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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 CAPN9 |
 Gene summary |
| Gene information | Gene symbol | CAPN9 | Gene ID | 10753 |
| Gene name | calpain 9 | |
| Synonyms | GC36|nCL-4 | |
| Cytomap | 1q42.2 | |
| Type of gene | protein-coding | |
| Description | calpain-9digestive tract-specific calpainnew calpain 4novel calpain large subunit-4 | |
| Modification date | 20180523 | |
| UniProtAcc | O14815 | |
| Context | PubMed: CAPN9 [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 CAPN9 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 CAPN9 |
| 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 CAPN9 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_19257 | 1 | 230883178:230883455:230891082:230891152:230895257:230895376 | 230891082:230891152 | ENSG00000135773.8 | ENST00000354537.1 |
| exon_skip_19263 | 1 | 230891082:230891152:230895257:230895376:230898398:230898532 | 230895257:230895376 | ENSG00000135773.8 | ENST00000354537.1,ENST00000271971.2 |
| exon_skip_19265 | 1 | 230903286:230903455:230904925:230905009:230907759:230907845 | 230904925:230905009 | ENSG00000135773.8 | ENST00000354537.1,ENST00000366666.2,ENST00000271971.2 |
| exon_skip_19267 | 1 | 230907759:230907845:230910299:230910377:230914718:230914879 | 230910299:230910377 | ENSG00000135773.8 | ENST00000366666.2,ENST00000271971.2 |
| exon_skip_19274 | 1 | 230907759:230907845:230914718:230914879:230915924:230916082 | 230914718:230914879 | ENSG00000135773.8 | ENST00000354537.1 |
| exon_skip_19279 | 1 | 230914718:230914879:230915924:230916082:230916245:230916454 | 230915924:230916082 | ENSG00000135773.8 | ENST00000354537.1,ENST00000366666.2,ENST00000271971.2 |
| exon_skip_19281 | 1 | 230921726:230921763:230923267:230923348:230925877:230925935 | 230923267:230923348 | ENSG00000135773.8 | ENST00000354537.1,ENST00000366666.2,ENST00000271971.2 |
| exon_skip_19284 | 1 | 230923267:230923348:230925877:230925935:230927609:230927674 | 230925877:230925935 | ENSG00000135773.8 | ENST00000354537.1,ENST00000366666.2,ENST00000271971.2 |
| exon_skip_19288 | 1 | 230930908:230931025:230933907:230933966:230937315:230937508 | 230933907:230933966 | ENSG00000135773.8 | ENST00000354537.1,ENST00000366666.2,ENST00000271971.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CAPN9 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_19257 | 1 | 230883178:230883455:230891082:230891152:230895257:230895376 | 230891082:230891152 | ENSG00000135773.8 | ENST00000354537.1 |
| exon_skip_19263 | 1 | 230891082:230891152:230895257:230895376:230898398:230898532 | 230895257:230895376 | ENSG00000135773.8 | ENST00000271971.2,ENST00000354537.1 |
| exon_skip_19265 | 1 | 230903286:230903455:230904925:230905009:230907759:230907845 | 230904925:230905009 | ENSG00000135773.8 | ENST00000271971.2,ENST00000354537.1,ENST00000366666.2 |
| exon_skip_19267 | 1 | 230907759:230907845:230910299:230910377:230914718:230914879 | 230910299:230910377 | ENSG00000135773.8 | ENST00000271971.2,ENST00000366666.2 |
| exon_skip_19274 | 1 | 230907759:230907845:230914718:230914879:230915924:230916082 | 230914718:230914879 | ENSG00000135773.8 | ENST00000354537.1 |
| exon_skip_19279 | 1 | 230914718:230914879:230915924:230916082:230916245:230916454 | 230915924:230916082 | ENSG00000135773.8 | ENST00000271971.2,ENST00000354537.1,ENST00000366666.2 |
| exon_skip_19281 | 1 | 230921726:230921763:230923267:230923348:230925877:230925935 | 230923267:230923348 | ENSG00000135773.8 | ENST00000271971.2,ENST00000354537.1,ENST00000366666.2 |
| exon_skip_19284 | 1 | 230923267:230923348:230925877:230925935:230927609:230927674 | 230925877:230925935 | ENSG00000135773.8 | ENST00000271971.2,ENST00000354537.1,ENST00000366666.2 |
