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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 LYAR |
 Gene summary |
| Gene information | Gene symbol | LYAR | Gene ID | 55646 |
| Gene name | Ly1 antibody reactive | |
| Synonyms | ZC2HC2|ZLYAR | |
| Cytomap | 4p16.3 | |
| Type of gene | protein-coding | |
| Description | cell growth-regulating nucleolar proteinLy1 antibody reactive homolog | |
| Modification date | 20180519 | |
| UniProtAcc | Q9NX58 | |
| Context | PubMed: LYAR [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 LYAR 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 LYAR |
| 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 LYAR |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_428231 | 4 | 4269430:4269750:4270256:4270342:4275309:4275396 | 4270256:4270342 | ENSG00000145220.9 | ENST00000343470.4,ENST00000452476.1 |
| exon_skip_428233 | 4 | 4270256:4270342:4275309:4275396:4276093:4276496 | 4275309:4275396 | ENSG00000145220.9 | ENST00000343470.4,ENST00000452476.1 |
| exon_skip_428236 | 4 | 4281173:4281257:4281368:4281476:4283509:4283624 | 4281368:4281476 | ENSG00000145220.9 | ENST00000343470.4,ENST00000452476.1 |
| exon_skip_428239 | 4 | 4285347:4285522:4288245:4288299:4291762:4291896 | 4288245:4288299 | ENSG00000145220.9 | ENST00000343470.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LYAR |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_428231 | 4 | 4269430:4269750:4270256:4270342:4275309:4275396 | 4270256:4270342 | ENSG00000145220.9 | ENST00000343470.4,ENST00000452476.1 |
| exon_skip_428233 | 4 | 4270256:4270342:4275309:4275396:4276093:4276496 | 4275309:4275396 | ENSG00000145220.9 | ENST00000343470.4,ENST00000452476.1 |
| exon_skip_428236 | 4 | 4281173:4281257:4281368:4281476:4283509:4283624 | 4281368:4281476 | ENSG00000145220.9 | ENST00000343470.4,ENST00000452476.1 |
| exon_skip_428239 | 4 | 4285347:4285522:4288245:4288299:4291762:4291896 | 4288245:4288299 | ENSG00000145220.9 | ENST00000343470.4 |
| 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 LYAR |
| 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 |
| ENST00000343470 | 4288245 | 4288299 | 3UTR-3UTR |
| ENST00000343470 | 4270256 | 4270342 | Frame-shift |
| ENST00000452476 | 4270256 | 4270342 | Frame-shift |
| ENST00000343470 | 4275309 | 4275396 | In-frame |
| ENST00000452476 | 4275309 | 4275396 | In-frame |
| ENST00000343470 | 4281368 | 4281476 | In-frame |
| ENST00000452476 | 4281368 | 4281476 | 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 |
| ENST00000343470 | 4288245 | 4288299 | 3UTR-3UTR |
| ENST00000343470 | 4270256 | 4270342 | Frame-shift |
| ENST00000452476 | 4270256 | 4270342 | Frame-shift |
| ENST00000343470 | 4275309 | 4275396 | In-frame |
| ENST00000452476 | 4275309 | 4275396 | In-frame |
| ENST00000343470 | 4281368 | 4281476 | In-frame |
| ENST00000452476 | 4281368 | 4281476 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LYAR |
| 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 |
| ENST00000343470 | 1586 | 379 | 4281368 | 4281476 | 479 | 586 | 79 | 115 |
| ENST00000452476 | 1485 | 379 | 4281368 | 4281476 | 381 | 488 | 79 | 115 |
| ENST00000343470 | 1586 | 379 | 4275309 | 4275396 | 1074 | 1160 | 277 | 306 |
| ENST00000452476 | 1485 | 379 | 4275309 | 4275396 | 976 | 1062 | 277 | 306 |
| 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 |
| ENST00000343470 | 1586 | 379 | 4281368 | 4281476 | 479 | 586 | 79 | 115 |
