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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 COCH |
 Gene summary |
| Gene information | Gene symbol | COCH | Gene ID | 1690 |
| Gene name | cochlin | |
| Synonyms | COCH-5B2|COCH5B2|DFNA9 | |
| Cytomap | 14q12 | |
| Type of gene | protein-coding | |
| Description | cochlincoagulation factor C homolog, cochlin (Limulus polyphemus) | |
| Modification date | 20180523 | |
| UniProtAcc | O43405 | |
| Context | PubMed: COCH [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 COCH 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 COCH |
| 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 COCH |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_105901 | 14 | 31343764:31343797:31344121:31344178:31344261:31344309 | 31344121:31344178 | ENSG00000100473.11 | ENST00000396618.3,ENST00000553772.1 |
| exon_skip_105902 | 14 | 31343950:31344178:31344261:31344309:31346777:31346934 | 31344261:31344309 | ENSG00000100473.11 | ENST00000216361.4,ENST00000396618.3,ENST00000553772.1,ENST00000475087.1 |
| exon_skip_105905 | 14 | 31346779:31346934:31348016:31348150:31348628:31348691 | 31348016:31348150 | ENSG00000100473.11 | ENST00000556908.1,ENST00000216361.4,ENST00000396618.3,ENST00000553833.1,ENST00000475087.1,ENST00000460581.2 |
| exon_skip_105908 | 14 | 31346779:31346934:31348628:31348691:31349657:31349702 | 31348628:31348691 | ENSG00000100473.11 | ENST00000557065.1 |
| exon_skip_105910 | 14 | 31353758:31353862:31354115:31354247:31354599:31354738 | 31354115:31354247 | ENSG00000100473.11 | ENST00000468826.2,ENST00000382493.4 |
| exon_skip_105912 | 14 | 31353758:31353862:31354599:31354826:31355001:31355518 | 31354599:31354826 | ENSG00000100473.11 | ENST00000216361.4,ENST00000396618.3,ENST00000475087.1,ENST00000460581.2 |
| exon_skip_105913 | 14 | 31354599:31354826:31355001:31355518:31358821:31358999 | 31355001:31355518 | ENSG00000100473.11 | ENST00000216361.4,ENST00000396618.3,ENST00000468826.2,ENST00000382493.4,ENST00000460581.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for COCH |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_105901 | 14 | 31343764:31343797:31344121:31344178:31344261:31344309 | 31344121:31344178 | ENSG00000100473.11 | ENST00000553772.1,ENST00000396618.3 |
| exon_skip_105902 | 14 | 31343950:31344178:31344261:31344309:31346777:31346934 | 31344261:31344309 | ENSG00000100473.11 | ENST00000216361.4,ENST00000553772.1,ENST00000396618.3,ENST00000475087.1 |
| exon_skip_105904 | 14 | 31344261:31344309:31346777:31346934:31349657:31349702 | 31346777:31346934 | ENSG00000100473.11 | ENST00000553772.1 |
| exon_skip_105905 | 14 | 31346779:31346934:31348016:31348150:31348628:31348691 | 31348016:31348150 | ENSG00000100473.11 | ENST00000216361.4,ENST00000396618.3,ENST00000475087.1,ENST00000556908.1,ENST00000460581.2,ENST00000553833.1 |
| exon_skip_105908 | 14 | 31346779:31346934:31348628:31348691:31349657:31349702 | 31348628:31348691 | ENSG00000100473.11 | ENST00000557065.1 |
| exon_skip_105910 | 14 | 31353758:31353862:31354115:31354247:31354599:31354738 | 31354115:31354247 | ENSG00000100473.11 | ENST00000382493.4,ENST00000468826.2 |
| exon_skip_105912 | 14 | 31353758:31353862:31354599:31354826:31355001:31355518 | 31354599:31354826 | ENSG00000100473.11 | ENST00000216361.4,ENST00000396618.3,ENST00000475087.1,ENST00000460581.2 |
| exon_skip_105913 | 14 | 31354599:31354826:31355001:31355518:31358821:31358999 | 31355001:31355518 | ENSG00000100473.11 | ENST00000216361.4,ENST00000396618.3,ENST00000460581.2,ENST00000382493.4,ENST00000468826.2 |
| 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 COCH |
| 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 |
| ENST00000396618 | 31344121 | 31344178 | 5CDS-5UTR |
| ENST00000396618 | 31348016 | 31348150 | Frame-shift |
| ENST00000396618 | 31354599 | 31354826 | Frame-shift |
| ENST00000396618 | 31355001 | 31355518 | Frame-shift |
| ENST00000396618 | 31344261 | 31344309 | 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 |
| ENST00000396618 | 31344121 | 31344178 | 5CDS-5UTR |
| ENST00000396618 | 31348016 | 31348150 | Frame-shift |
| ENST00000396618 | 31354599 | 31354826 | Frame-shift |
| ENST00000396618 | 31355001 | 31355518 | Frame-shift |
| ENST00000396618 | 31344261 | 31344309 | In-frame |
