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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 COL6A3 |
Gene summary |
Gene information | Gene symbol | COL6A3 | Gene ID | 1293 |
Gene name | collagen type VI alpha 3 chain | |
Synonyms | BTHLM1|DYT27|UCMD1 | |
Cytomap | 2q37.3 | |
Type of gene | protein-coding | |
Description | collagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3epididymis secretory sperm binding protein | |
Modification date | 20200328 | |
UniProtAcc | ||
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 COL6A3 |
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 |
CB | UP | 3.553375e+01 | 1.047059e+00 | 4.654515e-08 | 7.886237e-07 |
TC | UP | 5.868224e+01 | 1.395901e+00 | 1.101959e-14 | 3.134870e-12 |
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 |
CB | UP | ENST00000472056.5 | COL6A3-209:protein_coding:COL6A3 | 1.319170e+01 | 1.628217e+00 | 1.464525e-05 | 1.456137e-04 |
CB | UP | ENST00000473258.1 | COL6A3-210:lncRNA:COL6A3 | 4.504242e+00 | 1.034761e+00 | 2.345479e-03 | 1.051673e-02 |
TC | UP | ENST00000472056.5 | COL6A3-209:protein_coding:COL6A3 | 3.753368e+01 | 2.757190e+00 | 2.013453e-16 | 2.308022e-13 |
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 COL6A3 |
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_218190 | chr2 | 237376772:237377344:237378636:237379235:237380915:237381499 | 237378636:237379235 |
exon_skip_266424 | chr2 | 237333450:237333548:237334626:237334889:237336135:237336532 | 237334626:237334889 |
exon_skip_281679 | chr2 | 237377118:237377344:237378636:237379235:237380915:237381499 | 237378636:237379235 |
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 |
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Open reading frame (ORF) annotation in the exon skipping event for COL6A3 |
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 |
ENST00000295550 | 237378636 | 237379235 | In-frame |
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 |
ENST00000295550 | 237334626 | 237334889 | In-frame |
ENST00000295550 | 237378636 | 237379235 | In-frame |
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Infer the effects of exon skipping event on protein functional features for COL6A3 |
p-ENSG00000163359_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 |
ENST00000295550 | 10766 | 3177 | 237378636 | 237379235 | 2351 | 2949 | 632 | 832 |
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 |
ENST00000295550 | 10766 | 3177 | 237378636 | 237379235 | 2351 | 2949 | 632 | 832 |
ENST00000295550 | 10766 | 3177 | 237334626 | 237334889 | 9419 | 9681 | 2988 | 3076 |
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 |
P12111 | 632 | 832 | 633 | 832 | Alternative sequence | ID=VSP_045719;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
P12111 | 632 | 832 | 26 | 3177 | Chain | ID=PRO_0000005847;Note=Collagen alpha-3(VI) chain |
P12111 | 632 | 832 | 639 | 816 | Domain | Note=VWFA 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
P12111 | 632 | 832 | 659 | 659 | Natural variant | ID=VAR_047280;Note=R->H;Dbxref=dbSNP:rs36092870 |
P12111 | 632 | 832 | 677 | 677 | Natural variant | ID=VAR_058245;Note=In BTHLM1%3B unknown pathological significance. R->H;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15689448,ECO:0000269|PubMed:17886299;Dbxref=dbSNP:rs35227432,PMID:15689448,PMID:17886299 |
P12111 | 632 | 832 | 807 | 807 | Natural variant | ID=VAR_058246;Note=A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15689448;Dbxref=dbSNP:rs113155945,PMID:15689448 |
P12111 | 632 | 832 | 830 | 830 | Natural variant | ID=VAR_058247;Note=A->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15689448;Dbxref=dbSNP:rs77181645,PMID:15689448 |
P12111 | 632 | 832 | 26 | 2038 | Region | Note=Nonhelical region |
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 |
P12111 | 632 | 832 | 633 | 832 | Alternative sequence | ID=VSP_045719;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
P12111 | 632 | 832 | 26 | 3177 | Chain | ID=PRO_0000005847;Note=Collagen alpha-3(VI) chain |
P12111 | 632 | 832 | 639 | 816 | Domain | Note=VWFA 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
P12111 | 632 | 832 | 659 | 659 | Natural variant | ID=VAR_047280;Note=R->H;Dbxref=dbSNP:rs36092870 |
P12111 | 632 | 832 | 677 | 677 | Natural variant | ID=VAR_058245;Note=In BTHLM1%3B unknown pathological significance. R->H;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15689448,ECO:0000269|PubMed:17886299;Dbxref=dbSNP:rs35227432,PMID:15689448,PMID:17886299 |
P12111 | 632 | 832 | 807 | 807 | Natural variant | ID=VAR_058246;Note=A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15689448;Dbxref=dbSNP:rs113155945,PMID:15689448 |
P12111 | 632 | 832 | 830 | 830 | Natural variant | ID=VAR_058247;Note=A->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15689448;Dbxref=dbSNP:rs77181645,PMID:15689448 |
P12111 | 632 | 832 | 26 | 2038 | Region | Note=Nonhelical region |
P12111 | 2988 | 3076 | 1444 | 3177 | Alternative sequence | ID=VSP_043436;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P12111 | 2988 | 3076 | 26 | 3177 | Chain | ID=PRO_0000005847;Note=Collagen alpha-3(VI) chain |
P12111 | 2988 | 3076 | 2991 | 3085 | Domain | Note=Fibronectin type-III;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316 |
P12111 | 2988 | 3076 | 3037 | 3037 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
P12111 | 2988 | 3076 | 2988 | 2988 | Natural variant | ID=VAR_047286;Note=M->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:1689238,ECO:0000269|PubMed:17886299;Dbxref=dbSNP:rs11690358,PMID:1689238,PMID:17886299 |
P12111 | 2988 | 3076 | 3012 | 3012 | Natural variant | ID=VAR_047287;Note=A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:1689238;Dbxref=dbSNP:rs2270669,PMID:1689238 |
P12111 | 2988 | 3076 | 3043 | 3043 | Natural variant | ID=VAR_073838;Note=In DYT27. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26004199;Dbxref=dbSNP:rs552651651,PMID:26004199 |
P12111 | 2988 | 3076 | 3069 | 3069 | Natural variant | ID=VAR_047288;Note=T->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17886299;Dbxref=dbSNP:rs1131296,PMID:17886299 |
P12111 | 2988 | 3076 | 2376 | 3177 | Region | Note=Nonhelical region |
P12111 | 2988 | 3076 | 2992 | 2992 | Sequence conflict | Note=S->L;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in COL6A3 |
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 COL6A3 |
- 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 COL6A3 |
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 COL6A3 |
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 COL6A3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for COL6A3 |
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 COL6A3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |