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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
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 | 20200313 | |
UniProtAcc | D6RDJ1, Q9NX58, | |
Context |
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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Gene structures and expression levels for LYAR |
Skipped exons in the ROSMAP, MSBB, and Mayo 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. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for LYAR |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_289707 | chr4 | 4268530:4268615:4273583:4273669:4274367:4274769 | 4273583:4273669 |
exon_skip_293400 | chr4 | 4283621:4283795:4286519:4286572:4290036:4290154 | 4286519:4286572 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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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 ROSMAP based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000343470 | 4286519 | 4286572 | 3UTR-3UTR |
ENST00000343470 | 4273583 | 4273669 | In-frame |
ENST00000452476 | 4273583 | 4273669 | In-frame |
Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000343470 | 4286519 | 4286572 | 3UTR-3UTR |
ENST00000343470 | 4273583 | 4273669 | In-frame |
ENST00000452476 | 4273583 | 4273669 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LYAR |
p-ENSG00000145220_img4.png |
Loci of skipped exons in ROSMAP 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 | 4273583 | 4273669 | 1074 | 1159 | 277 | 306 |
ENST00000452476 | 1485 | 379 | 4273583 | 4273669 | 976 | 1061 | 277 | 306 |
Loci of skipped exons in MSBB 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 |
Loci of skipped exons in Mayo 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 | 4273583 | 4273669 | 1074 | 1159 | 277 | 306 |
ENST00000452476 | 1485 | 379 | 4273583 | 4273669 | 976 | 1061 | 277 | 306 |
Lost protein functional features of individual exon skipping events in ROSMAP. |
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 | 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 MSBB. |
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 |
Lost protein functional features of individual exon skipping events in Mayo. |
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 | 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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3'-UTR located exon skipping events that lost miRNA binding sites in LYAR |
3'-UTR exon skipping evnets lost miRNA binding. |
Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
Mayo | ENST00000343470 | 4286519 | 4286572 | hsa-miR-626 | chr4:4286557-4286564 | 8mer-1a | chr4:4286541-4286564 | 142.00 | -12.44 |
Mayo | ENST00000343470 | 4286519 | 4286572 | hsa-miR-6876-3p | chr4:4286557-4286564 | 8mer-1a | chr4:4286541-4286564 | 142.00 | -12.44 |
ROSMAP | ENST00000343470 | 4286519 | 4286572 | hsa-miR-626 | chr4:4286557-4286564 | 8mer-1a | chr4:4286541-4286564 | 142.00 | -12.44 |
ROSMAP | ENST00000343470 | 4286519 | 4286572 | hsa-miR-6876-3p | chr4:4286557-4286564 | 8mer-1a | chr4:4286541-4286564 | 142.00 | -12.44 |
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SNVs in the skipped exons for LYAR |
- Differential PSIs between mutated versus non-mutated samples. |
- Depth of Coverage in the skipped exon of the mutated samples. |
- Sashimi plot in the skipped exon of the mutated samples. |
- Non-synonymous mutations located in the skipped exons. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
- 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 |
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AD stage-associated exon skippint events for LYAR |
Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LYAR |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
CB | exon_skip_289707 | rs2980141 | chr4:4339608 | 3.402280e-07 | 1.428233e-04 |
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Correlation with RNA binding proteins (RBPs) for LYAR |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | RBM45 | exon_skip_293400 | 4.537348e-01 | 4.136009e-08 |
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RelatedDrugs for LYAR |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
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 |