| ENST00000452476 | 1485 | 379 | 4281368 | 4281476 | 381 | 488 | 79 | 115 |
| ENST00000343470 | 1586 | 379 | 4275309 | 4275396 | 1074 | 1160 | 277 | 306 |
| ENST00000452476 | 1485 | 379 | 4275309 | 4275396 | 976 | 1062 | 277 | 306 |
| 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 |
| Q9NX58 | 79 | 115 | 1 | 379 | Chain | ID=PRO_0000084528;Note=Cell growth-regulating nucleolar protein |
| Q9NX58 | 79 | 115 | 1 | 379 | Chain | ID=PRO_0000084528;Note=Cell growth-regulating nucleolar protein |
| Q9NX58 | 277 | 306 | 1 | 379 | Chain | ID=PRO_0000084528;Note=Cell growth-regulating nucleolar protein |
| Q9NX58 | 277 | 306 | 1 | 379 | Chain | ID=PRO_0000084528;Note=Cell growth-regulating nucleolar protein |
| Q9NX58 | 277 | 306 | 168 | 379 | Compositional bias | Note=Lys-rich |
| Q9NX58 | 277 | 306 | 168 | 379 | Compositional bias | Note=Lys-rich |
| 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 |
| Q9NX58 | 79 | 115 | 1 | 379 | Chain | ID=PRO_0000084528;Note=Cell growth-regulating nucleolar protein |
| Q9NX58 | 79 | 115 | 1 | 379 | Chain | ID=PRO_0000084528;Note=Cell growth-regulating nucleolar protein |
| Q9NX58 | 277 | 306 | 1 | 379 | Chain | ID=PRO_0000084528;Note=Cell growth-regulating nucleolar protein |
| Q9NX58 | 277 | 306 | 1 | 379 | Chain | ID=PRO_0000084528;Note=Cell growth-regulating nucleolar protein |
| Q9NX58 | 277 | 306 | 168 | 379 | Compositional bias | Note=Lys-rich |
| Q9NX58 | 277 | 306 | 168 | 379 | Compositional bias | Note=Lys-rich |
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SNVs in the skipped exons for LYAR |
| - 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 |
| HNSC | TCGA-CV-6441-01 | exon_skip_428231 | 4270257 | 4270342 | 4270287 | 4270287 | Frame_Shift_Del | A | - | p.N325fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_428231 | 4270257 | 4270342 | 4270294 | 4270294 | Frame_Shift_Del | G | - | p.P323fs |
| COAD | TCGA-CM-5861-01 | exon_skip_428233 | 4275310 | 4275396 | 4275372 | 4275372 | Frame_Shift_Del | T | - | p.K286fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_428236 | 4281369 | 4281476 | 4281438 | 4281438 | Frame_Shift_Del | G | - | p.P92fs |
| STAD | TCGA-BR-4368-01 | exon_skip_428231 | 4270257 | 4270342 | 4270269 | 4270270 | Frame_Shift_Ins | - | T | p.K331fs |
| STAD | TCGA-BR-4368-01 | exon_skip_428231 | 4270257 | 4270342 | 4270270 | 4270271 | Frame_Shift_Ins | - | T | p.K331fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_428236 | 4281369 | 4281476 | 4281472 | 4281473 | Frame_Shift_Ins | - | T | p.*81fs |
| KIRP | TCGA-KV-A74V-01 | exon_skip_428231 | 4270257 | 4270342 | 4270271 | 4270271 | Nonsense_Mutation | T | A | p.K331X |
| - 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 |
| NCIH2110_LUNG | 4281369 | 4281476 | 4281449 | 4281449 | Missense_Mutation | T | A | p.N89Y |
| FEPD_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 4281369 | 4281476 | 4281470 | 4281470 | Missense_Mutation | T | C | p.S82G |
| MM370_SKIN | 4270257 | 4270342 | 4270304 | 4270304 | Nonsense_Mutation | T | A | p.K320* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LYAR |
| 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 LYAR |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LYAR |
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RelatedDrugs for LYAR |
| 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 LYAR |
| 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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