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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 CLNS1A |
 Gene summary |
| Gene information | Gene symbol | CLNS1A | Gene ID | 1207 |
| Gene name | chloride nucleotide-sensitive channel 1A | |
| Synonyms | CLCI|CLNS1B|ICln | |
| Cytomap | 11q14.1 | |
| Type of gene | protein-coding | |
| Description | methylosome subunit pIClnchloride channel regulatory proteinchloride channel, nucleotide sensitive 1Achloride conductance regulatory protein IClnchloride ion current inducer proteini(Cln)reticulocyte pIClnreticulocyte protein ICln | |
| Modification date | 20180522 | |
| UniProtAcc | P54105 | |
| Context | PubMed: CLNS1A [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 |
| CLNS1A | GO:0000387 | spliceosomal snRNP assembly | 18984161 |
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Exon skipping events across known transcript of Ensembl for CLNS1A 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 CLNS1A |
| 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 CLNS1A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_75961 | 11 | 77330650:77330740:77332910:77333089:77333544:77333576 | 77332910:77333089 | ENSG00000074201.4 | ENST00000526009.1 |
| exon_skip_75963 | 11 | 77330650:77330740:77333544:77333718:77336007:77336076 | 77333544:77333718 | ENSG00000074201.4 | ENST00000263309.3,ENST00000525428.1,ENST00000528364.1,ENST00000527133.2 |
| exon_skip_75964 | 11 | 77330650:77330740:77333544:77333718:77340807:77340944 | 77333544:77333718 | ENSG00000074201.4 | ENST00000532069.1 |
| exon_skip_75970 | 11 | 77333687:77333718:77336007:77336115:77340807:77340944 | 77336007:77336115 | ENSG00000074201.4 | ENST00000263309.3 |
| exon_skip_75973 | 11 | 77336007:77336115:77336761:77336863:77340807:77340944 | 77336761:77336863 | ENSG00000074201.4 | ENST00000525064.1,ENST00000525428.1,ENST00000528364.1 |
| exon_skip_75974 | 11 | 77336007:77336115:77336761:77336863:77348634:77348796 | 77336761:77336863 | ENSG00000074201.4 | ENST00000527133.2 |
| exon_skip_75977 | 11 | 77336007:77336115:77340807:77340944:77348634:77348796 | 77340807:77340944 | ENSG00000074201.4 | ENST00000263309.3 |
| exon_skip_75979 | 11 | 77336763:77336863:77340807:77340944:77348634:77348796 | 77340807:77340944 | ENSG00000074201.4 | ENST00000525064.1,ENST00000525428.1,ENST00000528364.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CLNS1A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_75961 | 11 | 77330650:77330740:77332910:77333089:77333544:77333576 | 77332910:77333089 | ENSG00000074201.4 | ENST00000526009.1 |
| exon_skip_75963 | 11 | 77330650:77330740:77333544:77333718:77336007:77336076 | 77333544:77333718 | ENSG00000074201.4 | ENST00000525428.1,ENST00000263309.3,ENST00000528364.1,ENST00000527133.2 |
| exon_skip_75964 | 11 | 77330650:77330740:77333544:77333718:77340807:77340944 | 77333544:77333718 | ENSG00000074201.4 | ENST00000532069.1 |
| exon_skip_75970 | 11 | 77333687:77333718:77336007:77336115:77340807:77340944 | 77336007:77336115 | ENSG00000074201.4 | ENST00000263309.3 |
| exon_skip_75973 | 11 | 77336007:77336115:77336761:77336863:77340807:77340944 | 77336761:77336863 | ENSG00000074201.4 | ENST00000525428.1,ENST00000525064.1,ENST00000528364.1 |
| exon_skip_75974 | 11 | 77336007:77336115:77336761:77336863:77348634:77348796 | 77336761:77336863 | ENSG00000074201.4 | ENST00000527133.2 |
| exon_skip_75977 | 11 | 77336007:77336115:77340807:77340944:77348634:77348796 | 77340807:77340944 | ENSG00000074201.4 | ENST00000263309.3 |
| exon_skip_75979 | 11 | 77336763:77336863:77340807:77340944:77348634:77348796 | 77340807:77340944 | ENSG00000074201.4 | ENST00000525428.1,ENST00000525064.1,ENST00000528364.1 |
| 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 CLNS1A |
| 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 |
| ENST00000525428 | 77340807 | 77340944 | Frame-shift |
| ENST00000528364 | 77340807 | 77340944 | Frame-shift |
| ENST00000525428 | 77333544 | 77333718 | In-frame |
| ENST00000528364 | 77333544 | 77333718 | In-frame |
| ENST00000525428 | 77336761 | 77336863 | In-frame |
| ENST00000528364 | 77336761 | 77336863 | 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 |
| ENST00000525428 | 77340807 | 77340944 | Frame-shift |
| ENST00000528364 | 77340807 | 77340944 | Frame-shift |
| ENST00000525428 | 77333544 | 77333718 | In-frame |
| ENST00000528364 | 77333544 | 77333718 | In-frame |
| ENST00000525428 | 77336761 | 77336863 | In-frame |
| ENST00000528364 | 77336761 | 77336863 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CLNS1A |
| 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 |
| ENST00000525428 | 3010 | 237 | 77336761 | 77336863 | 354 | 455 | 87 | 121 |
| ENST00000528364 | 970 | 237 | 77336761 | 77336863 | 325 | 426 | 87 | 121 |
| ENST00000525428 | 3010 | 237 | 77333544 | 77333718 | 564 | 737 | 157 | 215 |
| ENST00000528364 | 970 | 237 | 77333544 | 77333718 | 535 | 708 | 157 | 215 |
