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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 AFF4 |
 Gene summary |
| Gene information | Gene symbol | AFF4 | Gene ID | 27125 |
| Gene name | AF4/FMR2 family member 4 | |
| Synonyms | AF5Q31|CHOPS|MCEF | |
| Cytomap | 5q31.1 | |
| Type of gene | protein-coding | |
| Description | AF4/FMR2 family member 4ALL1-fused gene from chromosome 5q31 proteinmajor CDK9 elongation factor-associated protein | |
| Modification date | 20200315 | |
| 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 |
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Gene structures and expression levels for AFF4 |
| 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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ENSG00000072364
| 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 |
| CB | UP | ENST00000425658.1 | AFF4-205:protein_coding:AFF4 | 1.119909e+01 | 9.668452e-01 | 2.382038e-06 | 3.134318e-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 AFF4 |
| 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_174132 | chr5 | 132885076:132885119:132886310:132886403:132887521:132887592 | 132886310:132886403 |
| exon_skip_238870 | chr5 | 132875395:132881186:132883340:132883560:132885076:132885119 | 132883340:132883560 |
| exon_skip_261958 | chr5 | 132902442:132902487:132904368:132904404:132932178:132932222 | 132904368:132904404 |
| exon_skip_262403 | chr5 | 132899587:132899641:132902442:132902487:132904368:132904404 | 132902442:132902487 |
| exon_skip_264745 | chr5 | 132897204:132897240:132898230:132898392:132899104:132899141 | 132898230:132898392 |
| exon_skip_32174 | chr5 | 132888097:132888160:132889079:132889173:132892164:132892404 | 132889079:132889173 |
| exon_skip_7515 | chr5 | 132893030:132893118:132896323:132897240:132898230:132898392 | 132896323:132897240 |
| exon_skip_77768 | chr5 | 132904368:132904404:132927121:132927207:132932178:132932222 | 132927121:132927207 |
| 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 AFF4 |
| 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 |
| ENST00000265343 | 132883340 | 132883560 | Frame-shift |
| ENST00000265343 | 132889079 | 132889173 | Frame-shift |
| ENST00000265343 | 132898230 | 132898392 | Frame-shift |
| ENST00000265343 | 132927121 | 132927207 | 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 |
| ENST00000265343 | 132889079 | 132889173 | Frame-shift |
| ENST00000265343 | 132898230 | 132898392 | Frame-shift |
| ENST00000265343 | 132902442 | 132902487 | Frame-shift |
| ENST00000265343 | 132896323 | 132897240 | In-frame |
| ENST00000265343 | 132927121 | 132927207 | In-frame |
| 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 |
| ENST00000265343 | 132883340 | 132883560 | Frame-shift |
| ENST00000265343 | 132886310 | 132886403 | Frame-shift |
| ENST00000265343 | 132889079 | 132889173 | Frame-shift |
| ENST00000265343 | 132898230 | 132898392 | Frame-shift |
| ENST00000265343 | 132902442 | 132902487 | Frame-shift |
| ENST00000265343 | 132927121 | 132927207 | In-frame |
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Infer the effects of exon skipping event on protein functional features for AFF4 |
p-ENSG00000072364_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 |
| ENST00000265343 | 9569 | 1163 | 132927121 | 132927207 | 1344 | 1429 | 321 | 349 |
| 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 |
| ENST00000265343 | 9569 | 1163 | 132927121 | 132927207 | 1344 | 1429 | 321 | 349 |
| ENST00000265343 | 9569 | 1163 | 132896323 | 132897240 | 1770 | 2686 | 463 | 768 |
| 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 |
| ENST00000265343 | 9569 | 1163 | 132927121 | 132927207 | 1344 | 1429 | 321 | 349 |
| 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 |
| Q9UHB7 | 321 | 349 | 1 | 1163 | Chain | ID=PRO_0000239393;Note=AF4/FMR2 family member 4 |
| Q9UHB7 | 321 | 349 | 102 | 461 | Compositional bias | Note=Ser-rich |
| Q9UHB7 | 321 | 349 | 315 | 323 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5JW9 |
| 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 |
| Q9UHB7 | 321 | 349 | 1 | 1163 | Chain | ID=PRO_0000239393;Note=AF4/FMR2 family member 4 |
| Q9UHB7 | 321 | 349 | 102 | 461 | Compositional bias | Note=Ser-rich |
| Q9UHB7 | 321 | 349 | 315 | 323 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5JW9 |
| Q9UHB7 | 463 | 768 | 354 | 1163 | Alternative sequence | ID=VSP_019219;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9UHB7 | 463 | 768 | 1 | 1163 | Chain | ID=PRO_0000239393;Note=AF4/FMR2 family member 4 |
| Q9UHB7 | 463 | 768 | 583 | 583 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| Q9UHB7 | 463 | 768 | 487 | 487 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:23186163,PMID:24275569 |
| Q9UHB7 | 463 | 768 | 490 | 490 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ESC8 |
| Q9UHB7 | 463 | 768 | 491 | 491 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ESC8 |
| Q9UHB7 | 463 | 768 | 549 | 549 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18691976,ECO:0000244|PubMed:19369195;Dbxref=PMID:18691976,PMID:19369195 |
| Q9UHB7 | 463 | 768 | 671 | 671 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19369195;Dbxref=PMID:18669648,PMID:19369195 |
| Q9UHB7 | 463 | 768 | 674 | 674 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18220336,ECO:0000244|PubMed:23186163;Dbxref=PMID:18220336,PMID:23186163 |
| Q9UHB7 | 463 | 768 | 680 | 680 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9UHB7 | 463 | 768 | 694 | 694 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| Q9UHB7 | 463 | 768 | 703 | 703 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:17081983,PMID:18669648,PMID:23186163 |
| Q9UHB7 | 463 | 768 | 706 | 706 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:17081983,PMID:18669648,PMID:23186163,PMID |
| Q9UHB7 | 463 | 768 | 712 | 712 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| Q9UHB7 | 463 | 768 | 757 | 757 | Natural variant | ID=VAR_064693;Note=Found in a clear cell renal carcinoma case%3B somatic mutation. S->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21248752;Dbxref=PMID:21248752 |
| 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 |
| Q9UHB7 | 321 | 349 | 1 | 1163 | Chain | ID=PRO_0000239393;Note=AF4/FMR2 family member 4 |
| Q9UHB7 | 321 | 349 | 102 | 461 | Compositional bias | Note=Ser-rich |
| Q9UHB7 | 321 | 349 | 315 | 323 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5JW9 |
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3'-UTR located exon skipping events that lost miRNA binding sites in AFF4 |
| 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 AFF4 |
| - 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 AFF4 |
| 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 AFF4 |
| 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 AFF4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| HCC | PTBP1 | exon_skip_77768 | 4.049784e-01 | 6.398057e-12 |
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RelatedDrugs for AFF4 |
| 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 AFF4 |
| 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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