
| ENST00000370096 | 103356006 | 103356060 | In-frame |
| ENST00000370096 | 103377714 | 103377768 | In-frame |
| ENST00000370096 | 103468770 | 103468824 | In-frame |
| ENST00000370096 | 103474018 | 103474072 | In-frame |
| ENST00000370096 | 103488297 | 103488552 | In-frame |
| ENST00000370096 | 103491771 | 103491888 | In-frame |
Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000370096 | 103354421 | 103354475 | In-frame |
| ENST00000370096 | 103356006 | 103356060 | In-frame |
| ENST00000370096 | 103377714 | 103377768 | In-frame |
| ENST00000370096 | 103468770 | 103468824 | In-frame |
| ENST00000370096 | 103474018 | 103474072 | In-frame |
| ENST00000370096 | 103488297 | 103488552 | In-frame |
| ENST00000370096 | 103491771 | 103491888 | In-frame |
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Infer the effects of exon skipping event on protein functional features for COL11A1 |
Exon skipping at the protein sequence level and followed lost functional features.* Click on the image to enlarge it in a new window. |
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Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000370096 | 7303 | 1806 | 103491771 | 103491888 | 1094 | 1210 | 260 | 299 |
| ENST00000370096 | 7303 | 1806 | 103488297 | 103488552 | 1304 | 1558 | 330 | 415 |
| ENST00000370096 | 7303 | 1806 | 103474018 | 103474072 | 1943 | 1996 | 543 | 561 |
| ENST00000370096 | 7303 | 1806 | 103468770 | 103468824 | 2258 | 2311 | 648 | 666 |
| ENST00000370096 | 7303 | 1806 | 103377714 | 103377768 | 4346 | 4399 | 1344 | 1362 |
| ENST00000370096 | 7303 | 1806 | 103356006 | 103356060 | 4616 | 4669 | 1434 | 1452 |
| ENST00000370096 | 7303 | 1806 | 103354421 | 103354475 | 4778 | 4831 | 1488 | 1506 |
Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000370096 | 7303 | 1806 | 103491771 | 103491888 | 1094 | 1210 | 260 | 299 |
| ENST00000370096 | 7303 | 1806 | 103488297 | 103488552 | 1304 | 1558 | 330 | 415 |
| ENST00000370096 | 7303 | 1806 | 103474018 | 103474072 | 1943 | 1996 | 543 | 561 |
| ENST00000370096 | 7303 | 1806 | 103468770 | 103468824 | 2258 | 2311 | 648 | 666 |
| ENST00000370096 | 7303 | 1806 | 103377714 | 103377768 | 4346 | 4399 | 1344 | 1362 |
| ENST00000370096 | 7303 | 1806 | 103356006 | 103356060 | 4616 | 4669 | 1434 | 1452 |
| ENST00000370096 | 7303 | 1806 | 103354421 | 103354475 | 4778 | 4831 | 1488 | 1506 |
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 feature | Description of feature |
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 feature | Description of feature |
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SNVs in the skipped exons for COL11A1 |
- Lollipop plot for presenting exon skipping associated SNVs.* Click on the image to enlarge it in a new window. |
- Differential PSIs between mutated versus non-mutated samples. |
- Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_28820 | 103468771 | 103468824 | 103468777 | 103468777 | Frame_Shift_Del | C | - | p.G676fs |
| LUSC | TCGA-39-5016-01 | exon_skip_28820 | 103468771 | 103468824 | 103468777 | 103468777 | Frame_Shift_Del | C | - | p.G676fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_28820 | 103468771 | 103468824 | 103468796 | 103468796 | Frame_Shift_Del | C | - | p.G670fs |
| COAD | TCGA-G4-6309-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.P558fs |
| ESCA | TCGA-L5-A43J-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.G557fs |
| ESCA | TCGA-L5-A43J-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.P558fs |
| ESCA | TCGA-L5-A4OI-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.G557fs |
| ESCA | TCGA-L5-A4OI-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.P558fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.G557fs |
| STAD | TCGA-CD-8536-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.P558fs |
| STAD | TCGA-CG-5723-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.P558fs |
| UCEC | TCGA-D1-A17A-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.G557fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_28826 | 103491356 | 103491508 | 103491416 | 103491416 | Frame_Shift_Del | T | - | p.K291fs |
| STAD | TCGA-D7-A4Z0-01 | exon_skip_28826 | 103491356 | 103491508 | 103491428 | 103491428 | Frame_Shift_Del | G | - | p.K288fs |
| KIRC | TCGA-BP-4965-01 | exon_skip_28821 | 103474019 | 103474072 | 103474038 | 103474039 | Frame_Shift_Ins | - | T | p.W567fs |
| COAD | TCGA-AZ-4315-01 | exon_skip_28821 | 103474019 | 103474072 | 103474066 | 103474067 | Frame_Shift_Ins | - | C | p.P558fs |
| COAD | TCGA-G4-6320-01 | exon_skip_28821 | 103474019 | 103474072 | 103474066 | 103474067 | Frame_Shift_Ins | - | C | p.P558fs |
| COAD | TCGA-G4-6628-01 | exon_skip_28821 | 103474019 | 103474072 | 103474066 | 103474067 | Frame_Shift_Ins | - | C | p.P558fs |
| STAD | TCGA-BR-7851-01 | exon_skip_28821 | 103474019 | 103474072 | 103474066 | 103474067 | Frame_Shift_Ins | - | C | p.P558fs |
| STAD | TCGA-HU-A4G8-01 | exon_skip_28821 | 103474019 | 103474072 | 103474066 | 103474067 | Frame_Shift_Ins | - | C | p.P558fs |
| STAD | TCGA-BR-7851-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474068 | Frame_Shift_Ins | - | C | p.G557fs |
| STAD | TCGA-HU-A4G8-01 | exon_skip_28821 | 103474019 | 103474072 | 103474067 | 103474068 | Frame_Shift_Ins | - | C | p.G557fs |
| LUAD | TCGA-44-2659-01 | exon_skip_28826 | 103491356 | 103491508 | 103491427 | 103491428 | Frame_Shift_Ins | - | G | p.I288fs |
| KIRC | TCGA-B0-4810-01 | exon_skip_28820 | 103468771 | 103468824 | 103468818 | 103468818 | Nonsense_Mutation | G | A | p.R663X |
| CESC | TCGA-Q1-A73O-01 | exon_skip_28821 | 103474019 | 103474072 | 103474021 | 103474021 | Nonsense_Mutation | G | A | p.Q573* |
| HNSC | TCGA-BA-6868-01 | exon_skip_28821 | 103474019 | 103474072 | 103474059 | 103474059 | Nonsense_Mutation | G | T | p.S548* |
| HNSC | TCGA-BA-6868-01 | exon_skip_28821 | 103474019 | 103474072 | 103474059 | 103474059 | Nonsense_Mutation | G | T | p.S560* |
| LUSC | TCGA-21-5786-01 | exon_skip_28823 | 103488298 | 103488552 | 103488510 | 103488510 | Nonsense_Mutation | C | A | p.G357* |
| COAD | TCGA-AD-6889-01 | exon_skip_28823 | 103488298 | 103488552 | 103488537 | 103488537 | Nonsense_Mutation | C | A | p.E336X |
| COAD | TCGA-CA-6717-01 | exon_skip_28826 | 103491356 | 103491508 | 103491411 | 103491411 | Nonsense_Mutation | G | T | p.S293X |
| SKCM | TCGA-D3-A3ML-06 | exon_skip_28815 | 103356007 | 103356060 | 103356006 | 103356006 | Splice_Site | C | T | . |
| LUAD | TCGA-49-6767-01 | exon_skip_28821 | 103474019 | 103474072 | 103474073 | 103474073 | Splice_Site | C | A | p.G544_splice |
- Depth of coverage in the three exons composing exon skipping event |
- Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 103474019 | 103474072 | 103474067 | 103474067 | Frame_Shift_Del | C | - | p.G545fs |
| NCIH847_LUNG | 103491772 | 103491888 | 103491809 | 103491809 | Frame_Shift_Del | C | - | p.G287fs |
| YD38_UPPER_AERODIGESTIVE_TRACT | 103354422 | 103354475 | 103354436 | 103354436 | Missense_Mutation | G | T | p.P1502T |
| MDAMB157_BREAST | 103356007 | 103356060 | 103356012 | 103356012 | Missense_Mutation | C | T | p.E1451K |
| HCC1438_LUNG | 103356007 | 103356060 | 103356017 | 103356017 | Missense_Mutation | T | G | p.K1449T |
| ONS76_CENTRAL_NERVOUS_SYSTEM | 103356007 | 103356060 | 103356024 | 103356024 | Missense_Mutation | C | T | p.G1447S |
| CAL148_BREAST | 103356007 | 103356060 | 103356041 | 103356041 | Missense_Mutation | C | A | p.G1441V |
| MEWO_SKIN | 103377715 | 103377768 | 103377722 | 103377722 | Missense_Mutation | C | T | p.G1360E |
