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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 CST3 |
 Gene summary |
| Gene information | Gene symbol | CST3 | Gene ID | 1471 |
| Gene name | cystatin C | |
| Synonyms | ARMD11|HEL-S-2 | |
| Cytomap | 20p11.21 | |
| Type of gene | protein-coding | |
| Description | cystatin-CbA218C14.4 (cystatin C)cystatin 3epididymis secretory protein Li 2gamma-traceneuroendocrine basic polypeptidepost-gamma-globulin | |
| Modification date | 20180527 | |
| UniProtAcc | P01034 | |
| Context | PubMed: CST3 [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 |
| CST3 | GO:0006952 | defense response | 6203523 |
| CST3 | GO:0010466 | negative regulation of peptidase activity | 6203523|7890620 |
| CST3 | GO:0045861 | negative regulation of proteolysis | 3488317 |
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Exon skipping events across known transcript of Ensembl for CST3 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 CST3 |
| 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 CST3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_355397 | 20 | 23608533:23610102:23614550:23614636:23615890:23615963 | 23614550:23614636 | ENSG00000101439.4 | ENST00000398411.1 |
| exon_skip_355401 | 20 | 23614550:23614636:23615890:23616004:23618256:23618569 | 23615890:23616004 | ENSG00000101439.4 | ENST00000376925.3,ENST00000398409.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CST3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_355397 | 20 | 23608533:23610102:23614550:23614636:23615890:23615963 | 23614550:23614636 | ENSG00000101439.4 | ENST00000398411.1 |
| exon_skip_355401 | 20 | 23614550:23614636:23615890:23616004:23618256:23618569 | 23615890:23616004 | ENSG00000101439.4 | ENST00000376925.3,ENST00000398409.1 |
| 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 CST3 |
| 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 |
| ENST00000398411 | 23614550 | 23614636 | 5CDS-5UTR |
| ENST00000376925 | 23615890 | 23616004 | In-frame |
| ENST00000398409 | 23615890 | 23616004 | 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 |
| ENST00000398411 | 23614550 | 23614636 | 5CDS-5UTR |
| ENST00000376925 | 23615890 | 23616004 | In-frame |
| ENST00000398409 | 23615890 | 23616004 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CST3 |
| 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 |
| ENST00000376925 | 890 | 146 | 23615890 | 23616004 | 408 | 521 | 81 | 119 |
| ENST00000398409 | 849 | 146 | 23615890 | 23616004 | 376 | 489 | 81 | 119 |
| 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 |
| ENST00000376925 | 890 | 146 | 23615890 | 23616004 | 408 | 521 | 81 | 119 |
| ENST00000398409 | 849 | 146 | 23615890 | 23616004 | 376 | 489 | 81 | 119 |
| 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 |
| P01034 | 81 | 119 | 67 | 101 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GAX |
| P01034 | 81 | 119 | 67 | 101 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GAX |
| P01034 | 81 | 119 | 27 | 146 | Chain | ID=PRO_0000006639;Note=Cystatin-C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:2541223,ECO:0000269|PubMed:3495457;Dbxref=PMID:2541223,PMID:3495457 |
| P01034 | 81 | 119 | 27 | 146 | Chain | ID=PRO_0000006639;Note=Cystatin-C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:2541223,ECO:0000269|PubMed:3495457;Dbxref=PMID:2541223,PMID:3495457 |
| P01034 | 81 | 119 | 99 | 109 | Disulfide bond | . |
| P01034 | 81 | 119 | 99 | 109 | Disulfide bond | . |
| P01034 | 81 | 119 | 106 | 108 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R4C |
| P01034 | 81 | 119 | 106 | 108 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R4C |
| P01034 | 81 | 119 | 115 | 118 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GAX |
| P01034 | 81 | 119 | 115 | 118 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GAX |
| P01034 | 81 | 119 | 81 | 85 | Motif | Note=Secondary area of contact |
| P01034 | 81 | 119 | 81 | 85 | Motif | Note=Secondary area of contact |
| P01034 | 81 | 119 | 94 | 94 | Natural variant | ID=VAR_002207;Note=In AMYL6. L->Q;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:1352269,ECO:0000269|PubMed:2541223;Dbxref=dbSNP:rs28939068,PMID:1352269,PMID:2541223 |
