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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 JMJD6 |
Gene summary |
Gene information | Gene symbol | JMJD6 | Gene ID | 23210 |
Gene name | jumonji domain containing 6, arginine demethylase and lysine hydroxylase | |
Synonyms | PSR|PTDSR|PTDSR1 | |
Cytomap | 17q25.1 | |
Type of gene | protein-coding | |
Description | bifunctional arginine demethylase and lysyl-hydroxylase JMJD6arginine demethylase and lysine hydroxylasehistone arginine demethylase JMJD6jmjC domain-containing protein 6jumonji domain containing 6jumonji domain-containing protein 6lysyl-hydroxylase | |
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 |
JMJD6 | GO:0006482 | protein demethylation | 24498420 |
JMJD6 | GO:0018395 | peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine | 19574390|22189873 |
JMJD6 | GO:0035513 | oxidative RNA demethylation | 24360279 |
JMJD6 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 24360279 |
JMJD6 | GO:0051260 | protein homooligomerization | 22189873|24360279 |
JMJD6 | GO:0070078 | histone H3-R2 demethylation | 17947579 |
JMJD6 | GO:0070078 | histone H3-R2 demethylation | 22189873 |
JMJD6 | GO:0070079 | histone H4-R3 demethylation | 17947579|24360279|24498420 |
JMJD6 | GO:0070079 | histone H4-R3 demethylation | 22189873 |
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Gene structures and expression levels for JMJD6 |
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 |
CB | UP | ENST00000397625.8 | JMJD6-202:protein_coding:JMJD6 | 1.087631e+02 | 1.558921e+00 | 3.803934e-06 | 4.650470e-05 |
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 JMJD6 |
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_101393 | chr17 | 76718500:76718860:76720360:76720498:76721798:76721933 | 76720360:76720498 |
exon_skip_118278 | chr17 | 76720360:76720498:76721263:76721351:76721798:76721933 | 76721263:76721351 |
exon_skip_161094 | chr17 | 76720360:76720498:76721263:76721356:76721798:76721930 | 76721263:76721356 |
exon_skip_210969 | chr17 | 76720360:76720498:76721263:76721351:76721798:76721930 | 76721263:76721351 |
exon_skip_229447 | chr17 | 76720397:76720498:76721263:76721351:76721798:76721933 | 76721263:76721351 |
exon_skip_65928 | chr17 | 76721798:76721933:76723772:76724058:76725467:76725855 | 76723772:76724058 |
exon_skip_83325 | chr17 | 76720360:76720498:76721263:76721356:76721798:76721933 | 76721263:76721356 |
exon_skip_84208 | chr17 | 76718500:76718860:76720360:76720498:76721798:76721930 | 76720360:76720498 |
exon_skip_94837 | chr17 | 76720397:76720498:76721263:76721356:76721798:76721933 | 76721263:76721356 |
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 JMJD6 |
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 |
ENST00000397625 | 76720360 | 76720498 | Frame-shift |
ENST00000397625 | 76723772 | 76724058 | Frame-shift |
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 |
ENST00000397625 | 76723772 | 76724058 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for JMJD6 |
p-ENSG00000070495_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 JMJD6 |
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 JMJD6 |
- 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 JMJD6 |
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 JMJD6 |
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 JMJD6 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | CNOT4 | exon_skip_161094 | -4.797847e-01 | 1.564978e-10 |
CB | PCBP4 | exon_skip_161094 | 6.051690e-01 | 2.940909e-17 |
CB | HNRNPA2B1 | exon_skip_161094 | -4.635489e-01 | 7.591349e-10 |
IFG | HNRNPK | exon_skip_83325 | -4.348545e-01 | 2.982791e-02 |
IFG | HNRNPA2B1 | exon_skip_83325 | -4.215549e-01 | 3.583295e-02 |
IFG | SRSF9 | exon_skip_83325 | -6.062529e-01 | 1.316348e-03 |
IFG | SRSF5 | exon_skip_83325 | -5.082034e-01 | 9.492617e-03 |
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RelatedDrugs for JMJD6 |
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 JMJD6 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |