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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 COG3 |
 Gene summary |
| Gene information | Gene symbol | COG3 | Gene ID | 83548 |
| Gene name | component of oligomeric golgi complex 3 | |
| Synonyms | SEC34 | |
| Cytomap | 13q14.13 | |
| Type of gene | protein-coding | |
| Description | conserved oligomeric Golgi complex subunit 3COG complex subunit 3p94tethering factor SEC34vesicle-docking protein SEC34 homolog | |
| Modification date | 20180523 | |
| UniProtAcc | Q96JB2 | |
| Context | PubMed: COG3 [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 |
| COG3 | GO:0006888 | ER to Golgi vesicle-mediated transport | 11929878 |
| COG3 | GO:0006891 | intra-Golgi vesicle-mediated transport | 11929878 |
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Exon skipping events across known transcript of Ensembl for COG3 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 COG3 |
| 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 COG3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_100247 | 13 | 46053139:46053201:46054259:46054425:46055364:46055439 | 46054259:46054425 | ENSG00000136152.10 | ENST00000349995.5 |
| exon_skip_100253 | 13 | 46065603:46065673:46066293:46066385:46067481:46067621 | 46066293:46066385 | ENSG00000136152.10 | ENST00000465942.1,ENST00000349995.5 |
| exon_skip_100258 | 13 | 46067555:46067621:46070286:46070447:46077378:46077484 | 46070286:46070447 | ENSG00000136152.10 | ENST00000465942.1,ENST00000349995.5 |
| exon_skip_100260 | 13 | 46083826:46083951:46085899:46085989:46090277:46090398 | 46085899:46085989 | ENSG00000136152.10 | ENST00000349995.5 |
| exon_skip_100264 | 13 | 46090281:46090398:46092896:46092985:46093094:46093229 | 46092896:46092985 | ENSG00000136152.10 | ENST00000349995.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for COG3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_100247 | 13 | 46053139:46053201:46054259:46054425:46055364:46055439 | 46054259:46054425 | ENSG00000136152.10 | ENST00000349995.5 |
| exon_skip_100253 | 13 | 46065603:46065673:46066293:46066385:46067481:46067621 | 46066293:46066385 | ENSG00000136152.10 | ENST00000349995.5,ENST00000465942.1 |
| exon_skip_100258 | 13 | 46067555:46067621:46070286:46070447:46077378:46077484 | 46070286:46070447 | ENSG00000136152.10 | ENST00000349995.5,ENST00000465942.1 |
| exon_skip_100260 | 13 | 46083826:46083951:46085899:46085989:46090277:46090398 | 46085899:46085989 | ENSG00000136152.10 | ENST00000349995.5 |
| exon_skip_100264 | 13 | 46090281:46090398:46092896:46092985:46093094:46093229 | 46092896:46092985 | ENSG00000136152.10 | ENST00000349995.5 |
| exon_skip_100266 | 13 | 46104816:46104915:46105285:46105444:46106144:46106228 | 46105285:46105444 | ENSG00000136152.10 | ENST00000486940.1 |
| 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 COG3 |
| 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 |
| ENST00000349995 | 46054259 | 46054425 | Frame-shift |
| ENST00000349995 | 46066293 | 46066385 | Frame-shift |
| ENST00000349995 | 46070286 | 46070447 | Frame-shift |
| ENST00000349995 | 46092896 | 46092985 | Frame-shift |
| ENST00000349995 | 46085899 | 46085989 | 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 |
| ENST00000349995 | 46054259 | 46054425 | Frame-shift |
| ENST00000349995 | 46066293 | 46066385 | Frame-shift |
| ENST00000349995 | 46070286 | 46070447 | Frame-shift |
| ENST00000349995 | 46092896 | 46092985 | Frame-shift |
| ENST00000349995 | 46085899 | 46085989 | In-frame |
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Infer the effects of exon skipping event on protein functional features for COG3 |
| 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 |
| ENST00000349995 | 4515 | 828 | 46085899 | 46085989 | 1832 | 1921 | 573 | 603 |
| 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 |
| ENST00000349995 | 4515 | 828 | 46085899 | 46085989 | 1832 | 1921 | 573 | 603 |
| 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 |
| Q96JB2 | 573 | 603 | 445 | 828 | Alternative sequence | ID=VSP_013653;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96JB2 | 573 | 603 | 2 | 828 | Chain | ID=PRO_0000213500;Note=Conserved oligomeric Golgi complex subunit 3 |
| 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 |
| Q96JB2 | 573 | 603 | 445 | 828 | Alternative sequence | ID=VSP_013653;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96JB2 | 573 | 603 | 2 | 828 | Chain | ID=PRO_0000213500;Note=Conserved oligomeric Golgi complex subunit 3 |
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SNVs in the skipped exons for COG3 |
| - 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 |
| KIRP | TCGA-Y8-A895-01 | exon_skip_100247 | 46054260 | 46054425 | 46054274 | 46054274 | Frame_Shift_Del | A | - | p.Y133fs |
| READ | TCGA-EI-6507-01 | 46085900 | 46085989 | 46085968 | 46085969 | Frame_Shift_Del | AG | - | p.596_596del | |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_100264 | 46092897 | 46092985 | 46092931 | 46092931 | Frame_Shift_Del | C | - | p.V655fs |
| PAAD | TCGA-LB-A7SX-01 | exon_skip_100247 | 46054260 | 46054425 | 46054424 | 46054425 | Frame_Shift_Ins | - | G | p.Q183fs |
| HNSC | TCGA-CV-7414-01 | exon_skip_100264 | 46092897 | 46092985 | 46092895 | 46092895 | Splice_Site | A | G | p.D644_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 |
| NCCSTCK140_STOMACH | 46054260 | 46054425 | 46054274 | 46054274 | Missense_Mutation | A | C | p.Y133S |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 46054260 | 46054425 | 46054274 | 46054274 | Missense_Mutation | A | C | p.Y133S |
| TOV112D_OVARY | 46070287 | 46070447 | 46070325 | 46070325 | Missense_Mutation | A | T | p.M456L |
| LS411N_LARGE_INTESTINE | 46070287 | 46070447 | 46070347 | 46070347 | Missense_Mutation | G | A | p.R463Q |
| KYSE510_OESOPHAGUS | 46070287 | 46070447 | 46070406 | 46070406 | Missense_Mutation | C | G | p.P483A |
| KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 46085900 | 46085989 | 46085936 | 46085936 | Missense_Mutation | T | C | p.S586P |
| PACADD137_PANCREAS | 46092897 | 46092985 | 46092924 | 46092924 | Missense_Mutation | T | C | p.M653T |
| DOK_UPPER_AERODIGESTIVE_TRACT | 46070287 | 46070447 | 46070358 | 46070358 | Nonsense_Mutation | C | T | p.R467* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COG3 |
| 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 COG3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for COG3 |
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RelatedDrugs for COG3 |
| 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 COG3 |
| 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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