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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for U2AF1 |
 Gene summary |
| Gene information | Gene symbol | U2AF1 | Gene ID | 7307 |
| Gene name | U2 small nuclear RNA auxiliary factor 1 | |
| Synonyms | FP793|RN|RNU2AF1|U2AF35|U2AFBP | |
| Cytomap | 21q22.3 | |
| Type of gene | protein-coding | |
| Description | splicing factor U2AF 35 kDa subunitU2 small nuclear RNA auxillary factor 1U2 small nuclear ribonucleoprotein auxillary factor, 35-KD subunitU2 snRNP auxiliary factor small subunitU2(RNU2) small nuclear RNA auxiliary factor binding proteinsplicing fac | |
| Modification date | 20180523 | |
| UniProtAcc | Q01081 | |
| Context | PubMed: U2AF1 [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 |
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Exon skipping events across known transcript of Ensembl for U2AF1 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. |
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Gene isoform structures and expression levels for U2AF1 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for U2AF1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_362463 | 21 | 44513299:44513359:44514580:44514673:44514764:44514898 | 44514580:44514673 | ENSG00000160201.7 | ENST00000475639.1,ENST00000486519.1,ENST00000459639.1,ENST00000380276.2,ENST00000291552.4,ENST00000464750.1,ENST00000398137.1 |
| exon_skip_362468 | 21 | 44514776:44514898:44515547:44515646:44515803:44515853 | 44515547:44515646 | ENSG00000160201.7 | ENST00000475639.1,ENST00000486519.1,ENST00000459639.1,ENST00000380276.2,ENST00000291552.4,ENST00000464750.1,ENST00000398137.1 |
| exon_skip_362476 | 21 | 44515811:44515853:44520562:44520629:44521475:44521542 | 44520562:44520629 | ENSG00000160201.7 | ENST00000464750.1,ENST00000463599.1,ENST00000398137.1 |
| exon_skip_362478 | 21 | 44515811:44515853:44520562:44520629:44524424:44524512 | 44520562:44520629 | ENSG00000160201.7 | ENST00000459639.1,ENST00000291552.4 |
| exon_skip_362484 | 21 | 44515811:44515853:44520562:44524512:44527560:44527634 | 44520562:44524512 | ENSG00000160201.7 | ENST00000475639.1 |
| exon_skip_362487 | 21 | 44515811:44515853:44520686:44520724:44524424:44524512 | 44520686:44520724 | ENSG00000160201.7 | ENST00000486519.1 |
| exon_skip_362488 | 21 | 44515811:44515853:44521475:44521542:44524424:44524512 | 44521475:44521542 | ENSG00000160201.7 | ENST00000380276.2 |
| exon_skip_362499 | 21 | 44520562:44520629:44521475:44521542:44524424:44524512 | 44521475:44521542 | ENSG00000160201.7 | ENST00000464750.1,ENST00000463599.1,ENST00000398137.1 |
| exon_skip_362501 | 21 | 44520562:44520629:44524424:44524512:44527560:44527634 | 44524424:44524512 | ENSG00000160201.7 | ENST00000291552.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for U2AF1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_362463 | 21 | 44513299:44513359:44514580:44514673:44514764:44514898 | 44514580:44514673 | ENSG00000160201.7 | ENST00000459639.1,ENST00000464750.1,ENST00000475639.1,ENST00000380276.2,ENST00000291552.4,ENST00000398137.1,ENST00000486519.1 |
| exon_skip_362468 | 21 | 44514776:44514898:44515547:44515646:44515803:44515853 | 44515547:44515646 | ENSG00000160201.7 | ENST00000459639.1,ENST00000464750.1,ENST00000475639.1,ENST00000380276.2,ENST00000291552.4,ENST00000398137.1,ENST00000486519.1 |
| exon_skip_362476 | 21 | 44515811:44515853:44520562:44520629:44521475:44521542 | 44520562:44520629 | ENSG00000160201.7 | ENST00000464750.1,ENST00000398137.1,ENST00000463599.1 |
| exon_skip_362478 | 21 | 44515811:44515853:44520562:44520629:44524424:44524512 | 44520562:44520629 | ENSG00000160201.7 | ENST00000459639.1,ENST00000291552.4 |
| exon_skip_362484 | 21 | 44515811:44515853:44520562:44524512:44527560:44527634 | 44520562:44524512 | ENSG00000160201.7 | ENST00000475639.1 |
| exon_skip_362487 | 21 | 44515811:44515853:44520686:44520724:44524424:44524512 | 44520686:44520724 | ENSG00000160201.7 | ENST00000486519.1 |
| exon_skip_362488 | 21 | 44515811:44515853:44521475:44521542:44524424:44524512 | 44521475:44521542 | ENSG00000160201.7 | ENST00000380276.2 |
| exon_skip_362499 | 21 | 44520562:44520629:44521475:44521542:44524424:44524512 | 44521475:44521542 | ENSG00000160201.7 | ENST00000464750.1,ENST00000398137.1,ENST00000463599.1 |
| exon_skip_362501 | 21 | 44520562:44520629:44524424:44524512:44527560:44527634 | 44524424:44524512 | ENSG00000160201.7 | ENST00000291552.4 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for U2AF1 |
| 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 |
| ENST00000291552 | 44520562 | 44520629 | Frame-shift |
| ENST00000291552 | 44524424 | 44524512 | Frame-shift |
| ENST00000291552 | 44514580 | 44514673 | In-frame |
| ENST00000291552 | 44515547 | 44515646 | 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 |
| ENST00000291552 | 44520562 | 44520629 | Frame-shift |
| ENST00000291552 | 44524424 | 44524512 | Frame-shift |
| ENST00000291552 | 44514580 | 44514673 | In-frame |
| ENST00000291552 | 44515547 | 44515646 | In-frame |
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Infer the effects of exon skipping event on protein functional features for U2AF1 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 |
| ENST00000291552 | 979 | 240 | 44515547 | 44515646 | 343 | 441 | 83 | 116 |
| ENST00000291552 | 979 | 240 | 44514580 | 44514673 | 576 | 668 | 161 | 191 |
| 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 |
| ENST00000291552 | 979 | 240 | 44515547 | 44515646 | 343 | 441 | 83 | 116 |
| ENST00000291552 | 979 | 240 | 44514580 | 44514673 | 576 | 668 | 161 | 191 |
| 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 |
| Q01081 | 83 | 116 | 76 | 240 | Alternative sequence | ID=VSP_042667;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01081 | 83 | 116 | 96 | 101 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JMT |
| Q01081 | 83 | 116 | 104 | 118 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JMT |
| Q01081 | 83 | 116 | 2 | 240 | Chain | ID=PRO_0000081994;Note=Splicing factor U2AF 35 kDa subunit |
| Q01081 | 83 | 116 | 65 | 147 | Domain | Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q01081 | 83 | 116 | 64 | 92 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JMT |
| Q01081 | 161 | 191 | 76 | 240 | Alternative sequence | ID=VSP_042667;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01081 | 161 | 191 | 2 | 240 | Chain | ID=PRO_0000081994;Note=Splicing factor U2AF 35 kDa subunit |
| Q01081 | 161 | 191 | 178 | 240 | Compositional bias | Note=Arg/Gly/Ser-rich (RS domain) |
| Q01081 | 161 | 191 | 165 | 165 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q01081 | 161 | 191 | 149 | 176 | Zinc finger | Note=C3H1-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00723 |
| 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 |
| Q01081 | 83 | 116 | 76 | 240 | Alternative sequence | ID=VSP_042667;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01081 | 83 | 116 | 96 | 101 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JMT |
| Q01081 | 83 | 116 | 104 | 118 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JMT |
| Q01081 | 83 | 116 | 2 | 240 | Chain | ID=PRO_0000081994;Note=Splicing factor U2AF 35 kDa subunit |
| Q01081 | 83 | 116 | 65 | 147 | Domain | Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q01081 | 83 | 116 | 64 | 92 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JMT |
| Q01081 | 161 | 191 | 76 | 240 | Alternative sequence | ID=VSP_042667;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01081 | 161 | 191 | 2 | 240 | Chain | ID=PRO_0000081994;Note=Splicing factor U2AF 35 kDa subunit |
| Q01081 | 161 | 191 | 178 | 240 | Compositional bias | Note=Arg/Gly/Ser-rich (RS domain) |
| Q01081 | 161 | 191 | 165 | 165 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q01081 | 161 | 191 | 149 | 176 | Zinc finger | Note=C3H1-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00723 |
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SNVs in the skipped exons for U2AF1 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - 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 |
| - 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 |
| HEC1A_ENDOMETRIUM | 44514581 | 44514673 | 44514587 | 44514587 | Missense_Mutation | C | T | p.R190H |
| CW2_LARGE_INTESTINE | 44520563 | 44520629 | 44520581 | 44520581 | Missense_Mutation | A | T | p.S61T |
| CW2_LARGE_INTESTINE | 44520563 | 44524512 | 44520581 | 44520581 | Missense_Mutation | A | T | p.S61T |
| SNUC5_LARGE_INTESTINE | 44520563 | 44520629 | 44520611 | 44520611 | Missense_Mutation | T | C | p.I51V |
| SNUC5_LARGE_INTESTINE | 44520563 | 44524512 | 44520611 | 44520611 | Missense_Mutation | T | C | p.I51V |
| HCC78_LUNG | 44524425 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| HCC78_LUNG | 44520563 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| NCIH1373_LUNG | 44524425 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| NCIH1373_LUNG | 44520563 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| SNU245_BILIARY_TRACT | 44524425 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| SNU245_BILIARY_TRACT | 44520563 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| LC2AD_LUNG | 44524425 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| LC2AD_LUNG | 44520563 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| NCIH441_LUNG | 44524425 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| NCIH441_LUNG | 44520563 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| NKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 44524425 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
| NKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 44520563 | 44524512 | 44524456 | 44524456 | Missense_Mutation | G | A | p.S34F |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for U2AF1 |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for U2AF1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for U2AF1 |
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RelatedDrugs for U2AF1 |
| 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 |
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RelatedDiseases for U2AF1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| U2AF1 | C0019693 | HIV Infections | 1 | CTD_human |
| U2AF1 | C0029456 | Osteoporosis | 1 | CTD_human |
| U2AF1 | C3463824 | MYELODYSPLASTIC SYNDROME | 1 | CTD_human |
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