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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 CAPN13 |
 Gene summary |
| Gene information | Gene symbol | CAPN13 | Gene ID | 92291 |
| Gene name | calpain 13 | |
| Synonyms | - | |
| Cytomap | 2p23.1 | |
| Type of gene | protein-coding | |
| Description | calpain-13CANP 13calcium-activated neutral proteinase 13 | |
| Modification date | 20180523 | |
| UniProtAcc | Q6MZZ7 | |
| Context | PubMed: CAPN13 [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 |
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Exon skipping events across known transcript of Ensembl for CAPN13 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 CAPN13 |
| 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 CAPN13 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_338039 | 2 | 30953595:30953652:30954209:30954265:30955303:30955350 | 30954209:30954265 | ENSG00000162949.12 | ENST00000534090.2,ENST00000490786.1,ENST00000450650.1,ENST00000295055.8 |
| exon_skip_338040 | 2 | 30957314:30957390:30959368:30959495:30960027:30961159 | 30959368:30959495 | ENSG00000162949.12 | ENST00000450650.1 |
| exon_skip_338043 | 2 | 30959368:30959495:30960027:30961159:30961265:30961323 | 30960027:30961159 | ENSG00000162949.12 | ENST00000450650.1 |
| exon_skip_338048 | 2 | 30964773:30964830:30965191:30965225:30966248:30966384 | 30965191:30965225 | ENSG00000162949.12 | ENST00000534090.2,ENST00000458085.2,ENST00000295055.8 |
| exon_skip_338051 | 2 | 30966248:30966445:30968588:30968600:30973968:30974092 | 30968588:30968600 | ENSG00000162949.12 | ENST00000465450.2,ENST00000295055.8 |
| exon_skip_338054 | 2 | 30973968:30974117:30975918:30976064:30977155:30977230 | 30975918:30976064 | ENSG00000162949.12 | ENST00000534090.2,ENST00000458085.2,ENST00000295055.8 |
| exon_skip_338056 | 2 | 30980911:30981003:30985947:30986022:30986997:30987129 | 30985947:30986022 | ENSG00000162949.12 | ENST00000534090.2,ENST00000465960.2,ENST00000458085.2,ENST00000295055.8 |
| exon_skip_338062 | 2 | 30993178:30993315:30998795:30998911:31000432:31000505 | 30998795:30998911 | ENSG00000162949.12 | ENST00000534090.2,ENST00000465960.2,ENST00000458085.2,ENST00000295055.8 |
| exon_skip_338066 | 2 | 31009993:31010223:31029046:31029132:31030167:31030292 | 31029046:31029132 | ENSG00000162949.12 | ENST00000458085.2,ENST00000485248.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CAPN13 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_338039 | 2 | 30953595:30953652:30954209:30954265:30955303:30955350 | 30954209:30954265 | ENSG00000162949.12 | ENST00000450650.1,ENST00000295055.8,ENST00000534090.2,ENST00000490786.1 |
| exon_skip_338040 | 2 | 30957314:30957390:30959368:30959495:30960027:30961159 | 30959368:30959495 | ENSG00000162949.12 | ENST00000450650.1 |
| exon_skip_338043 | 2 | 30959368:30959495:30960027:30961159:30961265:30961323 | 30960027:30961159 | ENSG00000162949.12 | ENST00000450650.1 |
| exon_skip_338048 | 2 | 30964773:30964830:30965191:30965225:30966248:30966384 | 30965191:30965225 | ENSG00000162949.12 | ENST00000295055.8,ENST00000534090.2,ENST00000458085.2 |
| exon_skip_338051 | 2 | 30966248:30966445:30968588:30968600:30973968:30974092 | 30968588:30968600 | ENSG00000162949.12 | ENST00000295055.8,ENST00000465450.2 |
| exon_skip_338054 | 2 | 30973968:30974117:30975918:30976064:30977155:30977230 | 30975918:30976064 | ENSG00000162949.12 | ENST00000295055.8,ENST00000534090.2,ENST00000458085.2 |
| exon_skip_338056 | 2 | 30980911:30981003:30985947:30986022:30986997:30987129 | 30985947:30986022 | ENSG00000162949.12 | ENST00000295055.8,ENST00000534090.2,ENST00000458085.2,ENST00000465960.2 |
| exon_skip_338062 | 2 | 30993178:30993315:30998795:30998911:31000432:31000505 | 30998795:30998911 | ENSG00000162949.12 | ENST00000295055.8,ENST00000534090.2,ENST00000458085.2,ENST00000465960.2 |
| exon_skip_338066 | 2 | 31009993:31010223:31029046:31029132:31030167:31030292 | 31029046:31029132 | ENSG00000162949.12 | ENST00000458085.2,ENST00000485248.2 |
| 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 CAPN13 |
| 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 |
| ENST00000295055 | 30954209 | 30954265 | Frame-shift |
| ENST00000295055 | 30965191 | 30965225 | Frame-shift |
| ENST00000295055 | 30975918 | 30976064 | Frame-shift |
| ENST00000295055 | 30998795 | 30998911 | Frame-shift |
| ENST00000295055 | 30968588 | 30968600 | In-frame |
| ENST00000295055 | 30985947 | 30986022 | 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 |
| ENST00000295055 | 30954209 | 30954265 | Frame-shift |
| ENST00000295055 | 30965191 | 30965225 | Frame-shift |
| ENST00000295055 | 30975918 | 30976064 | Frame-shift |
| ENST00000295055 | 30998795 | 30998911 | Frame-shift |
| ENST00000295055 | 30968588 | 30968600 | In-frame |
| ENST00000295055 | 30985947 | 30986022 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CAPN13 |
| 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 |
| ENST00000295055 | 2700 | 669 | 30985947 | 30986022 | 877 | 951 | 233 | 258 |
| 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 |
| ENST00000295055 | 2700 | 669 | 30985947 | 30986022 | 877 | 951 | 233 | 258 |
| 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 |
| Q6MZZ7 | 233 | 258 | 249 | 249 | Active site | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00239 |
| Q6MZZ7 | 233 | 258 | 1 | 669 | Chain | ID=PRO_0000259582;Note=Calpain-13 |
| Q6MZZ7 | 233 | 258 | 34 | 333 | Domain | Note=Calpain catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00239 |
| Q6MZZ7 | 233 | 258 | 249 | 249 | Natural variant | ID=VAR_028964;Note=H->Y;Dbxref=dbSNP:rs17010210 |
| 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 |
| Q6MZZ7 | 233 | 258 | 249 | 249 | Active site | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00239 |
| Q6MZZ7 | 233 | 258 | 1 | 669 | Chain | ID=PRO_0000259582;Note=Calpain-13 |
| Q6MZZ7 | 233 | 258 | 34 | 333 | Domain | Note=Calpain catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00239 |
| Q6MZZ7 | 233 | 258 | 249 | 249 | Natural variant | ID=VAR_028964;Note=H->Y;Dbxref=dbSNP:rs17010210 |
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SNVs in the skipped exons for CAPN13 |
| - 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 |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_338054 | 30975919 | 30976064 | 30975961 | 30975961 | Frame_Shift_Del | G | - | p.Q349fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_338062 | 30998796 | 30998911 | 30998828 | 30998828 | Frame_Shift_Del | A | - | p.S119fs |
| BLCA | TCGA-DK-A6AW-01 | exon_skip_338039 | 30954210 | 30954265 | 30954218 | 30954218 | Nonsense_Mutation | C | A | p.E659* |
| LGG | TCGA-DU-6392-01 | exon_skip_338040 | 30959369 | 30959495 | 30959398 | 30959398 | Nonsense_Mutation | G | A | p.R565* |
| SKCM | TCGA-DA-A95Z-06 | exon_skip_338040 | 30959369 | 30959495 | 30959398 | 30959398 | Nonsense_Mutation | G | A | p.R565* |
| PRAD | TCGA-EJ-7315-01 | exon_skip_338043 | 30960028 | 30961159 | 30961160 | 30961160 | Splice_Site | C | T | . |
| LUAD | TCGA-05-4382-01 | exon_skip_338054 | 30975919 | 30976064 | 30975918 | 30975918 | Splice_Site | C | A | p.G363_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 |
| NCIH2110_LUNG | 30959369 | 30959495 | 30959373 | 30959373 | Missense_Mutation | T | C | p.Y573C |
| HEC59_ENDOMETRIUM | 30959369 | 30959495 | 30959397 | 30959397 | Missense_Mutation | C | T | p.R565Q |
| ES2_OVARY | 30960028 | 30961159 | 30961117 | 30961117 | Missense_Mutation | A | G | p.L546S |
| BALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30960028 | 30961159 | 30961140 | 30961140 | Missense_Mutation | G | T | p.F538L |
| M14_SKIN | 30960028 | 30961159 | 30961154 | 30961154 | Missense_Mutation | G | A | p.P534S |
| MFE319_ENDOMETRIUM | 30975919 | 30976064 | 30975996 | 30975996 | Missense_Mutation | A | G | p.L337P |
| HCC1599_BREAST | 30975919 | 30976064 | 30976023 | 30976023 | Missense_Mutation | A | G | p.F328S |
| VMRCMELG_SKIN | 30985948 | 30986022 | 30985967 | 30985967 | Missense_Mutation | G | A | p.T252I |
| 22RV1_PROSTATE | 30975919 | 30976064 | 30975970 | 30975970 | Nonsense_Mutation | C | A | p.G346* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CAPN13 |
| 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 CAPN13 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CAPN13 |
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RelatedDrugs for CAPN13 |
| 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 CAPN13 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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