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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 COL4A2 |
 Gene summary |
| Gene information | Gene symbol | COL4A2 | Gene ID | 1284 |
| Gene name | collagen type IV alpha 2 chain | |
| Synonyms | ICH|POREN2 | |
| Cytomap | 13q34 | |
| Type of gene | protein-coding | |
| Description | collagen alpha-2(IV) chaincanstatin | |
| Modification date | 20180523 | |
| UniProtAcc | P08572 | |
| Context | PubMed: COL4A2 [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 |
| COL4A2 | GO:0016525 | negative regulation of angiogenesis | 10625665 |
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Exon skipping events across known transcript of Ensembl for COL4A2 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 COL4A2 |
| 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 COL4A2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_101281 | 13 | 110960415:110960470:111009818:111009899:111077080:111077215 | 111009818:111009899 | ENSG00000134871.13 | ENST00000360467.5,ENST00000400163.2 |
| exon_skip_101282 | 13 | 111009818:111009899:111077080:111077215:111077299:111077344 | 111077080:111077215 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101283 | 13 | 111090348:111090384:111090964:111091015:111092135:111092180 | 111090964:111091015 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101288 | 13 | 111121563:111121671:111125275:111125497:111130349:111130394 | 111125275:111125497 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101291 | 13 | 111137251:111137374:111138001:111138183:111141791:111141855 | 111138001:111138183 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101292 | 13 | 111138001:111138183:111141791:111141855:111142057:111142132 | 111141791:111141855 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101295 | 13 | 111143579:111143687:111144416:111144524:111145557:111145629 | 111144416:111144524 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101298 | 13 | 111144416:111144524:111145557:111145629:111147688:111147814 | 111145557:111145629 | ENSG00000134871.13 | ENST00000360467.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for COL4A2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_101281 | 13 | 110960415:110960470:111009818:111009899:111077080:111077215 | 111009818:111009899 | ENSG00000134871.13 | ENST00000400163.2,ENST00000360467.5 |
| exon_skip_101282 | 13 | 111009818:111009899:111077080:111077215:111077299:111077344 | 111077080:111077215 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101283 | 13 | 111090348:111090384:111090964:111091015:111092135:111092180 | 111090964:111091015 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101288 | 13 | 111121563:111121671:111125275:111125497:111130349:111130394 | 111125275:111125497 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101291 | 13 | 111137251:111137374:111138001:111138183:111141791:111141855 | 111138001:111138183 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101292 | 13 | 111138001:111138183:111141791:111141855:111142057:111142132 | 111141791:111141855 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101295 | 13 | 111143579:111143687:111144416:111144524:111145557:111145629 | 111144416:111144524 | ENSG00000134871.13 | ENST00000360467.5 |
| exon_skip_101298 | 13 | 111144416:111144524:111145557:111145629:111147688:111147814 | 111145557:111145629 | ENSG00000134871.13 | ENST00000360467.5 |
| 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 COL4A2 |
| 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 |
| ENST00000360467 | 111138001 | 111138183 | Frame-shift |
| ENST00000360467 | 111141791 | 111141855 | Frame-shift |
| ENST00000360467 | 111009818 | 111009899 | In-frame |
| ENST00000360467 | 111077080 | 111077215 | In-frame |
| ENST00000360467 | 111090964 | 111091015 | In-frame |
| ENST00000360467 | 111125275 | 111125497 | In-frame |
| ENST00000360467 | 111144416 | 111144524 | In-frame |
| ENST00000360467 | 111145557 | 111145629 | 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 |
| ENST00000360467 | 111138001 | 111138183 | Frame-shift |
| ENST00000360467 | 111141791 | 111141855 | Frame-shift |
| ENST00000360467 | 111009818 | 111009899 | In-frame |
| ENST00000360467 | 111077080 | 111077215 | In-frame |
| ENST00000360467 | 111090964 | 111091015 | In-frame |
| ENST00000360467 | 111125275 | 111125497 | In-frame |
| ENST00000360467 | 111144416 | 111144524 | In-frame |
| ENST00000360467 | 111145557 | 111145629 | In-frame |
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Infer the effects of exon skipping event on protein functional features for COL4A2 |
| 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 |
| ENST00000360467 | 6298 | 1712 | 111009818 | 111009899 | 406 | 486 | 33 | 60 |
| ENST00000360467 | 6298 | 1712 | 111077080 | 111077215 | 487 | 621 | 60 | 105 |
| ENST00000360467 | 6298 | 1712 | 111090964 | 111091015 | 1168 | 1218 | 287 | 304 |
| ENST00000360467 | 6298 | 1712 | 111125275 | 111125497 | 2510 | 2731 | 734 | 808 |
| ENST00000360467 | 6298 | 1712 | 111144416 | 111144524 | 3761 | 3868 | 1151 | 1187 |
| ENST00000360467 | 6298 | 1712 | 111145557 | 111145629 | 3869 | 3940 | 1187 | 1211 |
| 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 |
| ENST00000360467 | 6298 | 1712 | 111009818 | 111009899 | 406 | 486 | 33 | 60 |
| ENST00000360467 | 6298 | 1712 | 111077080 | 111077215 | 487 | 621 | 60 | 105 |
| ENST00000360467 | 6298 | 1712 | 111090964 | 111091015 | 1168 | 1218 | 287 | 304 |
| ENST00000360467 | 6298 | 1712 | 111125275 | 111125497 | 2510 | 2731 | 734 | 808 |
| ENST00000360467 | 6298 | 1712 | 111144416 | 111144524 | 3761 | 3868 | 1151 | 1187 |
| ENST00000360467 | 6298 | 1712 | 111145557 | 111145629 | 3869 | 3940 | 1187 | 1211 |
| 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 |
| P08572 | 33 | 60 | 26 | 183 | Propeptide | ID=PRO_0000005824;Note=N-terminal propeptide (7S domain) |
| P08572 | 60 | 105 | 26 | 183 | Propeptide | ID=PRO_0000005824;Note=N-terminal propeptide (7S domain) |
| P08572 | 287 | 304 | 184 | 1712 | Chain | ID=PRO_0000005825;Note=Collagen alpha-2(IV) chain |
| P08572 | 287 | 304 | 184 | 1484 | Region | Note=Triple-helical region |
| P08572 | 734 | 808 | 184 | 1712 | Chain | ID=PRO_0000005825;Note=Collagen alpha-2(IV) chain |
| P08572 | 734 | 808 | 184 | 1484 | Region | Note=Triple-helical region |
| P08572 | 1151 | 1187 | 184 | 1712 | Chain | ID=PRO_0000005825;Note=Collagen alpha-2(IV) chain |
| P08572 | 1151 | 1187 | 1152 | 1152 | Natural variant | ID=VAR_067838;Note=In POREN2%3B incomplete penetrance. G->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22209246;Dbxref=dbSNP:rs387906602,PMID:22209246 |
| P08572 | 1151 | 1187 | 184 | 1484 | Region | Note=Triple-helical region |
| P08572 | 1187 | 1211 | 184 | 1712 | Chain | ID=PRO_0000005825;Note=Collagen alpha-2(IV) chain |
| P08572 | 1187 | 1211 | 184 | 1484 | Region | Note=Triple-helical region |
| 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 |
| P08572 | 33 | 60 | 26 | 183 | Propeptide | ID=PRO_0000005824;Note=N-terminal propeptide (7S domain) |
| P08572 | 60 | 105 | 26 | 183 | Propeptide | ID=PRO_0000005824;Note=N-terminal propeptide (7S domain) |
| P08572 | 287 | 304 | 184 | 1712 | Chain | ID=PRO_0000005825;Note=Collagen alpha-2(IV) chain |
| P08572 | 287 | 304 | 184 | 1484 | Region | Note=Triple-helical region |
| P08572 | 734 | 808 | 184 | 1712 | Chain | ID=PRO_0000005825;Note=Collagen alpha-2(IV) chain |
