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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 C12orf4 |
 Gene summary |
| Gene information | Gene symbol | C12orf4 | Gene ID | 57102 |
| Gene name | chromosome 12 open reading frame 4 | |
| Synonyms | - | |
| Cytomap | 12p13.32 | |
| Type of gene | protein-coding | |
| Description | protein C12orf4 | |
| Modification date | 20180519 | |
| UniProtAcc | Q9NQ89 | |
| Context | PubMed: C12orf4 [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 C12orf4 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 C12orf4 |
| 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 C12orf4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_89314 | 12 | 4609480:4609506:4611476:4611648:4614471:4614546 | 4611476:4611648 | ENSG00000047621.7 | ENST00000544258.1 |
| exon_skip_89317 | 12 | 4614471:4614546:4626226:4626355:4627223:4627421 | 4626226:4626355 | ENSG00000047621.7 | ENST00000545746.1,ENST00000261250.3 |
| exon_skip_89319 | 12 | 4627223:4627421:4627939:4628046:4634419:4634541 | 4627939:4628046 | ENSG00000047621.7 | ENST00000541014.1,ENST00000545746.1,ENST00000261250.3 |
| exon_skip_89320 | 12 | 4634649:4634749:4639034:4639216:4643322:4643468 | 4639034:4639216 | ENSG00000047621.7 | ENST00000542080.1,ENST00000541014.1,ENST00000545746.1,ENST00000261250.3 |
| exon_skip_89321 | 12 | 4639034:4639216:4643322:4643468:4647574:4647609 | 4643322:4643468 | ENSG00000047621.7 | ENST00000541014.1 |
| exon_skip_89322 | 12 | 4643322:4643468:4645182:4645248:4647574:4647674 | 4645182:4645248 | ENSG00000047621.7 | ENST00000542080.1 |
| exon_skip_89323 | 12 | 4643322:4643468:4645182:4645377:4647574:4647609 | 4645182:4645377 | ENSG00000047621.7 | ENST00000545746.1 |
| exon_skip_89324 | 12 | 4643322:4643468:4645182:4645385:4647574:4647609 | 4645182:4645385 | ENSG00000047621.7 | ENST00000535030.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for C12orf4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_89314 | 12 | 4609480:4609506:4611476:4611648:4614471:4614546 | 4611476:4611648 | ENSG00000047621.7 | ENST00000544258.1 |
| exon_skip_89317 | 12 | 4614471:4614546:4626226:4626355:4627223:4627421 | 4626226:4626355 | ENSG00000047621.7 | ENST00000261250.3,ENST00000545746.1 |
| exon_skip_89319 | 12 | 4627223:4627421:4627939:4628046:4634419:4634541 | 4627939:4628046 | ENSG00000047621.7 | ENST00000261250.3,ENST00000545746.1,ENST00000541014.1 |
| exon_skip_89320 | 12 | 4634649:4634749:4639034:4639216:4643322:4643468 | 4639034:4639216 | ENSG00000047621.7 | ENST00000261250.3,ENST00000545746.1,ENST00000541014.1,ENST00000542080.1 |
| exon_skip_89321 | 12 | 4639034:4639216:4643322:4643468:4647574:4647609 | 4643322:4643468 | ENSG00000047621.7 | ENST00000541014.1 |
| exon_skip_89322 | 12 | 4643322:4643468:4645182:4645248:4647574:4647674 | 4645182:4645248 | ENSG00000047621.7 | ENST00000542080.1 |
| exon_skip_89323 | 12 | 4643322:4643468:4645182:4645377:4647574:4647609 | 4645182:4645377 | ENSG00000047621.7 | ENST00000545746.1 |
| exon_skip_89324 | 12 | 4643322:4643468:4645182:4645385:4647574:4647609 | 4645182:4645385 | ENSG00000047621.7 | ENST00000535030.1 |
| 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 C12orf4 |
| 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 |
| ENST00000545746 | 4645182 | 4645377 | 3UTR-3CDS |
| ENST00000261250 | 4627939 | 4628046 | Frame-shift |
| ENST00000545746 | 4627939 | 4628046 | Frame-shift |
| ENST00000261250 | 4639034 | 4639216 | Frame-shift |
| ENST00000545746 | 4639034 | 4639216 | Frame-shift |
| ENST00000261250 | 4626226 | 4626355 | In-frame |
| ENST00000545746 | 4626226 | 4626355 | 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 |
| ENST00000545746 | 4645182 | 4645377 | 3UTR-3CDS |
| ENST00000261250 | 4627939 | 4628046 | Frame-shift |
| ENST00000545746 | 4627939 | 4628046 | Frame-shift |
| ENST00000261250 | 4639034 | 4639216 | Frame-shift |
| ENST00000545746 | 4639034 | 4639216 | Frame-shift |
| ENST00000261250 | 4626226 | 4626355 | In-frame |
| ENST00000545746 | 4626226 | 4626355 | In-frame |
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Infer the effects of exon skipping event on protein functional features for C12orf4 |
| 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 |
| ENST00000261250 | 3843 | 552 | 4626226 | 4626355 | 1122 | 1250 | 344 | 387 |
| ENST00000545746 | 2185 | 552 | 4626226 | 4626355 | 1151 | 1279 | 344 | 387 |
| 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 |
| ENST00000261250 | 3843 | 552 | 4626226 | 4626355 | 1122 | 1250 | 344 | 387 |
| ENST00000545746 | 2185 | 552 | 4626226 | 4626355 | 1151 | 1279 | 344 | 387 |
| 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 |
| Q9NQ89 | 344 | 387 | 1 | 552 | Chain | ID=PRO_0000089842;Note=Protein C12orf4 |
