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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 SOX5 |
 Gene summary |
| Gene information | Gene symbol | SOX5 | Gene ID | 6660 |
| Gene name | SRY-box 5 | |
| Synonyms | L-SOX5|L-SOX5B|L-SOX5F|LAMSHF | |
| Cytomap | 12p12.1 | |
| Type of gene | protein-coding | |
| Description | transcription factor SOX-5SRY (sex determining region Y)-box 5 | |
| Modification date | 20180523 | |
| UniProtAcc | P35711 | |
| Context | PubMed: SOX5 [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 |
| SOX5 | GO:0032332 | positive regulation of chondrocyte differentiation | 21401405 |
| SOX5 | GO:0061036 | positive regulation of cartilage development | 21401405 |
| SOX5 | GO:0071560 | cellular response to transforming growth factor beta stimulus | 21401405 |
| SOX5 | GO:2000741 | positive regulation of mesenchymal stem cell differentiation | 21401405 |
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Exon skipping events across known transcript of Ensembl for SOX5 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 SOX5 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for SOX5 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_90572 | 12 | 23696144:23696318:23699249:23699358:23716191:23716337 | 23699249:23699358 | ENSG00000134532.11 | ENST00000546136.1,ENST00000537393.1,ENST00000309359.1,ENST00000545921.1,ENST00000451604.2,ENST00000396007.2 |
| exon_skip_90575 | 12 | 23716254:23716337:23728594:23728772:23757320:23757467 | 23728594:23728772 | ENSG00000134532.11 | ENST00000546136.1,ENST00000537393.1,ENST00000309359.1,ENST00000367206.3,ENST00000545921.1,ENST00000451604.2 |
| exon_skip_90576 | 12 | 23793745:23793831:23818377:23818498:23887617:23887649 | 23818377:23818498 | ENSG00000134532.11 | ENST00000546136.1,ENST00000535530.1,ENST00000537393.1,ENST00000541536.1,ENST00000309359.1,ENST00000367206.3,ENST00000545921.1,ENST00000451604.2,ENST00000536629.1,ENST00000381381.2 |
| exon_skip_90577 | 12 | 23793745:23793831:23818377:23818501:23887617:23887649 | 23818377:23818501 | ENSG00000134532.11 | ENST00000536911.1 |
| exon_skip_90580 | 12 | 24048831:24048958:24102497:24102595:24103875:24103954 | 24102497:24102595 | ENSG00000134532.11 | ENST00000441133.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SOX5 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_90572 | 12 | 23696144:23696318:23699249:23699358:23716191:23716337 | 23699249:23699358 | ENSG00000134532.11 | ENST00000546136.1,ENST00000309359.1,ENST00000451604.2,ENST00000537393.1,ENST00000396007.2,ENST00000545921.1 |
| exon_skip_90575 | 12 | 23716254:23716337:23728594:23728772:23757320:23757467 | 23728594:23728772 | ENSG00000134532.11 | ENST00000546136.1,ENST00000309359.1,ENST00000451604.2,ENST00000537393.1,ENST00000545921.1,ENST00000367206.3 |
| exon_skip_90576 | 12 | 23793745:23793831:23818377:23818498:23887617:23887649 | 23818377:23818498 | ENSG00000134532.11 | ENST00000546136.1,ENST00000309359.1,ENST00000381381.2,ENST00000451604.2,ENST00000537393.1,ENST00000541536.1,ENST00000545921.1,ENST00000367206.3,ENST00000535530.1,ENST00000536629.1 |
| exon_skip_90577 | 12 | 23793745:23793831:23818377:23818501:23887617:23887649 | 23818377:23818501 | ENSG00000134532.11 | ENST00000536911.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for SOX5 |
| 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 |
| ENST00000451604 | 23699249 | 23699358 | Frame-shift |
| ENST00000451604 | 23728594 | 23728772 | Frame-shift |
| ENST00000451604 | 23818377 | 23818498 | Frame-shift |
| 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 |
| ENST00000451604 | 23699249 | 23699358 | Frame-shift |
| ENST00000451604 | 23728594 | 23728772 | Frame-shift |
| ENST00000451604 | 23818377 | 23818498 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SOX5 |
| 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 |
| 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 |
| 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 SOX5 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - 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 |
| LUAD | TCGA-95-7043-01 | exon_skip_90575 | 23728595 | 23728772 | 23728652 | 23728652 | Frame_Shift_Del | G | - | p.L416fs |
| LUAD | TCGA-95-7043-01 | exon_skip_90575 | 23728595 | 23728772 | 23728652 | 23728652 | Frame_Shift_Del | G | - | p.L429fs |
| UCS | TCGA-N9-A4Q1-01 | exon_skip_90572 | 23699250 | 23699358 | 23699267 | 23699268 | Frame_Shift_Ins | - | T | p.E514fs |
| UCS | TCGA-N9-A4Q1-01 | exon_skip_90572 | 23699250 | 23699358 | 23699267 | 23699268 | Frame_Shift_Ins | - | T | p.L527fs |
| LUSC | TCGA-22-5491-01 | exon_skip_90572 | 23699250 | 23699358 | 23699316 | 23699316 | Nonsense_Mutation | T | A | p.K511* |
| SKCM | TCGA-D3-A3MR-06 | exon_skip_90572 | 23699250 | 23699358 | 23699316 | 23699316 | Nonsense_Mutation | T | A | p.K498* |
| SKCM | TCGA-D3-A3MR-06 | exon_skip_90572 | 23699250 | 23699358 | 23699316 | 23699316 | Nonsense_Mutation | T | A | p.K498X |
| LUAD | TCGA-53-7626-01 | exon_skip_90576 | 23818378 | 23818498 | 23818489 | 23818489 | Nonsense_Mutation | G | A | p.Q261* |
| LUAD | TCGA-53-7626-01 | exon_skip_90576 | 23818378 | 23818498 | 23818489 | 23818489 | Nonsense_Mutation | G | A | p.Q274* |
| LUAD | TCGA-53-7626-01 | exon_skip_90577 | 23818378 | 23818501 | 23818489 | 23818489 | Nonsense_Mutation | G | A | p.Q261* |
| LUAD | TCGA-53-7626-01 | exon_skip_90577 | 23818378 | 23818501 | 23818489 | 23818489 | Nonsense_Mutation | G | A | p.Q274* |
| CESC | TCGA-FU-A3HY-01 | exon_skip_90580 | 24102498 | 24102595 | 24102511 | 24102511 | Nonsense_Mutation | G | A | p.Q9* |
| LUAD | TCGA-78-7536-01 | exon_skip_90575 | 23728595 | 23728772 | 23728774 | 23728774 | Splice_Site | T | A | p.D389_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| SNU175_LARGE_INTESTINE | 23699250 | 23699358 | 23699351 | 23699352 | Frame_Shift_Ins | - | T | p.T499fs |
| HS888T_FIBROBLAST | 23699250 | 23699358 | 23699263 | 23699263 | Missense_Mutation | A | T | p.S528R |
| GCIY_STOMACH | 23728595 | 23728772 | 23728618 | 23728618 | Missense_Mutation | G | T | p.P440H |
| 59M_OVARY | 23728595 | 23728772 | 23728618 | 23728618 | Missense_Mutation | G | T | p.P440H |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 23728595 | 23728772 | 23728633 | 23728633 | Missense_Mutation | G | T | p.A435E |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 23728595 | 23728772 | 23728661 | 23728661 | Missense_Mutation | C | T | p.A426T |
| LB647SCLC_LUNG | 23728595 | 23728772 | 23728684 | 23728684 | Missense_Mutation | G | T | p.P418Q |
| BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 23818378 | 23818501 | 23818381 | 23818381 | Missense_Mutation | A | T | p.C310S |
| BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 23818378 | 23818498 | 23818381 | 23818381 | Missense_Mutation | A | T | p.C310S |
| NCIH226_LUNG | 23818378 | 23818501 | 23818396 | 23818396 | Missense_Mutation | T | C | p.S305G |
| NCIH226_LUNG | 23818378 | 23818498 | 23818396 | 23818396 | Missense_Mutation | T | C | p.S305G |
| HT115_LARGE_INTESTINE | 23818378 | 23818501 | 23818447 | 23818447 | Missense_Mutation | G | A | p.R288W |
| HT115_LARGE_INTESTINE | 23818378 | 23818498 | 23818447 | 23818447 | Missense_Mutation | G | A | p.R288W |
| LS411N_LARGE_INTESTINE | 24102498 | 24102595 | 24102522 | 24102522 | Missense_Mutation | G | T | p.P5H |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SOX5 |
| 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 SOX5 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SOX5 |
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RelatedDrugs for SOX5 |
| 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 SOX5 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SOX5 | C0004238 | Atrial Fibrillation | 1 | CTD_human |
| SOX5 | C0036341 | Schizophrenia | 1 | PSYGENET |
| SOX5 | C1510586 | Autism Spectrum Disorders | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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