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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 KDM3A |
 Gene summary |
| Gene information | Gene symbol | KDM3A | Gene ID | 55818 |
| Gene name | lysine demethylase 3A | |
| Synonyms | JHDM2A|JHMD2A|JMJD1|JMJD1A|TSGA | |
| Cytomap | 2p11.2 | |
| Type of gene | protein-coding | |
| Description | lysine-specific demethylase 3AjmjC domain-containing histone demethylation protein 2Ajumonji C domain-containing histone demethylase 2Ajumonji domain-containing protein 1Alysine (K)-specific demethylase 3Atestis-specific protein A | |
| Modification date | 20180523 | |
| UniProtAcc | Q9Y4C1 | |
| Context | PubMed: KDM3A [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 |
| KDM3A | GO:0009755 | hormone-mediated signaling pathway | 16603237 |
| KDM3A | GO:0030521 | androgen receptor signaling pathway | 16603237 |
| KDM3A | GO:0033169 | histone H3-K9 demethylation | 16603237 |
| KDM3A | GO:0046293 | formaldehyde biosynthetic process | 16603237 |
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Exon skipping events across known transcript of Ensembl for KDM3A 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 KDM3A |
| 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 KDM3A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_327464 | 2 | 86669170:86669356:86676929:86677085:86678225:86678246 | 86676929:86677085 | ENSG00000115548.12 | ENST00000441719.1,ENST00000312912.5,ENST00000427678.1,ENST00000409556.1,ENST00000409064.1,ENST00000452034.1 |
| exon_skip_327467 | 2 | 86684105:86684194:86687901:86687954:86691175:86691339 | 86687901:86687954 | ENSG00000115548.12 | ENST00000488971.1 |
| exon_skip_327469 | 2 | 86697326:86697531:86701898:86702113:86704999:86705152 | 86701898:86702113 | ENSG00000115548.12 | ENST00000441719.1,ENST00000312912.5,ENST00000542128.1,ENST00000409556.1,ENST00000409064.1 |
| exon_skip_327474 | 2 | 86705730:86705858:86707289:86707485:86709052:86709225 | 86707289:86707485 | ENSG00000115548.12 | ENST00000312912.5,ENST00000542128.1,ENST00000409556.1,ENST00000409064.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for KDM3A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_327463 | 2 | 86667923:86668085:86668394:86668567:86669140:86669356 | 86668394:86668567 | ENSG00000115548.12 | ENST00000409556.1 |
| exon_skip_327464 | 2 | 86669170:86669356:86676929:86677085:86678225:86678246 | 86676929:86677085 | ENSG00000115548.12 | ENST00000452034.1,ENST00000409556.1,ENST00000312912.5,ENST00000441719.1,ENST00000409064.1,ENST00000427678.1 |
| exon_skip_327465 | 2 | 86669170:86669356:86678225:86678336:86682207:86682266 | 86678225:86678336 | ENSG00000115548.12 | ENST00000542128.1 |
| exon_skip_327467 | 2 | 86684105:86684194:86687901:86687954:86691175:86691339 | 86687901:86687954 | ENSG00000115548.12 | ENST00000488971.1 |
| exon_skip_327469 | 2 | 86697326:86697531:86701898:86702113:86704999:86705152 | 86701898:86702113 | ENSG00000115548.12 | ENST00000409556.1,ENST00000312912.5,ENST00000441719.1,ENST00000409064.1,ENST00000542128.1 |
| exon_skip_327474 | 2 | 86705730:86705858:86707289:86707485:86709052:86709225 | 86707289:86707485 | ENSG00000115548.12 | ENST00000409556.1,ENST00000312912.5,ENST00000409064.1,ENST00000542128.1 |
| 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 KDM3A |
| 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 |
| ENST00000312912 | 86701898 | 86702113 | Frame-shift |
| ENST00000409064 | 86701898 | 86702113 | Frame-shift |
| ENST00000409556 | 86701898 | 86702113 | Frame-shift |
| ENST00000312912 | 86707289 | 86707485 | Frame-shift |
| ENST00000409064 | 86707289 | 86707485 | Frame-shift |
| ENST00000409556 | 86707289 | 86707485 | Frame-shift |
| ENST00000312912 | 86676929 | 86677085 | In-frame |
| ENST00000409064 | 86676929 | 86677085 | In-frame |
| ENST00000409556 | 86676929 | 86677085 | 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 |
| ENST00000409556 | 86668394 | 86668567 | 5UTR-5UTR |
| ENST00000312912 | 86701898 | 86702113 | Frame-shift |
| ENST00000409064 | 86701898 | 86702113 | Frame-shift |
| ENST00000409556 | 86701898 | 86702113 | Frame-shift |
| ENST00000312912 | 86707289 | 86707485 | Frame-shift |
| ENST00000409064 | 86707289 | 86707485 | Frame-shift |
| ENST00000409556 | 86707289 | 86707485 | Frame-shift |
