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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 CASC3 |
 Gene summary |
| Gene information | Gene symbol | CASC3 | Gene ID | 22794 |
| Gene name | CASC3, exon junction complex subunit | |
| Synonyms | BTZ|MLN51 | |
| Cytomap | 17q21.1 | |
| Type of gene | protein-coding | |
| Description | protein CASC3MLN 51barentszcancer susceptibility 3cancer susceptibility candidate 3cancer susceptibility candidate gene 3 proteinmetastatic lymph node 51metastatic lymph node gene 51 proteinprotein barentsz | |
| Modification date | 20180523 | |
| UniProtAcc | O15234 | |
| Context | PubMed: CASC3 [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 CASC3 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 CASC3 |
| 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 CASC3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_152378 | 17 | 38297459:38297487:38297822:38297860:38318005:38318117 | 38297822:38297860 | ENSG00000108349.10 | ENST00000581849.1,ENST00000584997.1,ENST00000418132.3,ENST00000264645.7 |
| exon_skip_152381 | 17 | 38318254:38318406:38318977:38319154:38319733:38319855 | 38318977:38319154 | ENSG00000108349.10 | ENST00000418132.3,ENST00000474190.1,ENST00000264645.7 |
| exon_skip_152382 | 17 | 38320164:38320419:38323049:38323114:38323750:38323865 | 38323049:38323114 | ENSG00000108349.10 | ENST00000264645.7 |
| exon_skip_152383 | 17 | 38323750:38323865:38324102:38324201:38324455:38324508 | 38324102:38324201 | ENSG00000108349.10 | ENST00000577605.1,ENST00000264645.7 |
| exon_skip_152386 | 17 | 38324102:38324201:38324455:38324670:38325576:38325632 | 38324455:38324670 | ENSG00000108349.10 | ENST00000264645.7 |
| exon_skip_152390 | 17 | 38325576:38325699:38325850:38325915:38326699:38328417 | 38325850:38325915 | ENSG00000108349.10 | ENST00000394114.2,ENST00000264645.7 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CASC3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_152378 | 17 | 38297459:38297487:38297822:38297860:38318005:38318117 | 38297822:38297860 | ENSG00000108349.10 | ENST00000418132.3,ENST00000264645.7,ENST00000581849.1,ENST00000584997.1 |
| exon_skip_152381 | 17 | 38318254:38318406:38318977:38319154:38319733:38319855 | 38318977:38319154 | ENSG00000108349.10 | ENST00000418132.3,ENST00000264645.7,ENST00000474190.1 |
| exon_skip_152382 | 17 | 38320164:38320419:38323049:38323114:38323750:38323865 | 38323049:38323114 | ENSG00000108349.10 | ENST00000264645.7 |
| exon_skip_152383 | 17 | 38323750:38323865:38324102:38324201:38324455:38324508 | 38324102:38324201 | ENSG00000108349.10 | ENST00000264645.7,ENST00000577605.1 |
| exon_skip_152386 | 17 | 38324102:38324201:38324455:38324670:38325576:38325632 | 38324455:38324670 | ENSG00000108349.10 | ENST00000264645.7 |
| exon_skip_152390 | 17 | 38325576:38325699:38325850:38325915:38326699:38328417 | 38325850:38325915 | ENSG00000108349.10 | ENST00000264645.7,ENST00000394114.2 |
| 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 CASC3 |
| 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 |
| ENST00000264645 | 38325850 | 38325915 | 3UTR-3CDS |
| ENST00000264645 | 38297822 | 38297860 | Frame-shift |
| ENST00000264645 | 38323049 | 38323114 | Frame-shift |
| ENST00000264645 | 38324455 | 38324670 | Frame-shift |
| ENST00000264645 | 38318977 | 38319154 | In-frame |
| ENST00000264645 | 38324102 | 38324201 | 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 |
| ENST00000264645 | 38325850 | 38325915 | 3UTR-3CDS |
| ENST00000264645 | 38297822 | 38297860 | Frame-shift |
| ENST00000264645 | 38323049 | 38323114 | Frame-shift |
| ENST00000264645 | 38324455 | 38324670 | Frame-shift |
| ENST00000264645 | 38318977 | 38319154 | In-frame |
| ENST00000264645 | 38324102 | 38324201 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CASC3 |
| 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 |
| ENST00000264645 | 4133 | 703 | 38318977 | 38319154 | 835 | 1011 | 203 | 261 |
| ENST00000264645 | 4133 | 703 | 38324102 | 38324201 | 1878 | 1976 | 550 | 583 |
| 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 |
| ENST00000264645 | 4133 | 703 | 38318977 | 38319154 | 835 | 1011 | 203 | 261 |
| ENST00000264645 | 4133 | 703 | 38324102 | 38324201 | 1878 | 1976 | 550 | 583 |
| 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 |
| O15234 | 203 | 261 | 1 | 703 | Chain | ID=PRO_0000089324;Note=Protein CASC3 |
| O15234 | 203 | 261 | 226 | 228 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2J0S |
| O15234 | 203 | 261 | 233 | 240 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2HYI |
| O15234 | 203 | 261 | 204 | 210 | Motif | Note=Nuclear localization signal 1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O15234 | 203 | 261 | 254 | 262 | Motif | Note=Nuclear localization signal 2;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O15234 | 203 | 261 | 218 | 218 | Mutagenesis | Note=Abolishes interaction with EIF4A3%2C EJC formation and localization in nucleus speckles. W->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16170325;Dbxref=PMID:16170325 |