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Infer the effects of exon skipping event on protein functional features for COCH |
| 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 |
| ENST00000396618 | 2553 | 550 | 31344261 | 31344309 | 91 | 138 | 11 | 27 |
| 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 |
| ENST00000396618 | 2553 | 550 | 31344261 | 31344309 | 91 | 138 | 11 | 27 |
| 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 |
| O43405 | 11 | 27 | 25 | 550 | Chain | ID=PRO_0000020968;Note=Cochlin |
| O43405 | 11 | 27 | 1 | 24 | Signal peptide | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| O43405 | 11 | 27 | 25 | 550 | Chain | ID=PRO_0000020968;Note=Cochlin |
| O43405 | 11 | 27 | 1 | 24 | Signal peptide | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for COCH |
| - 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-A3A0-01 | exon_skip_105905 | 31348017 | 31348150 | 31348036 | 31348036 | Frame_Shift_Del | G | - | p.G88fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_105905 | 31348017 | 31348150 | 31348036 | 31348036 | Frame_Shift_Del | G | - | p.G88fs |
| PAAD | TCGA-HZ-7918-01 | exon_skip_105913 | 31355002 | 31355518 | 31355263 | 31355270 | Frame_Shift_Del | GCTGTACA | - | p.AVQ296fs |
| SKCM | TCGA-D3-A51E-06 | exon_skip_105901 | 31344122 | 31344178 | 31344159 | 31344159 | Nonsense_Mutation | G | A | p.W5* |
| SKCM | TCGA-D3-A51E-06 | exon_skip_105901 | 31344122 | 31344178 | 31344159 | 31344159 | Nonsense_Mutation | G | A | p.W5X |
| UCEC | TCGA-BS-A0UF-01 | 31354600 | 31354826 | 31354788 | 31354788 | Nonsense_Mutation | G | T | p.E308* | |
| LUAD | TCGA-78-7167-01 | exon_skip_105902 | 31344262 | 31344309 | 31344261 | 31344261 | Splice_Site | G | C | p.G12_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 |
| MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31344122 | 31344178 | 31344164 | 31344164 | Missense_Mutation | C | T | p.P7L |
| KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31344122 | 31344178 | 31344164 | 31344164 | Missense_Mutation | C | T | p.P7L |
| KYSE270_OESOPHAGUS | 31344122 | 31344178 | 31344164 | 31344164 | Missense_Mutation | C | T | p.P7L |
| MEWO_SKIN | 31348017 | 31348150 | 31348039 | 31348039 | Missense_Mutation | G | A | p.G88R |
| SKPNDW_BONE | 31348017 | 31348150 | 31348109 | 31348109 | Missense_Mutation | C | A | p.S111Y |
| HCC2998_LARGE_INTESTINE | 31348017 | 31348150 | 31348113 | 31348113 | Missense_Mutation | A | C | p.Q112H |
| SNUC2A_LARGE_INTESTINE | 31348629 | 31348691 | 31348664 | 31348664 | Missense_Mutation | G | A | p.A137T |
| SNUC2B_LARGE_INTESTINE | 31348629 | 31348691 | 31348664 | 31348664 | Missense_Mutation | G | A | p.A137T |
| KYSE520_OESOPHAGUS | 31354600 | 31354826 | 31354680 | 31354680 | Missense_Mutation | G | A | p.V272I |
| ME1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31355002 | 31355518 | 31355012 | 31355012 | Missense_Mutation | G | A | p.R324Q |
| P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31355002 | 31355518 | 31355125 | 31355125 | Missense_Mutation | T | G | p.C362G |
| P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31355002 | 31355518 | 31355216 | 31355216 | Missense_Mutation | A | G | p.N392S |
| PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT | 31355002 | 31355518 | 31355423 | 31355423 | Missense_Mutation | T | C | p.I461T |
| HT115_LARGE_INTESTINE | 31348017 | 31348150 | 31348069 | 31348069 | Nonsense_Mutation | C | T | p.R98* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COCH |
| 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 |
| exon_skip_105913 | 14 | 31354599:31354826:31355001:31355518:31358821:31358999 | 31355001:31355518 | ENST00000216361.4,ENST00000396618.3,ENST00000468826.2,ENST00000382493.4,ENST00000460581.2 | LUAD | rs1045644 | chr14:31355096 | C/G | 6.61e-05 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for COCH |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for COCH |
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RelatedDrugs for COCH |
| 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 COCH |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| COCH | C1832425 | Deafness, Autosomal Dominant 9 | 8 | CTD_human;UNIPROT |
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