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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 CNGA1 |
 Gene summary |
| Gene information | Gene symbol | CNGA1 | Gene ID | 1259 |
| Gene name | cyclic nucleotide gated channel alpha 1 | |
| Synonyms | CNCG|CNCG1|CNG-1|CNG1|RCNC1|RCNCa|RCNCalpha|RP49 | |
| Cytomap | 4p12 | |
| Type of gene | protein-coding | |
| Description | cGMP-gated cation channel alpha-1CNG channel alpha-1cyclic nucleotide-gated cation channel 1cyclic nucleotide-gated channel, photoreceptorinterleukin-1 homologuerod photoreceptor cGMP-gated channel subunit alpha | |
| Modification date | 20180523 | |
| UniProtAcc | P29973 | |
| Context | PubMed: CNGA1 [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 CNGA1 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 CNGA1 |
| 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 CNGA1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_429386 | 4 | 47938030:47939846:47942779:47942886:47944057:47944165 | 47942779:47942886 | ENSG00000198515.9 | ENST00000358519.4,ENST00000402813.3,ENST00000420489.2,ENST00000514170.1,ENST00000544810.1 |
| exon_skip_429389 | 4 | 47942779:47942886:47944057:47944165:47945197:47945305 | 47944057:47944165 | ENSG00000198515.9 | ENST00000358519.4,ENST00000402813.3,ENST00000420489.2,ENST00000514170.1,ENST00000544810.1 |
| exon_skip_429391 | 4 | 47954599:47954720:47972912:47973117:47983409:47983550 | 47972912:47973117 | ENSG00000198515.9 | ENST00000544810.1 |
| exon_skip_429394 | 4 | 47954599:47954720:47983409:47983517:48012810:48012910 | 47983409:47983517 | ENSG00000198515.9 | ENST00000420489.2,ENST00000514170.1 |
| exon_skip_429401 | 4 | 47954599:47954720:48012810:48012910:48014905:48014961 | 48012810:48012910 | ENSG00000198515.9 | ENST00000504722.1 |
| exon_skip_429402 | 4 | 47954599:47954720:48012810:48012910:48018499:48018609 | 48012810:48012910 | ENSG00000198515.9 | ENST00000513178.1 |
| exon_skip_429407 | 4 | 47983409:47983517:48012810:48012910:48014905:48014961 | 48012810:48012910 | ENSG00000198515.9 | ENST00000420489.2 |
| exon_skip_429408 | 4 | 47983409:47983517:48012810:48012910:48018499:48018609 | 48012810:48012910 | ENSG00000198515.9 | ENST00000514170.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CNGA1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_429386 | 4 | 47938030:47939846:47942779:47942886:47944057:47944165 | 47942779:47942886 | ENSG00000198515.9 | ENST00000402813.3,ENST00000514170.1,ENST00000544810.1,ENST00000358519.4,ENST00000420489.2 |
| exon_skip_429389 | 4 | 47942779:47942886:47944057:47944165:47945197:47945305 | 47944057:47944165 | ENSG00000198515.9 | ENST00000402813.3,ENST00000514170.1,ENST00000544810.1,ENST00000358519.4,ENST00000420489.2 |
| exon_skip_429391 | 4 | 47954599:47954720:47972912:47973117:47983409:47983550 | 47972912:47973117 | ENSG00000198515.9 | ENST00000544810.1 |
| exon_skip_429394 | 4 | 47954599:47954720:47983409:47983517:48012810:48012910 | 47983409:47983517 | ENSG00000198515.9 | ENST00000514170.1,ENST00000420489.2 |
| exon_skip_429401 | 4 | 47954599:47954720:48012810:48012910:48014905:48014961 | 48012810:48012910 | ENSG00000198515.9 | ENST00000504722.1 |
| exon_skip_429402 | 4 | 47954599:47954720:48012810:48012910:48018499:48018609 | 48012810:48012910 | ENSG00000198515.9 | ENST00000513178.1 |
| exon_skip_429407 | 4 | 47983409:47983517:48012810:48012910:48014905:48014961 | 48012810:48012910 | ENSG00000198515.9 | ENST00000420489.2 |
| exon_skip_429408 | 4 | 47983409:47983517:48012810:48012910:48018499:48018609 | 48012810:48012910 | ENSG00000198515.9 | ENST00000514170.1 |
| 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 CNGA1 |
| 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 |
| ENST00000420489 | 47983409 | 47983517 | 3UTR-3UTR |
| ENST00000514170 | 47983409 | 47983517 | 3UTR-3UTR |
| ENST00000420489 | 48012810 | 48012910 | 3UTR-3UTR |
| ENST00000514170 | 48012810 | 48012910 | 3UTR-3UTR |
| ENST00000358519 | 47942779 | 47942886 | Frame-shift |
| ENST00000420489 | 47942779 | 47942886 | Frame-shift |
| ENST00000514170 | 47942779 | 47942886 | Frame-shift |
| ENST00000358519 | 47944057 | 47944165 | In-frame |
| ENST00000420489 | 47944057 | 47944165 | In-frame |
| ENST00000514170 | 47944057 | 47944165 | 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 |
| ENST00000420489 | 47983409 | 47983517 | 3UTR-3UTR |
| ENST00000514170 | 47983409 | 47983517 | 3UTR-3UTR |
| ENST00000420489 | 48012810 | 48012910 | 3UTR-3UTR |
| ENST00000514170 | 48012810 | 48012910 | 3UTR-3UTR |
| ENST00000358519 | 47942779 | 47942886 | Frame-shift |
| ENST00000420489 | 47942779 | 47942886 | Frame-shift |
| ENST00000514170 | 47942779 | 47942886 | Frame-shift |
| ENST00000358519 | 47944057 | 47944165 | In-frame |
| ENST00000420489 | 47944057 | 47944165 | In-frame |
| ENST00000514170 | 47944057 | 47944165 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CNGA1 |
| 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 |
| ENST00000358519 | 2644 | 690 | 47944057 | 47944165 | 562 | 669 | 150 | 185 |
| ENST00000420489 | 2763 | 690 | 47944057 | 47944165 | 716 | 823 | 150 | 185 |
| ENST00000514170 | 2854 | 690 | 47944057 | 47944165 | 770 | 877 | 150 | 185 |
| 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 |
| ENST00000358519 | 2644 | 690 | 47944057 | 47944165 | 562 | 669 | 150 | 185 |
| ENST00000420489 | 2763 | 690 | 47944057 | 47944165 | 716 | 823 | 150 | 185 |
| ENST00000514170 | 2854 | 690 | 47944057 | 47944165 | 770 | 877 | 150 | 185 |
| 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 |
| P29973 | 150 | 185 | 1 | 690 | Chain | ID=PRO_0000219308;Note=cGMP-gated cation channel alpha-1 |
| P29973 | 150 | 185 | 1 | 690 | Chain | ID=PRO_0000219308;Note=cGMP-gated cation channel alpha-1 |
| P29973 | 150 | 185 | 1 | 690 | Chain | ID=PRO_0000219308;Note=cGMP-gated cation channel alpha-1 |
| P29973 | 150 | 185 | 150 | 151 | Sequence conflict | Note=EE->HH;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P29973 | 150 | 185 | 150 | 151 | Sequence conflict | Note=EE->HH;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P29973 | 150 | 185 | 150 | 151 | Sequence conflict | Note=EE->HH;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P29973 | 150 | 185 | 1 | 164 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 1 | 164 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 1 | 164 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 165 | 185 | Transmembrane | Note=Helical%3B Name%3DH1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 165 | 185 | Transmembrane | Note=Helical%3B Name%3DH1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 165 | 185 | Transmembrane | Note=Helical%3B Name%3DH1;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 |
| P29973 | 150 | 185 | 1 | 690 | Chain | ID=PRO_0000219308;Note=cGMP-gated cation channel alpha-1 |
| P29973 | 150 | 185 | 1 | 690 | Chain | ID=PRO_0000219308;Note=cGMP-gated cation channel alpha-1 |
| P29973 | 150 | 185 | 1 | 690 | Chain | ID=PRO_0000219308;Note=cGMP-gated cation channel alpha-1 |
| P29973 | 150 | 185 | 150 | 151 | Sequence conflict | Note=EE->HH;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P29973 | 150 | 185 | 150 | 151 | Sequence conflict | Note=EE->HH;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P29973 | 150 | 185 | 150 | 151 | Sequence conflict | Note=EE->HH;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P29973 | 150 | 185 | 1 | 164 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 1 | 164 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 1 | 164 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 165 | 185 | Transmembrane | Note=Helical%3B Name%3DH1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 165 | 185 | Transmembrane | Note=Helical%3B Name%3DH1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29973 | 150 | 185 | 165 | 185 | Transmembrane | Note=Helical%3B Name%3DH1;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for CNGA1 |
| - 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-A51F-06 | exon_skip_429386 | 47942780 | 47942886 | 47942867 | 47942867 | Nonsense_Mutation | G | A | p.Q262* |
| CESC | TCGA-EK-A2R9-01 | exon_skip_429391 | 47972913 | 47973117 | 47973119 | 47973120 | Splice_Site | - | A | e1-2 |
| - 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 |
| SNUC5_LARGE_INTESTINE | 47942780 | 47942886 | 47942794 | 47942794 | Missense_Mutation | A | G | p.V217A |
| HEC1A_ENDOMETRIUM | 47942780 | 47942886 | 47942828 | 47942828 | Missense_Mutation | C | T | p.V206I |
| TGBC24TKB_BILIARY_TRACT | 47942780 | 47942886 | 47942872 | 47942872 | Missense_Mutation | T | A | p.E191V |
| YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 47944058 | 47944165 | 47944064 | 47944064 | Missense_Mutation | A | C | p.I184S |
| LU139_LUNG | 47944058 | 47944165 | 47944130 | 47944130 | Missense_Mutation | C | T | p.G162E |
| NCIH1838_LUNG | 47944058 | 47944165 | 47944133 | 47944133 | Missense_Mutation | G | A | p.S161L |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CNGA1 |
| 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 CNGA1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CNGA1 |
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RelatedDrugs for CNGA1 |
| 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 |
| P29973 | DB04209 | Dequalinium | cGMP-gated cation channel alpha-1 | small molecule | approved|investigational |
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RelatedDiseases for CNGA1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| CNGA1 | C0035334 | Retinitis Pigmentosa | 1 | CTD_human;HPO;ORPHANET |
| CNGA1 | C3151059 | RETINITIS PIGMENTOSA 49 | 1 | UNIPROT |
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