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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for MED4 |
 Gene summary |
| Gene information | Gene symbol | MED4 | Gene ID | 29079 |
| Gene name | mediator complex subunit 4 | |
| Synonyms | ARC36|DRIP36|HSPC126|TRAP36|VDRIP | |
| Cytomap | 13q14.2 | |
| Type of gene | protein-coding | |
| Description | mediator of RNA polymerase II transcription subunit 4TRAP/SMCC/PC2 subunit p36activator-recruited cofactor 36 kDa componentmediator, 34-kD subunit, homologvitamin D receptor-interacting protein, 36-kDvitamin D3 receptor-interacting protein complex 36 | |
| 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 |
| MED4 | GO:0006366 | transcription by RNA polymerase II | 10882111 |
| MED4 | GO:0006367 | transcription initiation from RNA polymerase II promoter | 12218053 |
| MED4 | GO:0045893 | positive regulation of transcription, DNA-templated | 10198638 |
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Gene structures and expression levels for MED4 |
| 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. |
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ENSG00000136146
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | UP | ENST00000481238.1 | TMED4-205:protein_coding:TMED4 | 7.934281e+01 | 8.315278e-01 | 2.642978e-05 | 1.026540e-03 |
| PG | UP | ENST00000289577.9 | TMED4-201:protein_coding:TMED4 | 2.668100e+01 | 1.530793e+00 | 3.129606e-04 | 6.322890e-03 |
| CB | DOWN | ENST00000495013.5 | MED4-204:non_stop_decay:MED4 | 1.151551e+01 | -8.694274e-01 | 1.616186e-07 | 3.185179e-06 |
| 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 MED4 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_125584 | chr13 | 48083371:48083428:48086282:48086452:48090352:48090418 | 48086282:48086452 |
| exon_skip_171768 | chr13 | 48081645:48081731:48083371:48083428:48086282:48086452 | 48083371:48083428 |
| exon_skip_232955 | chr13 | 48086282:48086452:48090352:48090418:48094954:48095068 | 48090352:48090418 |
| exon_skip_235227 | chr13 | 48090355:48090418:48093548:48093687:48094954:48095068 | 48093548:48093687 |
| exon_skip_75068 | chr13 | 48090352:48090418:48093548:48093687:48094954:48095068 | 48093548:48093687 |
| exon_skip_9477 | chr13 | 48081645:48081731:48083371:48083428:48086282:48086386 | 48083371:48083428 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_171768 | Mayo_CB | 7.751220e-01 | 8.788312e-01 | -1.037092e-01 | 4.885421e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for MED4 |
| 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 |
| ENST00000258648 | 48083371 | 48083428 | Frame-shift |
| ENST00000258648 | 48090352 | 48090418 | 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 |
| ENST00000258648 | 48083371 | 48083428 | Frame-shift |
| 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 |
| ENST00000258648 | 48083371 | 48083428 | Frame-shift |
| ENST00000258648 | 48090352 | 48090418 | Frame-shift |
| ENST00000258648 | 48086282 | 48086452 | In-frame |
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Infer the effects of exon skipping event on protein functional features for MED4 |
p-ENSG00000136146_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 |
| ENST00000258648 | 2039 | 270 | 48086282 | 48086452 | 219 | 388 | 64 | 120 |
| 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 |
| Q9NPJ6 | 64 | 120 | 2 | 270 | Chain | ID=PRO_0000096383;Note=Mediator of RNA polymerase II transcription subunit 4 |
| Q9NPJ6 | 64 | 120 | 90 | 131 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NPJ6 | 64 | 120 | 105 | 105 | Sequence conflict | Note=S->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NPJ6 | 64 | 120 | 120 | 120 | Sequence conflict | Note=I->T;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in MED4 |
| 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 MED4 |
| - 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 MED4 |
| 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 MED4 |
| 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 MED4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TRA2A | exon_skip_171768 | -5.798653e-01 | 1.154542e-15 |
| CB | SNRPA | exon_skip_171768 | -4.072070e-01 | 9.992408e-08 |
| CB | NUP42 | exon_skip_171768 | 5.173854e-01 | 2.890480e-12 |
| CB | TARDBP | exon_skip_232955 | -5.202831e-01 | 2.081511e-12 |
| CB | SAMD4A | exon_skip_232955 | -4.588716e-01 | 1.178467e-09 |
| CB | TRA2A | exon_skip_232955 | -5.194451e-01 | 2.289572e-12 |
| CB | RC3H1 | exon_skip_232955 | -4.368052e-01 | 8.600864e-09 |
| CB | HNRNPA2B1 | exon_skip_232955 | -4.593827e-01 | 1.123539e-09 |
| CB | HNRNPF | exon_skip_232955 | -4.049230e-01 | 1.195843e-07 |
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RelatedDrugs for MED4 |
| 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 MED4 |
| 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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