| exon_skip_19288 | 1 | 230930908:230931025:230933907:230933966:230937315:230937508 | 230933907:230933966 | ENSG00000135773.8 | ENST00000271971.2,ENST00000354537.1,ENST00000366666.2 |
| 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 CAPN9 |
| 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 |
| ENST00000271971 | 230895257 | 230895376 | Frame-shift |
| ENST00000271971 | 230915924 | 230916082 | Frame-shift |
| ENST00000271971 | 230925877 | 230925935 | Frame-shift |
| ENST00000271971 | 230933907 | 230933966 | Frame-shift |
| ENST00000271971 | 230904925 | 230905009 | In-frame |
| ENST00000271971 | 230910299 | 230910377 | In-frame |
| ENST00000271971 | 230923267 | 230923348 | 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 |
| ENST00000271971 | 230895257 | 230895376 | Frame-shift |
| ENST00000271971 | 230915924 | 230916082 | Frame-shift |
| ENST00000271971 | 230925877 | 230925935 | Frame-shift |
| ENST00000271971 | 230933907 | 230933966 | Frame-shift |
| ENST00000271971 | 230904925 | 230905009 | In-frame |
| ENST00000271971 | 230910299 | 230910377 | In-frame |
| ENST00000271971 | 230923267 | 230923348 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CAPN9 |
| 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 |
| ENST00000271971 | 2379 | 690 | 230904925 | 230905009 | 819 | 902 | 235 | 263 |
| ENST00000271971 | 2379 | 690 | 230910299 | 230910377 | 989 | 1066 | 292 | 317 |
| ENST00000271971 | 2379 | 690 | 230923267 | 230923348 | 1632 | 1712 | 506 | 533 |
| 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 |
| ENST00000271971 | 2379 | 690 | 230904925 | 230905009 | 819 | 902 | 235 | 263 |
| ENST00000271971 | 2379 | 690 | 230910299 | 230910377 | 989 | 1066 | 292 | 317 |
| ENST00000271971 | 2379 | 690 | 230923267 | 230923348 | 1632 | 1712 | 506 | 533 |
| 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 |
| O14815 | 235 | 263 | 254 | 254 | Active site | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17157313;Dbxref=PMID:17157313 |
| O14815 | 235 | 263 | 256 | 266 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 235 | 263 | 1 | 690 | Chain | ID=PRO_0000207722;Note=Calpain-9 |
| O14815 | 235 | 263 | 42 | 337 | Domain | Note=Calpain catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00239 |
| O14815 | 235 | 263 | 239 | 241 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 235 | 263 | 239 | 239 | Natural variant | ID=VAR_022192;Note=A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs28359647 |
| O14815 | 292 | 317 | 292 | 318 | Alternative sequence | ID=VSP_007553;Note=In isoform 2. SSPEWRSVGPAEQKRLCHTALDDGEFW->R;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10835488;Dbxref=PMID:10835488 |
| O14815 | 292 | 317 | 313 | 320 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 292 | 317 | 1 | 690 | Chain | ID=PRO_0000207722;Note=Calpain-9 |
| O14815 | 292 | 317 | 42 | 337 | Domain | Note=Calpain catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00239 |
| O14815 | 292 | 317 | 294 | 298 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 292 | 317 | 301 | 306 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 292 | 317 | 312 | 312 | Metal binding | Note=Calcium 2%3B via carbonyl oxygen |
| O14815 | 292 | 317 | 314 | 314 | Metal binding | Note=Calcium 2 |
| O14815 | 292 | 317 | 316 | 316 | Metal binding | Note=Calcium 2%3B via carbonyl oxygen |
| O14815 | 506 | 533 | 1 | 690 | Chain | ID=PRO_0000207722;Note=Calpain-9 |
| O14815 | 506 | 533 | 518 | 552 | Domain | Note=EF-hand 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
