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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 SOX6 |
Gene summary |
Gene information | Gene symbol | SOX6 | Gene ID | 55553 |
Gene name | SRY-box transcription factor 6 | |
Synonyms | HSSOX6|SOXD | |
Cytomap | 11p15.2 | |
Type of gene | protein-coding | |
Description | transcription factor SOX-6SRY (sex determining region Y)-box 6SRY-box 6SRY-box containing gene 6 | |
Modification date | 20200313 | |
UniProtAcc | ||
Context | - 31564203(MicroRNA-129-5p alleviates nerve injury and inflammatory response of Alzheimer's disease via downregulating SOX6) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
SOX6 | GO:0032332 | positive regulation of chondrocyte differentiation | 21401405 |
SOX6 | GO:0061036 | positive regulation of cartilage development | 21401405 |
SOX6 | GO:0071560 | cellular response to transforming growth factor beta stimulus | 21401405 |
SOX6 | GO:2000741 | positive regulation of mesenchymal stem cell differentiation | 21401405 |
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Gene structures and expression levels for SOX6 |
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 |
IFG | UP | ENST00000528252.5 | SOX6-210:protein_coding:SOX6 | 1.453668e+01 | 6.971015e+00 | 4.845564e-06 | 1.821357e-02 |
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 SOX6 |
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_249852 | chr11 | 16055752:16055901:16095996:16096118:16097609:16097688 | 16095996:16096118 |
exon_skip_30227 | chr11 | 16055758:16055901:16095996:16096118:16097609:16097688 | 16095996:16096118 |
exon_skip_88915 | chr11 | 16341012:16341252:16465701:16465816:16476315:16476388 | 16465701:16465816 |
exon_skip_8905 | chr11 | 16234640:16234671:16318446:16318653:16341012:16341252 | 16318446:16318653 |
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 SOX6 |
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 |
ENST00000528429 | 16318446 | 16318653 | Frame-shift |
ENST00000528429 | 16095996 | 16096118 | In-frame |
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 |
ENST00000528429 | 16095996 | 16096118 | 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 |
ENST00000528429 | 16095996 | 16096118 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SOX6 |
p-ENSG00000110693_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 |
ENST00000528429 | 2673 | 828 | 16095996 | 16096118 | 1047 | 1168 | 326 | 366 |
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 |
ENST00000528429 | 2673 | 828 | 16095996 | 16096118 | 1047 | 1168 | 326 | 366 |
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 |
ENST00000528429 | 2673 | 828 | 16095996 | 16096118 | 1047 | 1168 | 326 | 366 |
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 |
P35712 | 326 | 366 | 327 | 367 | Alternative sequence | ID=VSP_039694;Note=In isoform 2 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|PubMed:15489334;Dbxref=PMID:11230166,PMID:15489334 |
P35712 | 326 | 366 | 1 | 828 | Chain | ID=PRO_0000048729;Note=Transcription factor SOX-6 |
P35712 | 326 | 366 | 330 | 330 | Sequence conflict | Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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 |
P35712 | 326 | 366 | 327 | 367 | Alternative sequence | ID=VSP_039694;Note=In isoform 2 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|PubMed:15489334;Dbxref=PMID:11230166,PMID:15489334 |
P35712 | 326 | 366 | 1 | 828 | Chain | ID=PRO_0000048729;Note=Transcription factor SOX-6 |
P35712 | 326 | 366 | 330 | 330 | Sequence conflict | Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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 |
P35712 | 326 | 366 | 327 | 367 | Alternative sequence | ID=VSP_039694;Note=In isoform 2 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|PubMed:15489334;Dbxref=PMID:11230166,PMID:15489334 |
P35712 | 326 | 366 | 1 | 828 | Chain | ID=PRO_0000048729;Note=Transcription factor SOX-6 |
P35712 | 326 | 366 | 330 | 330 | Sequence conflict | Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SOX6 |
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 SOX6 |
- 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 SOX6 |
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 SOX6 |
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 SOX6 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SOX6 |
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 SOX6 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |