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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 PRDM2 |
 Gene summary |
| Gene information | Gene symbol | PRDM2 | Gene ID | 7799 |
| Gene name | PR/SET domain 2 | |
| Synonyms | HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2 | |
| Cytomap | 1p36.21 | |
| Type of gene | protein-coding | |
| Description | PR domain zinc finger protein 2GATA-3 binding protein G3BMTE-binding proteinPR domain 2PR domain containing 2, with ZNF domainPR domain-containing protein 2lysine N-methyltransferase 8retinoblastoma protein-binding zinc finger proteinretinoblastom | |
| 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 |
| PRDM2 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 8654390 |
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Gene structures and expression levels for PRDM2 |
| 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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ENSG00000116731
| 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 | ENST00000311066.9 | PRDM2-202:protein_coding:PRDM2 | 1.543101e+01 | 2.458963e+01 | 3.149532e-74 | 4.662913e-69 |
| 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 PRDM2 |
| 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_107442 | chr1 | 13749436:13749487:13769118:13769173:13773078:13773126 | 13769118:13769173 |
| exon_skip_146474 | chr1 | 13731018:13731117:13732779:13732855:13742005:13742157 | 13732779:13732855 |
| exon_skip_172568 | chr1 | 13749436:13749487:13773078:13773188:13816427:13816570 | 13773078:13773188 |
| exon_skip_177767 | chr1 | 13769118:13769173:13773078:13773188:13816427:13816570 | 13773078:13773188 |
| exon_skip_194543 | chr1 | 13773078:13773188:13778418:13782831:13816427:13816570 | 13778418:13782831 |
| exon_skip_235865 | chr1 | 13749436:13749487:13769039:13769173:13773078:13773126 | 13769039:13769173 |
| exon_skip_260198 | chr1 | 13773078:13773188:13816427:13816570:13823159:13823419 | 13816427:13816570 |
| exon_skip_271474 | chr1 | 13731018:13731117:13732779:13732882:13742005:13742157 | 13732779:13732882 |
| exon_skip_275199 | chr1 | 13773083:13773188:13778418:13782831:13786515:13787067 | 13778418:13782831 |
| exon_skip_28455 | chr1 | 13773078:13773188:13778418:13782831:13786515:13787067 | 13778418:13782831 |
| exon_skip_286391 | chr1 | 13731018:13731117:13742005:13742157:13749361:13749463 | 13742005:13742157 |
| exon_skip_50612 | chr1 | 13700240:13700300:13715541:13715614:13731000:13731117 | 13715541:13715614 |
| exon_skip_58881 | chr1 | 13742005:13742157:13749361:13749487:13773078:13773126 | 13749361:13749487 |
| exon_skip_85673 | chr1 | 13732779:13732882:13742005:13742157:13749361:13749463 | 13742005:13742157 |
| exon_skip_86517 | chr1 | 13778418:13782831:13816427:13816570:13823159:13823419 | 13816427:13816570 |
| exon_skip_97318 | chr1 | 13749436:13749487:13773078:13773188:13778418:13778463 | 13773078:13773188 |
| 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 PRDM2 |
| 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 |
| ENST00000235372 | 13732779 | 13732882 | Frame-shift |
| ENST00000235372 | 13749361 | 13749487 | Frame-shift |
| ENST00000235372 | 13778418 | 13782831 | Frame-shift |
| ENST00000235372 | 13742005 | 13742157 | In-frame |
| ENST00000235372 | 13773078 | 13773188 | 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 |
| ENST00000235372 | 13778418 | 13782831 | 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 |
| ENST00000235372 | 13816427 | 13816570 | 3UTR-3CDS |
| ENST00000235372 | 13732779 | 13732882 | Frame-shift |
| ENST00000235372 | 13749361 | 13749487 | Frame-shift |
| ENST00000235372 | 13778418 | 13782831 | Frame-shift |
| ENST00000235372 | 13773078 | 13773188 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PRDM2 |
p-ENSG00000116731_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 |
| ENST00000235372 | 7974 | 1718 | 13742005 | 13742157 | 1089 | 1240 | 77 | 128 |
| ENST00000235372 | 7974 | 1718 | 13773078 | 13773188 | 1369 | 1478 | 171 | 207 |
| 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 |
| ENST00000235372 | 7974 | 1718 | 13773078 | 13773188 | 1369 | 1478 | 171 | 207 |
| 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 |
| Q13029 | 77 | 128 | 1 | 201 | Alternative sequence | ID=VSP_018974;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q13029 | 77 | 128 | 72 | 80 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2QPW |
| Q13029 | 77 | 128 | 84 | 89 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2QPW |
| Q13029 | 77 | 128 | 106 | 110 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2JV0 |
| Q13029 | 77 | 128 | 113 | 118 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2QPW |
| Q13029 | 77 | 128 | 121 | 128 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2QPW |
| Q13029 | 77 | 128 | 1 | 1718 | Chain | ID=PRO_0000041634;Note=PR domain zinc finger protein 2 |
| Q13029 | 77 | 128 | 28 | 141 | Domain | Note=SET;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00190 |
| Q13029 | 77 | 128 | 93 | 95 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2QPW |
| Q13029 | 77 | 128 | 98 | 101 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2QPW |
| Q13029 | 77 | 128 | 106 | 106 | Mutagenesis | Note=Reduced histone methyltransferase activity. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14633678;Dbxref=PMID:14633678 |
| Q13029 | 77 | 128 | 81 | 83 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2QPW |
| Q13029 | 171 | 207 | 1 | 201 | Alternative sequence | ID=VSP_018974;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q13029 | 171 | 207 | 171 | 226 | Alternative sequence | ID=VSP_046421;Note=In isoform 4. GKKKSQENKNKGNKIQDIQLKTSEPDFTSANMRDSAEGPKEDEEKPSASALEQPAT->ATASAWRPDALHQRPRTSPGSIGRSKLQLQPSSRDHSSKSRHSGCSLTAPEVTWNQ;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q13029 | 171 | 207 | 1 | 1718 | Chain | ID=PRO_0000041634;Note=PR domain zinc finger protein 2 |
| Q13029 | 171 | 207 | 188 | 188 | Mutagenesis | Note=Loss of histone methyltransferase activity. I->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14633678;Dbxref=PMID:14633678 |
| Q13029 | 171 | 207 | 196 | 196 | Sequence conflict | Note=D->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q13029 | 171 | 207 | 200 | 200 | Sequence conflict | Note=A->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q13029 | 171 | 207 | 1 | 201 | Alternative sequence | ID=VSP_018974;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q13029 | 171 | 207 | 171 | 226 | Alternative sequence | ID=VSP_046421;Note=In isoform 4. GKKKSQENKNKGNKIQDIQLKTSEPDFTSANMRDSAEGPKEDEEKPSASALEQPAT->ATASAWRPDALHQRPRTSPGSIGRSKLQLQPSSRDHSSKSRHSGCSLTAPEVTWNQ;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q13029 | 171 | 207 | 1 | 1718 | Chain | ID=PRO_0000041634;Note=PR domain zinc finger protein 2 |
| Q13029 | 171 | 207 | 188 | 188 | Mutagenesis | Note=Loss of histone methyltransferase activity. I->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14633678;Dbxref=PMID:14633678 |
| Q13029 | 171 | 207 | 196 | 196 | Sequence conflict | Note=D->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q13029 | 171 | 207 | 200 | 200 | Sequence conflict | Note=A->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PRDM2 |
| 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 PRDM2 |
| - 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 PRDM2 |
| 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 |
| ADstage | MSBB | IFG | exon_skip_107442 | -4.244746e-01 | 2.436203e-02 | chr1 | + | 13749436 | 13749487 | 13769118 | 13769173 | 13773078 | 13773126 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PRDM2 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| CB | exon_skip_271474 | rs16852866 | chr1:13726979 | 1.213646e-04 | 2.004604e-02 |
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Correlation with RNA binding proteins (RBPs) for PRDM2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM3 | exon_skip_172568 | 4.698179e-01 | 8.969821e-10 |
| DLPFC | SRSF11 | exon_skip_235865 | -5.669936e-01 | 2.230090e-29 |
| DLPFC | FUBP1 | exon_skip_235865 | -4.200413e-01 | 1.704955e-15 |
| HCC | RBM6 | exon_skip_235865 | -4.440899e-01 | 1.777941e-14 |
| HCC | TRNAU1AP | exon_skip_235865 | -4.171777e-01 | 8.560911e-13 |
| HCC | PCBP4 | exon_skip_235865 | -4.117199e-01 | 1.802566e-12 |
| HCC | PTBP1 | exon_skip_235865 | -4.189620e-01 | 6.691599e-13 |
| HCC | SRSF5 | exon_skip_235865 | -4.249197e-01 | 2.908522e-13 |
| IFG | RBMS3 | exon_skip_194543 | 4.473748e-01 | 1.929425e-02 |
| IFG | ZNF326 | exon_skip_194543 | 4.020022e-01 | 3.765079e-02 |
| PCC | PTBP1 | exon_skip_235865 | -4.618359e-01 | 2.802890e-12 |
| TC | RBM24 | exon_skip_235865 | 5.897671e-01 | 4.401094e-16 |
| TC | RALYL | exon_skip_235865 | 6.245171e-01 | 2.334413e-18 |
| TC | CELF1 | exon_skip_235865 | 4.514757e-01 | 2.945536e-09 |
| TC | NOVA1 | exon_skip_235865 | 4.706672e-01 | 4.959918e-10 |
| TC | PCBP4 | exon_skip_172568 | 4.523427e-01 | 3.054964e-07 |
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RelatedDrugs for PRDM2 |
| 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 PRDM2 |
| 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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