| 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 |
| ENST00000525428 | 3010 | 237 | 77336761 | 77336863 | 354 | 455 | 87 | 121 |
| ENST00000528364 | 970 | 237 | 77336761 | 77336863 | 325 | 426 | 87 | 121 |
| ENST00000525428 | 3010 | 237 | 77333544 | 77333718 | 564 | 737 | 157 | 215 |
| ENST00000528364 | 970 | 237 | 77333544 | 77333718 | 535 | 708 | 157 | 215 |
| 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 |
| P54105 | 87 | 121 | 2 | 237 | Chain | ID=PRO_0000185155;Note=Methylosome subunit pICln |
| P54105 | 87 | 121 | 2 | 237 | Chain | ID=PRO_0000185155;Note=Methylosome subunit pICln |
| P54105 | 87 | 121 | 102 | 102 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:17487921,ECO:0000244|P |
| P54105 | 87 | 121 | 102 | 102 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:17487921,ECO:0000244|P |
| P54105 | 157 | 215 | 2 | 237 | Chain | ID=PRO_0000185155;Note=Methylosome subunit pICln |
| P54105 | 157 | 215 | 2 | 237 | Chain | ID=PRO_0000185155;Note=Methylosome subunit pICln |
| P54105 | 157 | 215 | 193 | 193 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 193 | 193 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 195 | 195 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 195 | 195 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 198 | 198 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 198 | 198 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 210 | 210 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 210 | 210 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| 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 |
| P54105 | 87 | 121 | 2 | 237 | Chain | ID=PRO_0000185155;Note=Methylosome subunit pICln |
| P54105 | 87 | 121 | 2 | 237 | Chain | ID=PRO_0000185155;Note=Methylosome subunit pICln |
| P54105 | 87 | 121 | 102 | 102 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:17487921,ECO:0000244|P |
| P54105 | 87 | 121 | 102 | 102 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:17487921,ECO:0000244|P |
| P54105 | 157 | 215 | 2 | 237 | Chain | ID=PRO_0000185155;Note=Methylosome subunit pICln |
| P54105 | 157 | 215 | 2 | 237 | Chain | ID=PRO_0000185155;Note=Methylosome subunit pICln |
| P54105 | 157 | 215 | 193 | 193 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 193 | 193 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 195 | 195 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 195 | 195 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 198 | 198 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 198 | 198 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 210 | 210 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P54105 | 157 | 215 | 210 | 210 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
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SNVs in the skipped exons for CLNS1A |
| - 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-D8-A1JK-01 | exon_skip_75963 exon_skip_75964 | 77333545 | 77333718 | 77333553 | 77333554 | Frame_Shift_Del | TC | - | p.D213fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_75963 exon_skip_75964 | 77333545 | 77333718 | 77333659 | 77333659 | Frame_Shift_Del | T | - | p.T178fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_75963 exon_skip_75964 | 77333545 | 77333718 | 77333678 | 77333678 | Frame_Shift_Del | T | - | p.E172fs |
| COAD | TCGA-AZ-4315-01 | exon_skip_75970 | 77336008 | 77336115 | 77336029 | 77336029 | Nonsense_Mutation | C | A | p.E151X |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-D8-A1JK-01 |
| Cancer type: BRCA | |
| ESID: exon_skip_75964 | |
| Skipped exon start: 77333545 | |
| Skipped exon end: 77333718 | |
| Mutation start: 77333553 | |
| Mutation end: 77333554 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: TC | |
| Mutation seq: - | |
| AAchange: p.D213fs | |
exon_skip_75963_BRCA_TCGA-D8-A1JK-01.png | |
| - 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 |
| SISO_CERVIX | 77333545 | 77333718 | 77333704 | 77333704 | Frame_Shift_Del | C | - | p.D163fs |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 77333545 | 77333718 | 77333704 | 77333704 | Frame_Shift_Del | C | - | p.D163fs |
| OV7_OVARY | 77333545 | 77333718 | 77333560 | 77333560 | Missense_Mutation | T | C | p.I211V |
| ESS1_ENDOMETRIUM | 77333545 | 77333718 | 77333601 | 77333601 | Missense_Mutation | C | A | p.S197I |
| HLFA_FIBROBLAST | 77336762 | 77336863 | 77336770 | 77336770 | Missense_Mutation | T | G | p.K119T |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CLNS1A |
| 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 CLNS1A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CLNS1A |
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RelatedDrugs for CLNS1A |
| 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 CLNS1A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| CLNS1A | C0025202 | melanoma | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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