| Q9NQ89 | 344 | 387 | 1 | 552 | Chain | ID=PRO_0000089842;Note=Protein C12orf4 |
| Q9NQ89 | 344 | 387 | 377 | 377 | Sequence conflict | Note=T->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQ89 | 344 | 387 | 377 | 377 | Sequence conflict | Note=T->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q9NQ89 | 344 | 387 | 1 | 552 | Chain | ID=PRO_0000089842;Note=Protein C12orf4 |
| Q9NQ89 | 344 | 387 | 1 | 552 | Chain | ID=PRO_0000089842;Note=Protein C12orf4 |
| Q9NQ89 | 344 | 387 | 377 | 377 | Sequence conflict | Note=T->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQ89 | 344 | 387 | 377 | 377 | Sequence conflict | Note=T->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for C12orf4 |
| - 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 |
| BRCA | TCGA-A8-A08L-01 | exon_skip_89319 | 4627940 | 4628046 | 4627964 | 4627967 | Frame_Shift_Del | CTAA | - | p.L270fs |
| BLCA | TCGA-DK-A6AW-01 | exon_skip_89317 | 4626227 | 4626355 | 4626293 | 4626293 | Nonsense_Mutation | C | A | p.E366* |
| KIRC | TCGA-A3-3374-01 | exon_skip_89319 | 4627940 | 4628046 | 4628042 | 4628042 | Nonsense_Mutation | C | A | p.E245* |
| HNSC | TCGA-UF-A71D-01 | exon_skip_89320 | 4639035 | 4639216 | 4639179 | 4639179 | Nonsense_Mutation | C | T | p.W121* |
| GBM | TCGA-06-0875-01 | exon_skip_89321 | 4643323 | 4643468 | 4643363 | 4643363 | Nonsense_Mutation | A | C | p.L95* |
| READ | TCGA-F5-6814-01 | exon_skip_89323 | 4645183 | 4645377 | 4645321 | 4645321 | Nonsense_Mutation | C | A | p.E14X |
| READ | TCGA-F5-6814-01 | exon_skip_89324 | 4645183 | 4645385 | 4645321 | 4645321 | Nonsense_Mutation | C | A | p.E14X |
| UCEC | TCGA-BS-A0TC-01 | exon_skip_89323 | 4645183 | 4645377 | 4645321 | 4645321 | Nonsense_Mutation | C | A | p.E14* |
| UCEC | TCGA-BS-A0TC-01 | exon_skip_89324 | 4645183 | 4645385 | 4645321 | 4645321 | Nonsense_Mutation | C | A | p.E14* |
| UCEC | TCGA-AP-A0LM-01 | exon_skip_89317 | 4626227 | 4626355 | 4626356 | 4626356 | Splice_Site | C | A | e8-1 |
| - 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 |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 4626227 | 4626355 | 4626311 | 4626311 | Frame_Shift_Del | G | - | p.R360fs |
| EFO27_OVARY | 4645183 | 4645385 | 4645320 | 4645321 | Frame_Shift_Del | TC | - | p.E14fs |
| EFO27_OVARY | 4645183 | 4645377 | 4645320 | 4645321 | Frame_Shift_Del | TC | - | p.E14fs |
| HEC1A_ENDOMETRIUM | 4626227 | 4626355 | 4626265 | 4626265 | Missense_Mutation | G | A | p.A375V |
| MERO48A_LUNG | 4627940 | 4628046 | 4628042 | 4628042 | Missense_Mutation | C | T | p.E245K |
| L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 4627940 | 4628046 | 4628042 | 4628042 | Missense_Mutation | C | T | p.E245K |
| HEC251_ENDOMETRIUM | 4639035 | 4639216 | 4639050 | 4639050 | Missense_Mutation | T | G | p.K164T |
| MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 4639035 | 4639216 | 4639183 | 4639183 | Missense_Mutation | T | C | p.S120G |
| SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 4645183 | 4645248 | 4645234 | 4645234 | Missense_Mutation | A | T | p.L43M |
| SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 4645183 | 4645385 | 4645234 | 4645234 | Missense_Mutation | A | T | p.L43M |
| SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 4645183 | 4645377 | 4645234 | 4645234 | Missense_Mutation | A | T | p.L43M |
| MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 4645183 | 4645385 | 4645270 | 4645270 | Missense_Mutation | G | A | p.P31S |
| MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 4645183 | 4645377 | 4645270 | 4645270 | Missense_Mutation | G | A | p.P31S |
| CORL303_LUNG | 4645183 | 4645385 | 4645294 | 4645294 | Missense_Mutation | T | C | p.S23G |
| CORL303_LUNG | 4645183 | 4645377 | 4645294 | 4645294 | Missense_Mutation | T | C | p.S23G |
| CAL39_VULVA | 4645183 | 4645385 | 4645323 | 4645323 | Missense_Mutation | C | G | p.R13T |
| CAL39_VULVA | 4645183 | 4645377 | 4645323 | 4645323 | Missense_Mutation | C | G | p.R13T |
| HEC251_ENDOMETRIUM | 4645183 | 4645385 | 4645321 | 4645321 | Nonsense_Mutation | C | A | p.E14* |
| HEC251_ENDOMETRIUM | 4645183 | 4645377 | 4645321 | 4645321 | Nonsense_Mutation | C | A | p.E14* |
| HT115_LARGE_INTESTINE | 4645183 | 4645385 | 4645321 | 4645321 | Nonsense_Mutation | C | A | p.E14* |
| HT115_LARGE_INTESTINE | 4645183 | 4645377 | 4645321 | 4645321 | Nonsense_Mutation | C | A | p.E14* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for C12orf4 |
| 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 C12orf4 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for C12orf4 |
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RelatedDrugs for C12orf4 |
| 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 C12orf4 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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