|
||||||
|
 | |
| |
| |
| 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 KDM2A |
 Gene summary |
| Gene information | Gene symbol | KDM2A | Gene ID | 22992 |
| Gene name | lysine demethylase 2A | |
| Synonyms | CXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA | |
| Cytomap | 11q13.2 | |
| Type of gene | protein-coding | |
| Description | lysine-specific demethylase 2ACXXC-type zinc finger protein 8F-box and leucine-rich repeat protein 11F-box/LRR-repeat protein 11[Histone-H3]-lysine-36 demethylase 1AjmjC domain-containing histone demethylation protein 1Ajumonji C domain-containing h | |
| Modification date | 20200320 | |
| 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 |
Top |
Gene structures and expression levels for KDM2A |
| 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. |
 |
ENSG00000173120
| 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 |
| CB | UP | ENST00000526258.5 | KDM2A-207:lncRNA:KDM2A | 8.559552e+02 | 1.124541e+00 | 5.310902e-06 | 6.166827e-05 |
| CB | UP | ENST00000529124.1 | KDM2A-211:lncRNA:KDM2A | 5.214593e+00 | 8.451368e-01 | 1.187349e-04 | 8.561832e-04 |
| CB | UP | ENST00000308783.9 | KDM2A-201:protein_coding:KDM2A | 5.692782e+01 | 8.070029e-01 | 1.590604e-04 | 1.098376e-03 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for KDM2A |
| 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_111332 | chr11 | 67231765:67231960:67243009:67243092:67245189:67245458 | 67243009:67243092 |
| exon_skip_169900 | chr11 | 67181846:67181892:67207510:67207688:67215340:67215446 | 67207510:67207688 |
| exon_skip_171619 | chr11 | 67215340:67215446:67215856:67215949:67217731:67217884 | 67215856:67215949 |
| exon_skip_191034 | chr11 | 67248281:67248370:67250086:67250798:67252694:67252857 | 67250086:67250798 |
| exon_skip_215998 | chr11 | 67240301:67240369:67243009:67243092:67245189:67245458 | 67243009:67243092 |
| exon_skip_242861 | chr11 | 67119976:67120049:67121234:67121358:67180079:67180217 | 67121234:67121358 |
| exon_skip_275370 | chr11 | 67217756:67217884:67219288:67219403:67228037:67228163 | 67219288:67219403 |
| exon_skip_61030 | chr11 | 67121269:67121358:67131952:67132073:67180079:67180217 | 67131952:67132073 |
| exon_skip_77236 | chr11 | 67248281:67248370:67250086:67250346:67252694:67252857 | 67250086:67250346 |
| exon_skip_90233 | chr11 | 67180079:67180217:67181320:67181398:67181846:67181892 | 67181320:67181398 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for KDM2A |
| 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 |
| ENST00000529006 | 67207510 | 67207688 | Frame-shift |
| ENST00000529006 | 67243009 | 67243092 | 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 |
| ENST00000529006 | 67215856 | 67215949 | Frame-shift |
| ENST00000529006 | 67243009 | 67243092 | 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 |
| ENST00000529006 | 67181320 | 67181398 | Frame-shift |
| ENST00000529006 | 67207510 | 67207688 | Frame-shift |
| ENST00000529006 | 67215856 | 67215949 | Frame-shift |
| ENST00000529006 | 67219288 | 67219403 | Frame-shift |
| ENST00000529006 | 67250086 | 67250798 | Frame-shift |
| ENST00000529006 | 67243009 | 67243092 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for KDM2A |
p-ENSG00000173120_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 |
| ENST00000529006 | 6984 | 1162 | 67243009 | 67243092 | 1927 | 2009 | 493 | 521 |
| 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 |
| ENST00000529006 | 6984 | 1162 | 67243009 | 67243092 | 1927 | 2009 | 493 | 521 |
| 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 |
| ENST00000529006 | 6984 | 1162 | 67243009 | 67243092 | 1927 | 2009 | 493 | 521 |
| 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 |
| Q9Y2K7 | 493 | 521 | 1 | 542 | Alternative sequence | ID=VSP_046938;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.3 |
| Q9Y2K7 | 493 | 521 | 499 | 501 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2YU1 |
| Q9Y2K7 | 493 | 521 | 1 | 1162 | Chain | ID=PRO_0000119855;Note=Lysine-specific demethylase 2A |
| Q9Y2K7 | 493 | 521 | 505 | 505 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| Q9Y2K7 | 493 | 521 | 485 | 498 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2YU1 |
| Q9Y2K7 | 493 | 521 | 504 | 507 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2YU1 |
| Q9Y2K7 | 493 | 521 | 518 | 518 | Sequence conflict | Note=K->I;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q9Y2K7 | 493 | 521 | 1 | 542 | Alternative sequence | ID=VSP_046938;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.3 |
| Q9Y2K7 | 493 | 521 | 499 | 501 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2YU1 |
| Q9Y2K7 | 493 | 521 | 1 | 1162 | Chain | ID=PRO_0000119855;Note=Lysine-specific demethylase 2A |
| Q9Y2K7 | 493 | 521 | 505 | 505 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| Q9Y2K7 | 493 | 521 | 485 | 498 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2YU1 |
| Q9Y2K7 | 493 | 521 | 504 | 507 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2YU1 |
| Q9Y2K7 | 493 | 521 | 518 | 518 | Sequence conflict | Note=K->I;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q9Y2K7 | 493 | 521 | 1 | 542 | Alternative sequence | ID=VSP_046938;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.3 |
| Q9Y2K7 | 493 | 521 | 499 | 501 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2YU1 |
| Q9Y2K7 | 493 | 521 | 1 | 1162 | Chain | ID=PRO_0000119855;Note=Lysine-specific demethylase 2A |
| Q9Y2K7 | 493 | 521 | 505 | 505 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| Q9Y2K7 | 493 | 521 | 485 | 498 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2YU1 |
| Q9Y2K7 | 493 | 521 | 504 | 507 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2YU1 |
| Q9Y2K7 | 493 | 521 | 518 | 518 | Sequence conflict | Note=K->I;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in KDM2A |
| 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 |
Top |
SNVs in the skipped exons for KDM2A |
| - 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 |
Top |
AD stage-associated exon skippint events for KDM2A |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for KDM2A |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for KDM2A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for KDM2A |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for KDM2A |
| 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)
|