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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 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 | 20180523 | |
| UniProtAcc | P29375 | |
| Context | PubMed: KDM5A [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 |
| KDM5A | GO:0033169 | histone H3-K9 demethylation | 18270511 |
| KDM5A | GO:0034720 | histone H3-K4 demethylation | 18270511 |
| KDM5A | GO:0045893 | positive regulation of transcription, DNA-templated | 11358960 |
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Exon skipping events across known transcript of Ensembl for KDM5A 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 KDM5A |
| 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 KDM5A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_89176 | 12 | 394621:394828:395291:395373:401924:402091 | 395291:395373 | ENSG00000073614.7 | ENST00000540838.1 |
| exon_skip_89179 | 12 | 404738:404959:406206:406366:416111:416255 | 406206:406366 | ENSG00000073614.7 | ENST00000382815.4,ENST00000399788.2 |
| exon_skip_89182 | 12 | 427271:427627:430160:430275:431582:431733 | 430160:430275 | ENSG00000073614.7 | ENST00000382815.4,ENST00000399788.2,ENST00000544760.1 |
| exon_skip_89183 | 12 | 431582:431733:432247:432372:432765:432947 | 432247:432372 | ENSG00000073614.7 | ENST00000382815.4,ENST00000399788.2,ENST00000544760.1 |
| exon_skip_89187 | 12 | 438000:438195:440984:441104:442652:442815 | 440984:441104 | ENSG00000073614.7 | ENST00000382815.4,ENST00000399788.2,ENST00000544760.1 |
| exon_skip_89190 | 12 | 440984:441104:442652:442815:443406:443494 | 442652:442815 | ENSG00000073614.7 | ENST00000382815.4,ENST00000399788.2,ENST00000544760.1 |
| exon_skip_89196 | 12 | 475211:475270:493196:493319:495062:495140 | 493196:493319 | ENSG00000073614.7 | ENST00000382815.4,ENST00000536014.1,ENST00000399788.2 |
| exon_skip_89198 | 12 | 495062:495140:496413:496440:498092:498430 | 496413:496440 | ENSG00000073614.7 | ENST00000543507.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for KDM5A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_89176 | 12 | 394621:394828:395291:395373:401924:402091 | 395291:395373 | ENSG00000073614.7 | ENST00000540838.1 |
| exon_skip_89179 | 12 | 404738:404959:406206:406366:416111:416255 | 406206:406366 | ENSG00000073614.7 | ENST00000399788.2,ENST00000382815.4 |
| exon_skip_89182 | 12 | 427271:427627:430160:430275:431582:431733 | 430160:430275 | ENSG00000073614.7 | ENST00000399788.2,ENST00000382815.4,ENST00000544760.1 |
| exon_skip_89183 | 12 | 431582:431733:432247:432372:432765:432947 | 432247:432372 | ENSG00000073614.7 | ENST00000399788.2,ENST00000382815.4,ENST00000544760.1 |
| exon_skip_89187 | 12 | 438000:438195:440984:441104:442652:442815 | 440984:441104 | ENSG00000073614.7 | ENST00000399788.2,ENST00000382815.4,ENST00000544760.1 |
| exon_skip_89190 | 12 | 440984:441104:442652:442815:443406:443494 | 442652:442815 | ENSG00000073614.7 | ENST00000399788.2,ENST00000382815.4,ENST00000544760.1 |
| exon_skip_89196 | 12 | 475211:475270:493196:493319:495062:495140 | 493196:493319 | ENSG00000073614.7 | ENST00000399788.2,ENST00000382815.4,ENST00000536014.1 |
| exon_skip_89198 | 12 | 495062:495140:496413:496440:498092:498430 | 496413:496440 | ENSG00000073614.7 | ENST00000543507.1 |
| 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 KDM5A |
| 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 |
| ENST00000399788 | 406206 | 406366 | Frame-shift |
| ENST00000399788 | 430160 | 430275 | Frame-shift |
| ENST00000399788 | 432247 | 432372 | Frame-shift |
| ENST00000399788 | 442652 | 442815 | Frame-shift |
| ENST00000399788 | 440984 | 441104 | In-frame |
| ENST00000399788 | 493196 | 493319 | 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 |
| ENST00000399788 | 406206 | 406366 | Frame-shift |
| ENST00000399788 | 430160 | 430275 | Frame-shift |
| ENST00000399788 | 432247 | 432372 | Frame-shift |
| ENST00000399788 | 442652 | 442815 | Frame-shift |
| ENST00000399788 | 440984 | 441104 | In-frame |
| ENST00000399788 | 493196 | 493319 | In-frame |
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Infer the effects of exon skipping event on protein functional features for KDM5A |
| 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 |
| ENST00000399788 | 10780 | 1690 | 493196 | 493319 | 607 | 729 | 81 | 122 |
| ENST00000399788 | 10780 | 1690 | 440984 | 441104 | 2017 | 2136 | 551 | 591 |
| 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 |
| ENST00000399788 | 10780 | 1690 | 493196 | 493319 | 607 | 729 | 81 | 122 |
| ENST00000399788 | 10780 | 1690 | 440984 | 441104 | 2017 | 2136 | 551 | 591 |
| 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 |
| P29375 | 81 | 122 | 1 | 1690 | Chain | ID=PRO_0000200584;Note=Lysine-specific demethylase 5A |
| P29375 | 81 | 122 | 84 | 174 | Domain | Note=ARID;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00355 |
| P29375 | 81 | 122 | 85 | 100 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
| P29375 | 81 | 122 | 117 | 126 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
| P29375 | 81 | 122 | 112 | 112 | Mutagenesis | Note=Decreases DNA-binding. R->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18270511;Dbxref=PMID:18270511 |
| P29375 | 81 | 122 | 77 | 82 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
| P29375 | 551 | 591 | 553 | 557 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
| P29375 | 551 | 591 | 562 | 565 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
| P29375 | 551 | 591 | 570 | 586 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
| P29375 | 551 | 591 | 1 | 1690 | Chain | ID=PRO_0000200584;Note=Lysine-specific demethylase 5A |
| P29375 | 551 | 591 | 437 | 603 | Domain | Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00538 |
| P29375 | 551 | 591 | 589 | 591 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
| P29375 | 551 | 591 | 571 | 571 | Metal binding | Note=Iron%3B catalytic;Ontology_term=ECO:0000255,ECO:0000305,ECO:0000305,ECO:0000305,ECO:0000305;evidence=ECO:0000255|PROSITE-ProRule:PRU00538,ECO:0000305|PubMed:26645689,ECO:0000305|PubMed:27214401,ECO:0000305|PubMed:27427228,ECO:0000305|PubMed:27499454; |
| 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 |
| P29375 | 81 | 122 | 1 | 1690 | Chain | ID=PRO_0000200584;Note=Lysine-specific demethylase 5A |
| P29375 | 81 | 122 | 84 | 174 | Domain | Note=ARID;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00355 |
| P29375 | 81 | 122 | 85 | 100 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
| P29375 | 81 | 122 | 117 | 126 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
| P29375 | 81 | 122 | 112 | 112 | Mutagenesis | Note=Decreases DNA-binding. R->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18270511;Dbxref=PMID:18270511 |
| P29375 | 81 | 122 | 77 | 82 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
| P29375 | 551 | 591 | 553 | 557 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
| P29375 | 551 | 591 | 562 | 565 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
| P29375 | 551 | 591 | 570 | 586 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BGY |
| P29375 | 551 | 591 | 1 | 1690 | Chain | ID=PRO_0000200584;Note=Lysine-specific demethylase 5A |
| P29375 | 551 | 591 | 437 | 603 | Domain | Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00538 |
| P29375 | 551 | 591 | 589 | 591 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V9P |
| P29375 | 551 | 591 | 571 | 571 | Metal binding | Note=Iron%3B catalytic;Ontology_term=ECO:0000255,ECO:0000305,ECO:0000305,ECO:0000305,ECO:0000305;evidence=ECO:0000255|PROSITE-ProRule:PRU00538,ECO:0000305|PubMed:26645689,ECO:0000305|PubMed:27214401,ECO:0000305|PubMed:27427228,ECO:0000305|PubMed:27499454; |