| P01034 | 81 | 119 | 94 | 94 | Natural variant | ID=VAR_002207;Note=In AMYL6. L->Q;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:1352269,ECO:0000269|PubMed:2541223;Dbxref=dbSNP:rs28939068,PMID:1352269,PMID:2541223 |
| 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 |
| P01034 | 81 | 119 | 67 | 101 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GAX |
| P01034 | 81 | 119 | 67 | 101 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GAX |
| P01034 | 81 | 119 | 27 | 146 | Chain | ID=PRO_0000006639;Note=Cystatin-C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:2541223,ECO:0000269|PubMed:3495457;Dbxref=PMID:2541223,PMID:3495457 |
| P01034 | 81 | 119 | 27 | 146 | Chain | ID=PRO_0000006639;Note=Cystatin-C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:2541223,ECO:0000269|PubMed:3495457;Dbxref=PMID:2541223,PMID:3495457 |
| P01034 | 81 | 119 | 99 | 109 | Disulfide bond | . |
| P01034 | 81 | 119 | 99 | 109 | Disulfide bond | . |
| P01034 | 81 | 119 | 106 | 108 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R4C |
| P01034 | 81 | 119 | 106 | 108 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R4C |
| P01034 | 81 | 119 | 115 | 118 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GAX |
| P01034 | 81 | 119 | 115 | 118 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GAX |
| P01034 | 81 | 119 | 81 | 85 | Motif | Note=Secondary area of contact |
| P01034 | 81 | 119 | 81 | 85 | Motif | Note=Secondary area of contact |
| P01034 | 81 | 119 | 94 | 94 | Natural variant | ID=VAR_002207;Note=In AMYL6. L->Q;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:1352269,ECO:0000269|PubMed:2541223;Dbxref=dbSNP:rs28939068,PMID:1352269,PMID:2541223 |
| P01034 | 81 | 119 | 94 | 94 | Natural variant | ID=VAR_002207;Note=In AMYL6. L->Q;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:1352269,ECO:0000269|PubMed:2541223;Dbxref=dbSNP:rs28939068,PMID:1352269,PMID:2541223 |
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SNVs in the skipped exons for CST3 |
| - 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 |
| BLCA | TCGA-GV-A6ZA-01 | exon_skip_355397 | 23614551 | 23614636 | 23614618 | 23614618 | Nonsense_Mutation | G | A | p.Q126* |
| OV | TCGA-13-1487-01 | exon_skip_355401 | 23615891 | 23616004 | 23615890 | 23615890 | Splice_Site | C | A | p.R119_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 |
| KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 23614551 | 23614636 | 23614558 | 23614558 | Missense_Mutation | C | T | p.A146T |
| JSC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 23614551 | 23614636 | 23614597 | 23614597 | Missense_Mutation | G | T | p.Q133K |
| NCIH358_LUNG | 23615891 | 23616004 | 23615922 | 23615922 | Missense_Mutation | C | A | p.C109F |
| NB12_AUTONOMIC_GANGLIA | 23615891 | 23616004 | 23615934 | 23615934 | Missense_Mutation | T | G | p.N105T |
| SNU1040_LARGE_INTESTINE | 23615891 | 23616004 | 23615955 | 23615955 | Missense_Mutation | G | A | p.T98M |
| COV504_OVARY | 23615891 | 23616004 | 23615988 | 23615988 | Missense_Mutation | T | G | p.N87T |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CST3 |
| 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 CST3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CST3 |
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RelatedDrugs for CST3 |
| 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 CST3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| CST3 | C0002395 | Alzheimer's Disease | 2 | CTD_human |
| CST3 | C0022658 | Kidney Diseases | 2 | CTD_human |
| CST3 | C1527338 | Hereditary Cerebral Amyloid Angiopathy, Icelandic Type | 2 | ORPHANET;UNIPROT |
| CST3 | C2677774 | Age-Related Macular Degeneration type 11 | 2 | CTD_human;UNIPROT |
| CST3 | C0007222 | Cardiovascular Diseases | 1 | CTD_human |
| CST3 | C0023467 | Leukemia, Myelocytic, Acute | 1 | CTD_human |
| CST3 | C0025286 | Meningioma | 1 | CTD_human |
| CST3 | C0029172 | Oral Submucous Fibrosis | 1 | CTD_human |
| CST3 | C0268393 | Familial Cerebral Amyloid Angiopathy | 1 | CTD_human |
| CST3 | C1862939 | AMYOTROPHIC LATERAL SCLEROSIS 1 | 1 | CTD_human |
| CST3 | C2609414 | Acute kidney injury | 1 | CTD_human |
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