| O14815 | 506 | 533 | 522 | 522 | Natural variant | ID=VAR_022198;Note=R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs12731961 |
| O14815 | 506 | 533 | 338 | 521 | Region | Note=Domain III |
| O14815 | 506 | 533 | 522 | 690 | Region | Note=Domain IV |
| 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 |
| O14815 | 235 | 263 | 254 | 254 | Active site | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17157313;Dbxref=PMID:17157313 |
| O14815 | 235 | 263 | 256 | 266 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 235 | 263 | 1 | 690 | Chain | ID=PRO_0000207722;Note=Calpain-9 |
| O14815 | 235 | 263 | 42 | 337 | Domain | Note=Calpain catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00239 |
| O14815 | 235 | 263 | 239 | 241 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 235 | 263 | 239 | 239 | Natural variant | ID=VAR_022192;Note=A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs28359647 |
| O14815 | 292 | 317 | 292 | 318 | Alternative sequence | ID=VSP_007553;Note=In isoform 2. SSPEWRSVGPAEQKRLCHTALDDGEFW->R;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10835488;Dbxref=PMID:10835488 |
| O14815 | 292 | 317 | 313 | 320 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 292 | 317 | 1 | 690 | Chain | ID=PRO_0000207722;Note=Calpain-9 |
| O14815 | 292 | 317 | 42 | 337 | Domain | Note=Calpain catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00239 |
| O14815 | 292 | 317 | 294 | 298 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 292 | 317 | 301 | 306 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ZIV |
| O14815 | 292 | 317 | 312 | 312 | Metal binding | Note=Calcium 2%3B via carbonyl oxygen |
| O14815 | 292 | 317 | 314 | 314 | Metal binding | Note=Calcium 2 |
| O14815 | 292 | 317 | 316 | 316 | Metal binding | Note=Calcium 2%3B via carbonyl oxygen |
| O14815 | 506 | 533 | 1 | 690 | Chain | ID=PRO_0000207722;Note=Calpain-9 |
| O14815 | 506 | 533 | 518 | 552 | Domain | Note=EF-hand 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
| O14815 | 506 | 533 | 522 | 522 | Natural variant | ID=VAR_022198;Note=R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs12731961 |
| O14815 | 506 | 533 | 338 | 521 | Region | Note=Domain III |
| O14815 | 506 | 533 | 522 | 690 | Region | Note=Domain IV |
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SNVs in the skipped exons for CAPN9 |
| - 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-A39Y-01 | exon_skip_19263 | 230895258 | 230895376 | 230895325 | 230895325 | Frame_Shift_Del | C | - | p.I117fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_19263 | 230895258 | 230895376 | 230895370 | 230895370 | Frame_Shift_Del | T | - | p.H132fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_19284 | 230925878 | 230925935 | 230925930 | 230925930 | Frame_Shift_Del | A | - | p.Q525fs |
| UCEC | TCGA-AX-A05Z-01 | exon_skip_19257 | 230891083 | 230891152 | 230891101 | 230891101 | Nonsense_Mutation | G | T | p.E78* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_19257 | 230891083 | 230891152 | 230891101 | 230891101 | Nonsense_Mutation | G | T | p.E78* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_19257 | 230891083 | 230891152 | 230891101 | 230891101 | Nonsense_Mutation | G | T | p.E78X |
| LGG | TCGA-DU-6392-01 | exon_skip_19263 | 230895258 | 230895376 | 230895265 | 230895265 | Nonsense_Mutation | C | A | p.C97* |
| LUSC | TCGA-66-2742-01 | exon_skip_19274 | 230914719 | 230914879 | 230914831 | 230914831 | Nonsense_Mutation | G | T | p.G356* |
| SKCM | TCGA-WE-A8K5-06 | exon_skip_19279 | 230915925 | 230916082 | 230915935 | 230915935 | Nonsense_Mutation | G | A | p.W349* |
| LUAD | TCGA-78-7156-01 | exon_skip_19265 | 230904926 | 230905009 | 230904925 | 230904925 | Splice_Site | G | C | p.T236_splice |
