|
||||||
|
 | |
| |
| |
| 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 PRDM16 |
 Gene summary |
| Gene information | Gene symbol | PRDM16 | Gene ID | 63976 |
| Gene name | PR/SET domain 16 | |
| Synonyms | CMD1LL|KMT8F|LVNC8|MEL1|PFM13 | |
| Cytomap | 1p36.32 | |
| Type of gene | protein-coding | |
| Description | histone-lysine N-methyltransferase PRDM16MDS1/EVI1-like gene 1PR domain 16PR domain containing 16PR domain zinc finger protein 16transcription factor MEL1 | |
| 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 |
| PRDM16 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 19049980 |
| PRDM16 | GO:0030512 | negative regulation of transforming growth factor beta receptor signaling pathway | 14656887 |
| PRDM16 | GO:0045892 | negative regulation of transcription, DNA-templated | 12816872 |
| PRDM16 | GO:0045893 | positive regulation of transcription, DNA-templated | 25578880 |
Top |
Gene structures and expression levels for PRDM16 |
| 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. |
 |
ENSG00000142611
| 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 |
| STG | UP | ENST00000270722.10 | PRDM16-201:protein_coding:PRDM16 | 1.344847e+02 | 8.918649e-01 | 1.566263e-05 | 3.637679e-03 |
| CB | DOWN | ENST00000321336.1 | PRDM16-DT-201:lncRNA:PRDM16 | 1.370840e+01 | -1.042620e+00 | 6.137680e-10 | 2.920947e-08 |
| TC | DOWN | ENST00000453118.5 | PRDM16-DT-207:lncRNA:PRDM16 | 3.218560e+01 | -8.223997e-01 | 3.921036e-03 | 2.790574e-02 |
| TC | UP | ENST00000378391.6 | PRDM16-203:protein_coding:PRDM16 | 9.455617e+00 | 8.332077e-01 | 6.382878e-03 | 4.016299e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PRDM16 |
| 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_164011 | chr1 | 3244132:3244137:3385149:3385286:3396491:3396593 | 3385149:3385286 |
| exon_skip_164095 | chr1 | 3244132:3244137:3385152:3385286:3396491:3396593 | 3385152:3385286 |
| exon_skip_167273 | chr1 | 3430872:3431108:3431966:3432140:3433677:3434095 | 3431966:3432140 |
| exon_skip_184930 | chr1 | 3430872:3431108:3431966:3432140:3433677:3433925 | 3431966:3432140 |
| exon_skip_295024 | chr1 | 3425581:3425750:3426051:3426225:3430872:3431108 | 3426051:3426225 |
| exon_skip_34123 | chr1 | 3430872:3431108:3431966:3432140:3433734:3435421 | 3431966:3432140 |
| exon_skip_49010 | chr1 | 3385152:3385286:3396491:3396593:3402791:3402992 | 3396491:3396593 |
| 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 PRDM16 |
| 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 |
| ENST00000270722 | 3431966 | 3432140 | Frame-shift |
| ENST00000270722 | 3385152 | 3385286 | 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 |
| ENST00000270722 | 3431966 | 3432140 | 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 |
| ENST00000270722 | 3396491 | 3396593 | Frame-shift |
| ENST00000270722 | 3426051 | 3426225 | Frame-shift |
| ENST00000270722 | 3431966 | 3432140 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for PRDM16 |
p-ENSG00000142611_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 |
| ENST00000270722 | 8707 | 1276 | 3385152 | 3385286 | 489 | 622 | 146 | 191 |
| 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 |
| Q9HAZ2 | 146 | 191 | 1 | 184 | Alternative sequence | ID=VSP_038063;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9HAZ2 | 146 | 191 | 191 | 191 | Alternative sequence | ID=VSP_038064;Note=In isoform 3. Q->QV;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| Q9HAZ2 | 146 | 191 | 161 | 163 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N1I |
| Q9HAZ2 | 146 | 191 | 183 | 188 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N1I |
| Q9HAZ2 | 146 | 191 | 191 | 198 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N1I |
| Q9HAZ2 | 146 | 191 | 1 | 1276 | Chain | ID=PRO_0000047773;Note=PR domain zinc finger protein 16 |
| Q9HAZ2 | 146 | 191 | 82 | 211 | Domain | Note=SET;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00190 |
| Q9HAZ2 | 146 | 191 | 167 | 170 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N1I |
| Q9HAZ2 | 146 | 191 | 178 | 180 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N1I |
| Q9HAZ2 | 146 | 191 | 153 | 155 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N1I |
| 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 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in PRDM16 |
| 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 PRDM16 |
| - 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 PRDM16 |
| 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 PRDM16 |
| 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 PRDM16 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for PRDM16 |
| 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 PRDM16 |
| 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)
|