| ENST00000312912 | 86676929 | 86677085 | In-frame |
| ENST00000409064 | 86676929 | 86677085 | In-frame |
| ENST00000409556 | 86676929 | 86677085 | In-frame |
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Infer the effects of exon skipping event on protein functional features for KDM3A |
| 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 |
| ENST00000312912 | 4901 | 1321 | 86676929 | 86677085 | 514 | 669 | 62 | 114 |
| ENST00000409064 | 4638 | 1321 | 86676929 | 86677085 | 245 | 400 | 62 | 114 |
| ENST00000409556 | 4945 | 1321 | 86676929 | 86677085 | 552 | 707 | 62 | 114 |
| 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 |
| ENST00000312912 | 4901 | 1321 | 86676929 | 86677085 | 514 | 669 | 62 | 114 |
| ENST00000409064 | 4638 | 1321 | 86676929 | 86677085 | 245 | 400 | 62 | 114 |
| ENST00000409556 | 4945 | 1321 | 86676929 | 86677085 | 552 | 707 | 62 | 114 |
| 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 |
| Q9Y4C1 | 62 | 114 | 1 | 1321 | Chain | ID=PRO_0000084285;Note=Lysine-specific demethylase 3A |
| Q9Y4C1 | 62 | 114 | 1 | 1321 | Chain | ID=PRO_0000084285;Note=Lysine-specific demethylase 3A |
| Q9Y4C1 | 62 | 114 | 1 | 1321 | Chain | ID=PRO_0000084285;Note=Lysine-specific demethylase 3A |
| 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 |
| Q9Y4C1 | 62 | 114 | 1 | 1321 | Chain | ID=PRO_0000084285;Note=Lysine-specific demethylase 3A |
| Q9Y4C1 | 62 | 114 | 1 | 1321 | Chain | ID=PRO_0000084285;Note=Lysine-specific demethylase 3A |
| Q9Y4C1 | 62 | 114 | 1 | 1321 | Chain | ID=PRO_0000084285;Note=Lysine-specific demethylase 3A |
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SNVs in the skipped exons for KDM3A |
| - 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 |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_327464 | 86676930 | 86677085 | 86676942 | 86676942 | Frame_Shift_Del | T | - | p.F67fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_327469 | 86701899 | 86702113 | 86701989 | 86701989 | Frame_Shift_Del | T | - | p.P605fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_327469 | 86701899 | 86702113 | 86701996 | 86701996 | Frame_Shift_Del | A | - | p.K608fs |
| CESC | TCGA-C5-A7CH-01 | exon_skip_327474 | 86707290 | 86707485 | 86707395 | 86707395 | Frame_Shift_Del | G | - | p.G808fs |
| STAD | TCGA-BR-4184-01 | exon_skip_327464 | 86676930 | 86677085 | 86677062 | 86677062 | Nonsense_Mutation | C | T | p.R107* |
| STAD | TCGA-BR-4184-01 | exon_skip_327464 | 86676930 | 86677085 | 86677062 | 86677062 | Nonsense_Mutation | C | T | p.R107X |
| - 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 |
| CAKI2_KIDNEY | 86676930 | 86677085 | 86677065 | 86677066 | Frame_Shift_Ins | - | T | p.I108fs |
| SW1116_LARGE_INTESTINE | 86676930 | 86677085 | 86676943 | 86676943 | Missense_Mutation | T | A | p.F67Y |
| TGBC11TKB_STOMACH | 86676930 | 86677085 | 86676961 | 86676961 | Missense_Mutation | G | T | p.R73M |
| UMUC14_URINARY_TRACT | 86676930 | 86677085 | 86677083 | 86677083 | Missense_Mutation | A | G | p.I114V |
| CALU6_LUNG | 86701899 | 86702113 | 86702056 | 86702056 | Missense_Mutation | C | T | p.H628Y |
| AN3CA_ENDOMETRIUM | 86701899 | 86702113 | 86702061 | 86702061 | Missense_Mutation | C | A | p.F629L |
| RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 86707290 | 86707485 | 86707300 | 86707300 | Missense_Mutation | C | G | p.A776G |
| MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 86707290 | 86707485 | 86707312 | 86707312 | Missense_Mutation | C | A | p.P780Q |
| SN12C_KIDNEY | 86707290 | 86707485 | 86707374 | 86707374 | Missense_Mutation | G | A | p.E801K |
| CAL72_BONE | 86707290 | 86707485 | 86707380 | 86707380 | Missense_Mutation | G | T | p.A803S |
| HCC2998_LARGE_INTESTINE | 86707290 | 86707485 | 86707464 | 86707464 | Missense_Mutation | A | C | p.N831H |
| PEO1_OVARY | 86676930 | 86677085 | 86677038 | 86677038 | Nonsense_Mutation | C | T | p.R99* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for KDM3A |
| 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 KDM3A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for KDM3A |
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RelatedDrugs for KDM3A |
| 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 KDM3A |
| 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)
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