| LUAD | TCGA-67-3771-01 | 230910300 | 230910377 | 230910379 | 230910379 | Splice_Site | T | A | p.W318_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 |
| SNU503_LARGE_INTESTINE | 230914719 | 230914879 | 230914742 | 230914742 | Frame_Shift_Del | C | - | p.A326fs |
| KYSE50_OESOPHAGUS | 230915925 | 230916082 | 230916075 | 230916075 | Frame_Shift_Del | T | - | p.I422fs |
| SISO_CERVIX | 230904926 | 230905009 | 230904961 | 230904962 | Frame_Shift_Ins | - | T | p.F248fs |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 230904926 | 230905009 | 230904961 | 230904962 | Frame_Shift_Ins | - | T | p.F248fs |
| SNU81_LARGE_INTESTINE | 230895258 | 230895376 | 230895339 | 230895339 | Missense_Mutation | G | A | p.S122N |
| CAL78_BONE | 230904926 | 230905009 | 230904932 | 230904932 | Missense_Mutation | A | C | p.S238R |
| OCILY132_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 230904926 | 230905009 | 230904957 | 230904957 | Missense_Mutation | C | T | p.T246M |
| KP4_PANCREAS | 230904926 | 230905009 | 230904957 | 230904957 | Missense_Mutation | C | T | p.T246M |
| CW2_LARGE_INTESTINE | 230904926 | 230905009 | 230904962 | 230904962 | Missense_Mutation | T | G | p.F248V |
| RL952_ENDOMETRIUM | 230904926 | 230905009 | 230904983 | 230904983 | Missense_Mutation | G | A | p.A255T |
| KYAE1_OESOPHAGUS | 230910300 | 230910377 | 230910335 | 230910335 | Missense_Mutation | A | G | p.Q304R |
| FTC238_THYROID | 230910300 | 230910377 | 230910341 | 230910341 | Missense_Mutation | G | A | p.R306H |
| FTC133_THYROID | 230910300 | 230910377 | 230910341 | 230910341 | Missense_Mutation | G | A | p.R306H |
| RKO_LARGE_INTESTINE | 230914719 | 230914879 | 230914771 | 230914771 | Missense_Mutation | C | T | p.L336F |
| NY_BONE | 230914719 | 230914879 | 230914780 | 230914780 | Missense_Mutation | G | A | p.D339N |
| CAL51_BREAST | 230914719 | 230914879 | 230914844 | 230914844 | Missense_Mutation | G | A | p.R360H |
| RKO_LARGE_INTESTINE | 230914719 | 230914879 | 230914867 | 230914867 | Missense_Mutation | C | T | p.R368C |
| SW900_LUNG | 230915925 | 230916082 | 230915930 | 230915930 | Missense_Mutation | T | G | p.F374V |
| WM793_SKIN | 230915925 | 230916082 | 230916032 | 230916032 | Missense_Mutation | C | G | p.L408V |
| LS180_LARGE_INTESTINE | 230915925 | 230916082 | 230916057 | 230916057 | Missense_Mutation | T | C | p.L416P |
| HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 230915925 | 230916082 | 230916072 | 230916072 | Missense_Mutation | C | T | p.A421V |
| SNU668_STOMACH | 230923268 | 230923348 | 230923320 | 230923320 | Missense_Mutation | G | A | p.R524Q |
| DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 230925878 | 230925935 | 230925883 | 230925883 | Missense_Mutation | G | T | p.M535I |
| TCYIK_CERVIX | 230925878 | 230925935 | 230925930 | 230925930 | Missense_Mutation | A | G | p.Q551R |
| 22RV1_PROSTATE | 230933908 | 230933966 | 230933915 | 230933915 | Missense_Mutation | C | A | p.F665L |
| LB831BLC_URINARY_TRACT | 230914719 | 230914879 | 230914838 | 230914838 | Nonsense_Mutation | G | A | p.W358* |
| LB831EBV_MATCHED_NORMAL_TISSUE | 230914719 | 230914879 | 230914838 | 230914838 | Nonsense_Mutation | G | A | p.W358* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CAPN9 |
| 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 CAPN9 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CAPN9 |
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RelatedDrugs for CAPN9 |
| 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 CAPN9 |
| 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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