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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
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|DFNA37|STL2 | |
Cytomap | 1p21.1 | |
Type of gene | protein-coding | |
Description | collagen alpha-1(XI) chaincollagen XI, alpha-1 polypeptidecollagen, type XI, alpha 1deafness, autosomal dominant 37 | |
Modification date | 20200313 | |
UniProtAcc | A0A0U1RRA7, A0A2R8Y4I5, A0A2R8Y4M5, | |
Context |
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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Gene structures and expression levels for COL11A1 |
Skipped exons in the ROSMAP, MSBB, and Mayo 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. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for COL11A1 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_232600 | chr1 | 102979382:102979435:102979597:102979612:102984138:102984191 | 102979597:102979612 |
exon_skip_235604 | chr1 | 103025521:103025613:103025800:103025952:103026216:103026332 | 103025800:103025952 |
exon_skip_291703 | chr1 | 103021707:103021769:103022742:103022996:103025521:103025613 | 103022742:103022996 |
exon_skip_96971 | chr1 | 102898941:102898994:102912159:102912212:102913637:102913690 | 102912159:102912212 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
exon_skip_232600 | Mayo_TC | 3.625676e-01 | 4.914545e-01 | -1.288870e-01 | 2.597629e-05 |
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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 ROSMAP based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000370096 | 102912159 | 102912212 | In-frame |
ENST00000370096 | 103022742 | 103022996 | In-frame |
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Infer the effects of exon skipping event on protein functional features for COL11A1 |
p-ENSG00000060718_img4.png |
Loci of skipped exons in ROSMAP 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 |
Loci of skipped exons in MSBB 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 |
Loci of skipped exons in Mayo 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 | 7278 | 1806 | 103022742 | 103022996 | 1279 | 1532 | 330 | 414 |
ENST00000370096 | 7278 | 1806 | 102912159 | 102912212 | 4321 | 4373 | 1344 | 1361 |
Lost protein functional features of individual exon skipping events in ROSMAP. |
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 MSBB. |
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 Mayo. |
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 |
P12107 | 330 | 414 | 300 | 415 | Alternative sequence | ID=VSP_046318;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
P12107 | 330 | 414 | 36 | 511 | Propeptide | ID=PRO_0000005774;Note=N-terminal propeptide;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
P12107 | 330 | 414 | 230 | 419 | Region | Note=Nonhelical region |
P12107 | 1344 | 1361 | 512 | 1563 | Chain | ID=PRO_0000005775;Note=Collagen alpha-1(XI) chain |
P12107 | 1344 | 1361 | 529 | 1542 | Region | Note=Triple-helical region |
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3'-UTR located exon skipping events that lost miRNA binding sites in COL11A1 |
3'-UTR exon skipping evnets lost miRNA binding. |
Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for COL11A1 |
- Differential PSIs between mutated versus non-mutated samples. |
- Depth of Coverage in the skipped exon of the mutated samples. |
- Sashimi plot in the skipped exon of the mutated samples. |
- Non-synonymous mutations located in the skipped exons. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
- 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 |
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AD stage-associated exon skippint events for COL11A1 |
Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COL11A1 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for COL11A1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
TC | NUP42 | exon_skip_232600 | 4.529339e-01 | 7.064625e-08 |
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RelatedDrugs for COL11A1 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
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 |