| O15234 | 203 | 261 | 220 | 221 | Mutagenesis | Note=Abolishes interaction with EIF4A3%2C EJC formation and localization in nucleus speckles. HD->AA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16170325;Dbxref=PMID:16170325 |
| O15234 | 203 | 261 | 240 | 241 | Mutagenesis | Note=Abolishes interaction with EIF4A3%2C EJC formation and localization in nucleus speckles. YG->AA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16170325;Dbxref=PMID:16170325 |
| O15234 | 203 | 261 | 137 | 283 | Region | Note=Necessary for RNA-binding%2C interaction with MAGOH and localization in nucleus speckles;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15166247;Dbxref=PMID:15166247 |
| O15234 | 203 | 261 | 137 | 283 | Region | Note=Sufficient to form the EJC |
| O15234 | 203 | 261 | 244 | 246 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3EX7 |
| O15234 | 550 | 583 | 1 | 703 | Chain | ID=PRO_0000089324;Note=Protein CASC3 |
| O15234 | 550 | 583 | 377 | 703 | Region | Note=Necessary for localization in cytoplasmic stress granules |
| 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 |
| O15234 | 203 | 261 | 1 | 703 | Chain | ID=PRO_0000089324;Note=Protein CASC3 |
| O15234 | 203 | 261 | 226 | 228 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2J0S |
| O15234 | 203 | 261 | 233 | 240 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2HYI |
| O15234 | 203 | 261 | 204 | 210 | Motif | Note=Nuclear localization signal 1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O15234 | 203 | 261 | 254 | 262 | Motif | Note=Nuclear localization signal 2;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O15234 | 203 | 261 | 218 | 218 | Mutagenesis | Note=Abolishes interaction with EIF4A3%2C EJC formation and localization in nucleus speckles. W->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16170325;Dbxref=PMID:16170325 |
| O15234 | 203 | 261 | 220 | 221 | Mutagenesis | Note=Abolishes interaction with EIF4A3%2C EJC formation and localization in nucleus speckles. HD->AA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16170325;Dbxref=PMID:16170325 |
| O15234 | 203 | 261 | 240 | 241 | Mutagenesis | Note=Abolishes interaction with EIF4A3%2C EJC formation and localization in nucleus speckles. YG->AA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16170325;Dbxref=PMID:16170325 |
| O15234 | 203 | 261 | 137 | 283 | Region | Note=Necessary for RNA-binding%2C interaction with MAGOH and localization in nucleus speckles;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15166247;Dbxref=PMID:15166247 |
| O15234 | 203 | 261 | 137 | 283 | Region | Note=Sufficient to form the EJC |
| O15234 | 203 | 261 | 244 | 246 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3EX7 |
| O15234 | 550 | 583 | 1 | 703 | Chain | ID=PRO_0000089324;Note=Protein CASC3 |
| O15234 | 550 | 583 | 377 | 703 | Region | Note=Necessary for localization in cytoplasmic stress granules |
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SNVs in the skipped exons for CASC3 |
| - 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 |
| SKCM | TCGA-D3-A1Q4-06 | exon_skip_152383 | 38324103 | 38324201 | 38324121 | 38324121 | Frame_Shift_Del | T | - | p.I557fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_152386 | 38324456 | 38324670 | 38324506 | 38324506 | Frame_Shift_Del | C | - | p.P603fs |
| KIRP | TCGA-DZ-6133-01 | exon_skip_152381 | 38318978 | 38319154 | 38319005 | 38319005 | Nonsense_Mutation | G | A | p.W212* |
| KIRP | TCGA-DZ-6133-01 | exon_skip_152381 | 38318978 | 38319154 | 38319005 | 38319005 | Nonsense_Mutation | G | A | p.W212X |
| SARC | TCGA-SI-A71Q-01 | exon_skip_152383 | 38324103 | 38324201 | 38324174 | 38324174 | Nonsense_Mutation | C | T | p.Q575* |
| LUAD | TCGA-78-7537-01 | exon_skip_152381 | 38318978 | 38319154 | 38319155 | 38319155 | Splice_Site | G | T | p.R262_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 |
| HCC38_BREAST | 38324456 | 38324670 | 38324646 | 38324651 | In_Frame_Del | GCCTCA | - | p.PH648del |
| GSU_STOMACH | 38318978 | 38319154 | 38318995 | 38318995 | Missense_Mutation | G | A | p.R209Q |
| HCC2108_LUNG | 38318978 | 38319154 | 38319055 | 38319055 | Missense_Mutation | C | A | p.A229D |
| MORCPR_LUNG | 38318978 | 38319154 | 38319055 | 38319055 | Missense_Mutation | C | A | p.A229D |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38318978 | 38319154 | 38319103 | 38319103 | Missense_Mutation | G | A | p.R245H |
| CP66MEL_SKIN | 38318978 | 38319154 | 38319132 | 38319132 | Missense_Mutation | C | T | p.P255S |
| SNU324_PANCREAS | 38324103 | 38324201 | 38324165 | 38324165 | Missense_Mutation | A | G | p.M572V |
| LNCAPCLONEFGC_PROSTATE | 38324456 | 38324670 | 38324491 | 38324491 | Missense_Mutation | A | G | p.N596D |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38324456 | 38324670 | 38324668 | 38324668 | Nonsense_Mutation | C | T | p.Q655* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CASC3 |
| 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 CASC3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CASC3 |
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RelatedDrugs for CASC3 |
| 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 CASC3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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