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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 KDM5A |
Gene summary |
Gene information | Gene symbol | KDM5A | Gene ID | 5927 |
Gene name | lysine demethylase 5A | |
Synonyms | RBBP-2|RBBP2|RBP2 | |
Cytomap | 12p13.33 | |
Type of gene | protein-coding | |
Description | lysine-specific demethylase 5AJumonji, AT rich interactive domain 1A (RBP2-like)histone demethylase JARID1Ajumonji/ARID domain-containing protein 1Alysine (K)-specific demethylase 5Aretinoblastoma binding protein 2 | |
Modification date | 20200313 | |
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 |
KDM5A | GO:0034720 | histone H3-K4 demethylation | 18270511 |
KDM5A | GO:0045893 | positive regulation of transcription, DNA-templated | 11358960 |
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Gene structures and expression levels for KDM5A |
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 KDM5A |
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_10264 | chr12 | 352205:352324:354076:354234:355158:355249 | 354076:354234 |
exon_skip_110602 | chr12 | 318106:318461:320995:321109:322417:322567 | 320995:321109 |
exon_skip_134327 | chr12 | 295573:295793:297041:297200:306946:307089 | 297041:297200 |
exon_skip_213539 | chr12 | 285527:285662:286126:286207:292759:292925 | 286126:286207 |
exon_skip_283464 | chr12 | 285456:285662:286126:286207:292759:292925 | 286126:286207 |
exon_skip_291775 | chr12 | 318285:318461:320995:321109:322417:322567 | 320995:321109 |
exon_skip_35547 | chr12 | 322417:322567:323082:323206:323600:323781 | 323082:323206 |
exon_skip_3763 | chr12 | 318111:318461:320995:321109:322417:322567 | 320995:321109 |
exon_skip_64787 | chr12 | 365970:366104:384031:384153:385897:385974 | 384031:384153 |
exon_skip_75842 | chr12 | 318123:318461:320995:321109:322417:322567 | 320995:321109 |
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 KDM5A |
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 |
ENST00000399788 | 297041 | 297200 | Frame-shift |
ENST00000399788 | 320995 | 321109 | Frame-shift |
ENST00000399788 | 323082 | 323206 | Frame-shift |
ENST00000399788 | 354076 | 354234 | In-frame |
ENST00000399788 | 384031 | 384153 | 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 |
ENST00000399788 | 297041 | 297200 | Frame-shift |
ENST00000399788 | 320995 | 321109 | Frame-shift |
ENST00000399788 | 323082 | 323206 | Frame-shift |
ENST00000399788 | 384031 | 384153 | In-frame |
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 |
ENST00000399788 | 297041 | 297200 | Frame-shift |
ENST00000399788 | 320995 | 321109 | Frame-shift |
ENST00000399788 | 323082 | 323206 | Frame-shift |
ENST00000399788 | 384031 | 384153 | In-frame |
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Infer the effects of exon skipping event on protein functional features for KDM5A |
p-ENSG00000073614_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 |
ENST00000399788 | 10780 | 1690 | 384031 | 384153 | 607 | 728 | 81 | 121 |
ENST00000399788 | 10780 | 1690 | 354076 | 354234 | 1234 | 1391 | 290 | 342 |
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 |
ENST00000399788 | 10780 | 1690 | 384031 | 384153 | 607 | 728 | 81 | 121 |
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 |
ENST00000399788 | 10780 | 1690 | 384031 | 384153 | 607 | 728 | 81 | 121 |
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 |
P29375 | 81 | 121 | 1 | 1690 | Chain | ID=PRO_0000200584;Note=Lysine-specific demethylase 5A |
P29375 | 81 | 121 | 84 | 174 | Domain | Note=ARID;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00355 |
P29375 | 81 | 121 | 85 | 100 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
P29375 | 81 | 121 | 117 | 126 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
P29375 | 81 | 121 | 112 | 112 | Mutagenesis | Note=Decreases DNA-binding. R->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18270511;Dbxref=PMID:18270511 |
P29375 | 81 | 121 | 77 | 82 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
P29375 | 290 | 342 | 1 | 1690 | Chain | ID=PRO_0000200584;Note=Lysine-specific demethylase 5A |
P29375 | 290 | 342 | 293 | 343 | Zinc finger | Note=PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00146 |
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 |
P29375 | 81 | 121 | 1 | 1690 | Chain | ID=PRO_0000200584;Note=Lysine-specific demethylase 5A |
P29375 | 81 | 121 | 84 | 174 | Domain | Note=ARID;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00355 |
P29375 | 81 | 121 | 85 | 100 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
P29375 | 81 | 121 | 117 | 126 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
P29375 | 81 | 121 | 112 | 112 | Mutagenesis | Note=Decreases DNA-binding. R->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18270511;Dbxref=PMID:18270511 |
P29375 | 81 | 121 | 77 | 82 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
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 |
P29375 | 81 | 121 | 1 | 1690 | Chain | ID=PRO_0000200584;Note=Lysine-specific demethylase 5A |
P29375 | 81 | 121 | 84 | 174 | Domain | Note=ARID;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00355 |
P29375 | 81 | 121 | 85 | 100 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
P29375 | 81 | 121 | 117 | 126 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
P29375 | 81 | 121 | 112 | 112 | Mutagenesis | Note=Decreases DNA-binding. R->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18270511;Dbxref=PMID:18270511 |
P29375 | 81 | 121 | 77 | 82 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
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3'-UTR located exon skipping events that lost miRNA binding sites in KDM5A |
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 |
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SNVs in the skipped exons for KDM5A |
- 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 KDM5A |
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 |
CDR | MSBB | IFG | exon_skip_283464 | 3.749662e-01 | 4.928943e-02 | chr12 | - | 285456 | 285662 | 286126 | 286207 | 292759 | 292925 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for KDM5A |
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 KDM5A |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | TRA2A | exon_skip_35547 | -4.462838e-01 | 2.576157e-07 |
IFG | RBM3 | exon_skip_283464 | -4.021407e-01 | 3.388789e-02 |
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RelatedDrugs for KDM5A |
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 KDM5A |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |