|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for AFF1 |
 Gene summary |
| Gene information | Gene symbol | AFF1 | Gene ID | 4299 |
| Gene name | AF4/FMR2 family member 1 | |
| Synonyms | AF4|MLLT2|PBM1 | |
| Cytomap | 4q21.3-q22.1 | |
| Type of gene | protein-coding | |
| Description | AF4/FMR2 family member 1ALL1-fused gene from chromosome 4 proteinmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 2pre-B-cell monocytic leukemia partner 1proto-oncogene AF4 | |
| Modification date | 20180523 | |
| UniProtAcc | P51825 | |
| Context | PubMed: AFF1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
Top |
Exon skipping events across known transcript of Ensembl for AFF1 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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. |
 |
Top |
Gene isoform structures and expression levels for AFF1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for AFF1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_424845 | 4 | 87869649:87869723:87967317:87967438:87967846:87968042 | 87967317:87967438 | ENSG00000172493.16 | ENST00000511442.1,ENST00000507468.1,ENST00000395146.4,ENST00000503477.1 |
| exon_skip_424849 | 4 | 87928420:87928576:87967317:87967438:87967846:87968042 | 87967317:87967438 | ENSG00000172493.16 | ENST00000307808.6 |
| exon_skip_424852 | 4 | 88005274:88005316:88011135:88011222:88012944:88012976 | 88011135:88011222 | ENSG00000172493.16 | ENST00000514970.1,ENST00000511722.1,ENST00000507468.1,ENST00000395146.4,ENST00000544085.1,ENST00000307808.6 |
| exon_skip_424853 | 4 | 88012944:88012981:88016066:88016121:88026779:88026834 | 88016066:88016121 | ENSG00000172493.16 | ENST00000514970.1,ENST00000511722.1,ENST00000395146.4,ENST00000544085.1,ENST00000307808.6,ENST00000503477.1 |
| exon_skip_424856 | 4 | 88026779:88026834:88026959:88026997:88029310:88029452 | 88026959:88026997 | ENSG00000172493.16 | ENST00000514970.1,ENST00000511722.1,ENST00000395146.4,ENST00000544085.1,ENST00000307808.6 |
| exon_skip_424859 | 4 | 88026959:88026997:88029310:88029467:88035518:88036451 | 88029310:88029467 | ENSG00000172493.16 | ENST00000395146.4,ENST00000544085.1,ENST00000307808.6 |
| exon_skip_424860 | 4 | 88052944:88053016:88053422:88053560:88055622:88055846 | 88053422:88053560 | ENSG00000172493.16 | ENST00000395146.4,ENST00000544085.1 |
| exon_skip_424861 | 4 | 88052944:88053016:88053422:88053560:88055625:88055846 | 88053422:88053560 | ENSG00000172493.16 | ENST00000307808.6 |
| exon_skip_424863 | 4 | 88053422:88053560:88055622:88055846:88056731:88057263 | 88055622:88055846 | ENSG00000172493.16 | ENST00000395146.4,ENST00000544085.1 |
| exon_skip_424865 | 4 | 88053422:88053560:88055625:88055846:88056731:88057263 | 88055625:88055846 | ENSG00000172493.16 | ENST00000307808.6 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for AFF1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_424845 | 4 | 87869649:87869723:87967317:87967438:87967846:87968042 | 87967317:87967438 | ENSG00000172493.16 | ENST00000395146.4,ENST00000507468.1,ENST00000503477.1,ENST00000511442.1 |
| exon_skip_424849 | 4 | 87928420:87928576:87967317:87967438:87967846:87968042 | 87967317:87967438 | ENSG00000172493.16 | ENST00000307808.6 |
| exon_skip_424852 | 4 | 88005274:88005316:88011135:88011222:88012944:88012976 | 88011135:88011222 | ENSG00000172493.16 | ENST00000395146.4,ENST00000507468.1,ENST00000307808.6,ENST00000511722.1,ENST00000544085.1,ENST00000514970.1 |
| exon_skip_424853 | 4 | 88012944:88012981:88016066:88016121:88026779:88026834 | 88016066:88016121 | ENSG00000172493.16 | ENST00000395146.4,ENST00000503477.1,ENST00000307808.6,ENST00000511722.1,ENST00000544085.1,ENST00000514970.1 |
| exon_skip_424856 | 4 | 88026779:88026834:88026959:88026997:88029310:88029452 | 88026959:88026997 | ENSG00000172493.16 | ENST00000395146.4,ENST00000307808.6,ENST00000511722.1,ENST00000544085.1,ENST00000514970.1 |
| exon_skip_424859 | 4 | 88026959:88026997:88029310:88029467:88035518:88036451 | 88029310:88029467 | ENSG00000172493.16 | ENST00000395146.4,ENST00000307808.6,ENST00000544085.1 |
| exon_skip_424860 | 4 | 88052944:88053016:88053422:88053560:88055622:88055846 | 88053422:88053560 | ENSG00000172493.16 | ENST00000395146.4,ENST00000544085.1 |
| exon_skip_424861 | 4 | 88052944:88053016:88053422:88053560:88055625:88055846 | 88053422:88053560 | ENSG00000172493.16 | ENST00000307808.6 |
| exon_skip_424863 | 4 | 88053422:88053560:88055622:88055846:88056731:88057263 | 88055622:88055846 | ENSG00000172493.16 | ENST00000395146.4,ENST00000544085.1 |
| exon_skip_424865 | 4 | 88053422:88053560:88055625:88055846:88056731:88057263 | 88055625:88055846 | ENSG00000172493.16 | ENST00000307808.6 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for AFF1 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000307808 | 87967317 | 87967438 | Frame-shift |
| ENST00000307808 | 88016066 | 88016121 | Frame-shift |
| ENST00000307808 | 88026959 | 88026997 | Frame-shift |
| ENST00000307808 | 88029310 | 88029467 | Frame-shift |
| ENST00000307808 | 88055625 | 88055846 | Frame-shift |
| ENST00000307808 | 88011135 | 88011222 | In-frame |
| ENST00000307808 | 88053422 | 88053560 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000307808 | 87967317 | 87967438 | Frame-shift |
| ENST00000307808 | 88016066 | 88016121 | Frame-shift |
| ENST00000307808 | 88026959 | 88026997 | Frame-shift |
| ENST00000307808 | 88029310 | 88029467 | Frame-shift |
| ENST00000307808 | 88055625 | 88055846 | Frame-shift |
| ENST00000307808 | 88011135 | 88011222 | In-frame |
| ENST00000307808 | 88053422 | 88053560 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for AFF1 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| Loci of skipped exons in TCGA 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 |
| ENST00000307808 | 9407 | 1210 | 88011135 | 88011222 | 1504 | 1590 | 361 | 390 |
| ENST00000307808 | 9407 | 1210 | 88053422 | 88053560 | 3573 | 3710 | 1051 | 1096 |
| Loci of skipped exons in GTEx 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 |
| ENST00000307808 | 9407 | 1210 | 88011135 | 88011222 | 1504 | 1590 | 361 | 390 |
| ENST00000307808 | 9407 | 1210 | 88053422 | 88053560 | 3573 | 3710 | 1051 | 1096 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 |
| P51825 | 361 | 390 | 1 | 1210 | Chain | ID=PRO_0000215910;Note=AF4/FMR2 family member 1 |
| P51825 | 1051 | 1096 | 1096 | 1096 | Alternative sequence | ID=VSP_046096;Note=In isoform 2 and isoform 3. A->AR;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:8443374;Dbxref=PMID:14702039,PMID:8443374 |
| P51825 | 1051 | 1096 | 1 | 1210 | Chain | ID=PRO_0000215910;Note=AF4/FMR2 family member 1 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| 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 |
| P51825 | 361 | 390 | 1 | 1210 | Chain | ID=PRO_0000215910;Note=AF4/FMR2 family member 1 |
| P51825 | 1051 | 1096 | 1096 | 1096 | Alternative sequence | ID=VSP_046096;Note=In isoform 2 and isoform 3. A->AR;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:8443374;Dbxref=PMID:14702039,PMID:8443374 |
| P51825 | 1051 | 1096 | 1 | 1210 | Chain | ID=PRO_0000215910;Note=AF4/FMR2 family member 1 |
Top |
SNVs in the skipped exons for AFF1 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| STAD | TCGA-FP-A4BE-01 | exon_skip_424849 exon_skip_424845 | 87967318 | 87967438 | 87967391 | 87967392 | Frame_Shift_Del | AA | - | p.37_38del |
| STAD | TCGA-FP-A4BE-01 | exon_skip_424849 exon_skip_424845 | 87967318 | 87967438 | 87967391 | 87967392 | Frame_Shift_Del | AA | - | p.E37fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_424853 | 88016067 | 88016121 | 88016086 | 88016086 | Frame_Shift_Del | A | - | p.S409fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_424861 exon_skip_424860 | 88053423 | 88053560 | 88053440 | 88053440 | Frame_Shift_Del | T | - | p.I1057fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_424861 exon_skip_424860 | 88053423 | 88053560 | 88053466 | 88053466 | Frame_Shift_Del | A | - | p.K1067fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_424861 exon_skip_424860 | 88053423 | 88053560 | 88053466 | 88053466 | Frame_Shift_Del | A | - | p.C1072X |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_424861 exon_skip_424860 | 88053423 | 88053560 | 88053466 | 88053466 | Frame_Shift_Del | A | - | p.K1067fs |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_424861 exon_skip_424860 | 88053423 | 88053560 | 88053466 | 88053466 | Frame_Shift_Del | A | - | p.C1072X |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_424861 exon_skip_424860 | 88053423 | 88053560 | 88053466 | 88053466 | Frame_Shift_Del | A | - | p.K1067fs |
| SKCM | TCGA-QB-AA9O-06 | exon_skip_424849 exon_skip_424845 | 87967318 | 87967438 | 87967346 | 87967346 | Nonsense_Mutation | C | T | p.R16* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_424849 exon_skip_424845 | 87967318 | 87967438 | 87967346 | 87967346 | Nonsense_Mutation | C | T | p.R16* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_424849 exon_skip_424845 | 87967318 | 87967438 | 87967346 | 87967346 | Nonsense_Mutation | C | T | p.R23X |
| LUSC | TCGA-46-3765-01 | exon_skip_424849 exon_skip_424845 | 87967318 | 87967438 | 87967424 | 87967424 | Nonsense_Mutation | G | T | p.G49* |
| UCEC | TCGA-D1-A17Q-01 | exon_skip_424859 | 88029311 | 88029467 | 88029435 | 88029435 | Nonsense_Mutation | G | T | p.E494* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| DV90_LUNG | 87967318 | 87967438 | 87967419 | 87967419 | Frame_Shift_Del | T | - | p.L40fs |
| DU145_PROSTATE | 87967318 | 87967438 | 87967368 | 87967368 | Missense_Mutation | G | A | p.R23H |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 88053423 | 88053560 | 88053439 | 88053439 | Missense_Mutation | A | C | p.I1057L |
| FTC133_THYROID | 88053423 | 88053560 | 88053448 | 88053448 | Missense_Mutation | A | G | p.M1060V |
| NCIH358_LUNG | 88055623 | 88055846 | 88055679 | 88055679 | Missense_Mutation | G | T | p.G1115V |
| NCIH358_LUNG | 88055626 | 88055846 | 88055679 | 88055679 | Missense_Mutation | G | T | p.G1115V |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 88053423 | 88053560 | 88053424 | 88053424 | Splice_Site | A | T | p.M1052L |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for AFF1 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for AFF1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for AFF1 |
Top |
RelatedDrugs for AFF1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for AFF1 |
| 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)
|