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SNVs in the skipped exons for KDM5A |
| - 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 |
| STAD | TCGA-HU-A4GX-01 | exon_skip_89183 | 432248 | 432372 | 432249 | 432249 | Frame_Shift_Del | T | - | p.D759fs |
| STAD | TCGA-HU-A4GX-01 | exon_skip_89183 | 432248 | 432372 | 432249 | 432249 | Frame_Shift_Del | T | - | p.K758fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_89183 | 432248 | 432372 | 432324 | 432324 | Frame_Shift_Del | T | - | p.K733fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_89183 | 432248 | 432372 | 432324 | 432324 | Frame_Shift_Del | T | - | p.K733fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_89183 | 432248 | 432372 | 432324 | 432324 | Frame_Shift_Del | T | - | p.K733fs |
| LUAD | TCGA-44-2656-01 | exon_skip_89190 | 442653 | 442815 | 442810 | 442811 | Frame_Shift_Ins | - | C | p.E499fs |
| LUAD | TCGA-17-Z026-01 | exon_skip_89179 | 406207 | 406366 | 406210 | 406210 | Nonsense_Mutation | G | A | p.Q1411* |
| STAD | TCGA-BR-8680-01 | exon_skip_89182 | 430161 | 430275 | 430229 | 430229 | Nonsense_Mutation | C | A | p.E825* |
| STAD | TCGA-BR-8680-01 | exon_skip_89182 | 430161 | 430275 | 430229 | 430229 | Nonsense_Mutation | C | A | p.E825X |
| THYM | TCGA-ZB-A963-01 | exon_skip_89190 | 442653 | 442815 | 442727 | 442727 | Nonsense_Mutation | C | A | p.E527X |
| - 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 |
| JHUEM1_ENDOMETRIUM | 442653 | 442815 | 442811 | 442811 | Frame_Shift_Del | C | - | p.E499fs |
| CHLA218_BONE | 406207 | 406366 | 406347 | 406348 | Frame_Shift_Ins | - | A | p.S1365fs |
| HEC251_ENDOMETRIUM | 406207 | 406366 | 406233 | 406233 | Missense_Mutation | G | T | p.S1403Y |
| NCIH513_PLEURA | 406207 | 406366 | 406324 | 406324 | Missense_Mutation | G | C | p.L1373V |
| KMS12BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 430161 | 430275 | 430171 | 430171 | Missense_Mutation | C | T | p.R844Q |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 430161 | 430275 | 430175 | 430175 | Missense_Mutation | C | T | p.A843T |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 430161 | 430275 | 430268 | 430268 | Missense_Mutation | G | A | p.P812S |
| HDLM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 432248 | 432372 | 432307 | 432307 | Missense_Mutation | T | C | p.Y739C |
| NCIH526_LUNG | 432248 | 432372 | 432365 | 432365 | Missense_Mutation | A | G | p.Y720H |
| NCIH630_LARGE_INTESTINE | 432248 | 432372 | 432367 | 432367 | Missense_Mutation | C | T | p.R719H |
| SNU1040_LARGE_INTESTINE | 432248 | 432372 | 432368 | 432368 | Missense_Mutation | G | A | p.R719C |
| RERFLCAD1_LUNG | 442653 | 442815 | 442718 | 442718 | Missense_Mutation | G | A | p.P530S |
| GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 442653 | 442815 | 442750 | 442750 | Missense_Mutation | C | T | p.R519K |
| SISO_CERVIX | 406207 | 406366 | 406207 | 406207 | Splice_Site | C | A | p.G1412C |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 406207 | 406366 | 406207 | 406207 | Splice_Site | C | A | p.G1412C |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 430161 | 430275 | 430275 | 430275 | Splice_Site | T | C | p.R809R |
| TOV21G_OVARY | 432248 | 432372 | 432249 | 432249 | Splice_Site | T | - | p.K758fs |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 442653 | 442815 | 442653 | 442653 | Splice_Site | A | G | p.P551P |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for KDM5A |
| 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 KDM5A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for KDM5A |
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RelatedDrugs for KDM5A |
| 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 KDM5A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| KDM5A | C3714756 | Intellectual Disability | 1 | CTD_human |
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