| SW872_SOFT_TISSUE | 103468771 | 103468824 | 103468811 | 103468811 | Missense_Mutation | A | C | p.L653W |
| NCIH810_LUNG | 103474019 | 103474072 | 103474029 | 103474029 | Missense_Mutation | G | C | p.P558R |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 103474019 | 103474072 | 103474057 | 103474057 | Missense_Mutation | A | C | p.S549A |
| M14_SKIN | 103488298 | 103488552 | 103488336 | 103488336 | Missense_Mutation | G | A | p.P403S |
| LS411N_LARGE_INTESTINE | 103488298 | 103488552 | 103488346 | 103488346 | Missense_Mutation | T | G | p.E399D |
| BFTC905_URINARY_TRACT | 103488298 | 103488552 | 103488354 | 103488354 | Missense_Mutation | G | C | p.P397A |
| HLE_LIVER | 103488298 | 103488552 | 103488388 | 103488388 | Missense_Mutation | T | A | p.E385D |
| HLF_LIVER | 103488298 | 103488552 | 103488388 | 103488388 | Missense_Mutation | T | A | p.E385D |
| HCC2998_LARGE_INTESTINE | 103488298 | 103488552 | 103488396 | 103488396 | Missense_Mutation | A | C | p.F383V |
| CHLA258_BONE | 103488298 | 103488552 | 103488405 | 103488405 | Missense_Mutation | C | T | p.E380K |
| HEC251_ENDOMETRIUM | 103488298 | 103488552 | 103488405 | 103488405 | Missense_Mutation | C | T | p.E380K |
| NCIH1648_LUNG | 103488298 | 103488552 | 103488423 | 103488423 | Missense_Mutation | C | A | p.V374L |
| HUCCT1_BILIARY_TRACT | 103488298 | 103488552 | 103488444 | 103488444 | Missense_Mutation | C | T | p.G367S |
| YD38_UPPER_AERODIGESTIVE_TRACT | 103488298 | 103488552 | 103488455 | 103488455 | Missense_Mutation | T | C | p.K363R |
| KHYG_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 103488298 | 103488552 | 103488473 | 103488473 | Missense_Mutation | T | A | p.D357V |
| SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 103488298 | 103488552 | 103488489 | 103488489 | Missense_Mutation | T | A | p.R352W |
| MZ7MEL_SKIN | 103488298 | 103488552 | 103488522 | 103488522 | Missense_Mutation | C | T | p.E341K |
| JHOS2_OVARY | 103491772 | 103491888 | 103491860 | 103491860 | Missense_Mutation | T | C | p.D270G |
| NCIH2066_LUNG | 103488298 | 103488552 | 103488391 | 103488391 | Nonsense_Mutation | A | T | p.Y384* |
| A101D_SKIN | 103488298 | 103488552 | 103488540 | 103488540 | Nonsense_Mutation | C | A | p.E335* |
| HS294T_SKIN | 103488298 | 103488552 | 103488540 | 103488540 | Nonsense_Mutation | C | A | p.E335* |
| NCIH630_LARGE_INTESTINE | 103356007 | 103356060 | 103356059 | 103356059 | Splice_Site | C | T | p.G1435E |
| CROAP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 103377715 | 103377768 | 103377716 | 103377716 | Splice_Site | C | T | p.R1362Q |
| HEC1_ENDOMETRIUM | 103474019 | 103474072 | 103474019 | 103474019 | Splice_Site | C | A | p.Q561H |
| CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 103488298 | 103488552 | 103488298 | 103488298 | Splice_Site | G | A | p.S415S |
| CORL24_LUNG | 103488298 | 103488552 | 103488552 | 103488552 | Splice_Site | G | T | p.P331T |
| NCIH838_LUNG | 103491772 | 103491888 | 103491772 | 103491772 | Splice_Site | C | A | p.E299D |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COL11A1 |
sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA 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 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for COL11A1 |
Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| COL11A1 | C1858084 | STICKLER SYNDROME, TYPE II (disorder) | 3 | CTD_human;ORPHANET;UNIPROT |
| COL11A1 | C0017605 | Angle Closure Glaucoma | 2 | CTD_human |
| COL11A1 | C0021818 | Intervertebral Disk Displacement | 1 | CTD_human |
| COL11A1 | C0029422 | Osteochondrodysplasias | 1 | CTD_human |
| COL11A1 | C0029927 | Ovarian Cysts | 1 | CTD_human |
| COL11A1 | C0265235 | Marshall syndrome | 1 | CTD_human;ORPHANET |
| COL11A1 | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
| COL11A1 | C3278138 | FIBROCHONDROGENESIS 1 | 1 | UNIPROT |