| P08572 | 734 | 808 | 184 | 1484 | Region | Note=Triple-helical region |
| P08572 | 1151 | 1187 | 184 | 1712 | Chain | ID=PRO_0000005825;Note=Collagen alpha-2(IV) chain |
| P08572 | 1151 | 1187 | 1152 | 1152 | Natural variant | ID=VAR_067838;Note=In POREN2%3B incomplete penetrance. G->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22209246;Dbxref=dbSNP:rs387906602,PMID:22209246 |
| P08572 | 1151 | 1187 | 184 | 1484 | Region | Note=Triple-helical region |
| P08572 | 1187 | 1211 | 184 | 1712 | Chain | ID=PRO_0000005825;Note=Collagen alpha-2(IV) chain |
| P08572 | 1187 | 1211 | 184 | 1484 | Region | Note=Triple-helical region |
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SNVs in the skipped exons for COL4A2 |
| - 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 |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_101281 | 111009819 | 111009899 | 111009849 | 111009849 | Nonsense_Mutation | G | T | p.G44* |
| LIHC | TCGA-WX-AA46-01 | exon_skip_101288 | 111125276 | 111125497 | 111125290 | 111125290 | Nonsense_Mutation | C | T | p.R740X |
| THYM | TCGA-XU-A92U-01 | exon_skip_101298 | 111145558 | 111145629 | 111145566 | 111145566 | Nonsense_Mutation | G | T | p.G1191X |
| - 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 |
| IGR39_SKIN | 111077081 | 111077215 | 111077119 | 111077120 | Frame_Shift_Ins | - | T | p.P74fs |
| IGR37_SKIN | 111077081 | 111077215 | 111077119 | 111077120 | Frame_Shift_Ins | - | T | p.P74fs |
| MALME3M_SKIN | 111009819 | 111009899 | 111009861 | 111009861 | Missense_Mutation | A | G | p.S48G |
| HEC59_ENDOMETRIUM | 111009819 | 111009899 | 111009889 | 111009889 | Missense_Mutation | A | G | p.K57R |
| HCT15_LARGE_INTESTINE | 111077081 | 111077215 | 111077195 | 111077195 | Missense_Mutation | A | G | p.T99A |
| WM88_SKIN | 111077081 | 111077215 | 111077207 | 111077207 | Missense_Mutation | G | A | p.G103S |
| LS411N_LARGE_INTESTINE | 111125276 | 111125497 | 111125429 | 111125429 | Missense_Mutation | A | C | p.D786A |
| SW1463_LARGE_INTESTINE | 111138002 | 111138183 | 111138082 | 111138082 | Missense_Mutation | A | C | p.K1036Q |
| MDAPCA2B_PROSTATE | 111138002 | 111138183 | 111138094 | 111138094 | Missense_Mutation | G | A | p.G1040R |
| CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 111138002 | 111138183 | 111138112 | 111138112 | Missense_Mutation | G | A | p.G1046S |
| HCC56_LARGE_INTESTINE | 111141792 | 111141855 | 111141796 | 111141796 | Missense_Mutation | A | G | p.D1071G |
| IHH4_THYROID | 111141792 | 111141855 | 111141796 | 111141796 | Missense_Mutation | A | G | p.D1071G |
| OVK18_OVARY | 111144417 | 111144524 | 111144482 | 111144482 | Missense_Mutation | G | T | p.G1174C |
| HEC108_ENDOMETRIUM | 111125276 | 111125497 | 111125276 | 111125276 | Splice_Site | G | T | p.G735V |
| BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 111138002 | 111138183 | 111138183 | 111138183 | Splice_Site | G | A | p.R1069R |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 111145558 | 111145629 | 111145559 | 111145559 | Splice_Site | T | G | p.G1188G |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COL4A2 |
| 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 COL4A2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for COL4A2 |
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RelatedDrugs for COL4A2 |
| 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 COL4A2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| COL4A2 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| COL4A2 | C0027726 | Nephrotic Syndrome | 1 | CTD_human |
| COL4A2 | C0149925 | Small cell carcinoma of lung | 1 | CTD_human |
| COL4A2 | C3280970 | PORENCEPHALY 2 | 1 | UNIPROT |
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