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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 LIG4 |
Gene summary |
Gene information | Gene symbol | LIG4 | Gene ID | 3981 |
Gene name | DNA ligase 4 | |
Synonyms | LIG4S | |
Cytomap | 13q33.3 | |
Type of gene | protein-coding | |
Description | DNA ligase 4DNA joinaseDNA ligase IVDNA repair enzymeligase IV, DNA, ATP-dependentpolydeoxyribonucleotide synthase [ATP] 4polynucleotide ligasesealase | |
Modification date | 20200321 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
LIG4 | GO:0000012 | single strand break repair | 8798671 |
LIG4 | GO:0006266 | DNA ligation | 12517771 |
LIG4 | GO:0006297 | nucleotide-excision repair, DNA gap filling | 12517771 |
LIG4 | GO:0006302 | double-strand break repair | 9242410|19589734 |
LIG4 | GO:0006303 | double-strand break repair via nonhomologous end joining | 12517771 |
LIG4 | GO:0033151 | V(D)J recombination | 9809069 |
LIG4 | GO:0051103 | DNA ligation involved in DNA repair | 12517771 |
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Gene structures and expression levels for LIG4 |
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 LIG4 |
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_175627 | chr13 | 108207446:108211296:108214538:108214807:108215484:108215535 | 108214538:108214807 |
exon_skip_249822 | chr13 | 108207446:108211296:108214538:108214807:108215484:108215523 | 108214538:108214807 |
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 LIG4 |
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 |
ENST00000611712 | 108214538 | 108214807 | 3UTR-3UTR |
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 |
ENST00000611712 | 108214538 | 108214807 | 3UTR-3UTR |
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Infer the effects of exon skipping event on protein functional features for LIG4 |
p-ENSG00000174405_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 |
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 |
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 |
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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in LIG4 |
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 | ENST00000611712 | 108214538 | 108214807 | hsa-miR-4308 | chr13:108214669-108214676 | 8mer-1a | chr13:108214658-108214676 | 150.00 | -18.48 |
Mayo | ENST00000611712 | 108214538 | 108214807 | hsa-miR-6764-3p | chr13:108214570-108214577 | 8mer-1a | chr13:108214563-108214584 | 158.00 | -17.88 |
Mayo | ENST00000611712 | 108214538 | 108214807 | hsa-miR-629-3p | chr13:108214686-108214693 | 8mer-1a | chr13:108214683-108214706 | 155.00 | -24.17 |
Mayo | ENST00000611712 | 108214538 | 108214807 | hsa-miR-3191-5p | chr13:108214571-108214578 | 8mer-1a | chr13:108214563-108214584 | 158.00 | -17.88 |
Mayo | ENST00000611712 | 108214538 | 108214807 | hsa-miR-6824-3p | chr13:108214570-108214577 | 8mer-1a | chr13:108214563-108214584 | 158.00 | -17.88 |
Mayo | ENST00000611712 | 108214538 | 108214807 | hsa-miR-6894-3p | chr13:108214655-108214662 | 8mer-1a | chr13:108214644-108214668 | 180.00 | -26.70 |
ROSMAP | ENST00000611712 | 108214538 | 108214807 | hsa-miR-4308 | chr13:108214669-108214676 | 8mer-1a | chr13:108214658-108214676 | 150.00 | -18.48 |
ROSMAP | ENST00000611712 | 108214538 | 108214807 | hsa-miR-6764-3p | chr13:108214570-108214577 | 8mer-1a | chr13:108214563-108214584 | 158.00 | -17.88 |
ROSMAP | ENST00000611712 | 108214538 | 108214807 | hsa-miR-629-3p | chr13:108214686-108214693 | 8mer-1a | chr13:108214683-108214706 | 155.00 | -24.17 |
ROSMAP | ENST00000611712 | 108214538 | 108214807 | hsa-miR-3191-5p | chr13:108214571-108214578 | 8mer-1a | chr13:108214563-108214584 | 158.00 | -17.88 |
ROSMAP | ENST00000611712 | 108214538 | 108214807 | hsa-miR-6824-3p | chr13:108214570-108214577 | 8mer-1a | chr13:108214563-108214584 | 158.00 | -17.88 |
ROSMAP | ENST00000611712 | 108214538 | 108214807 | hsa-miR-6894-3p | chr13:108214655-108214662 | 8mer-1a | chr13:108214644-108214668 | 180.00 | -26.70 |
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SNVs in the skipped exons for LIG4 |
- 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 LIG4 |
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 LIG4 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for LIG4 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for LIG4 |
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 LIG4 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |