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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 LEF1 |
 Gene summary |
| Gene information | Gene symbol | LEF1 | Gene ID | 51176 |
| Gene name | lymphoid enhancer binding factor 1 | |
| Synonyms | LEF-1|TCF10|TCF1ALPHA|TCF7L3 | |
| Cytomap | 4q25 | |
| Type of gene | protein-coding | |
| Description | lymphoid enhancer-binding factor 1T cell-specific transcription factor 1-alphaTCF1-alpha | |
| Modification date | 20180527 | |
| UniProtAcc | Q9UJU2 | |
| Context | PubMed: LEF1 [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 |
| LEF1 | GO:0006366 | transcription by RNA polymerase II | 23001182 |
| LEF1 | GO:0008284 | positive regulation of cell proliferation | 19351848 |
| LEF1 | GO:0010628 | positive regulation of gene expression | 16344550 |
| LEF1 | GO:0016055 | Wnt signaling pathway | 10644691 |
| LEF1 | GO:0030854 | positive regulation of granulocyte differentiation | 19620402 |
| LEF1 | GO:0032696 | negative regulation of interleukin-13 production | 18445004 |
| LEF1 | GO:0032713 | negative regulation of interleukin-4 production | 18445004 |
| LEF1 | GO:0032714 | negative regulation of interleukin-5 production | 18445004 |
| LEF1 | GO:0043392 | negative regulation of DNA binding | 18445004 |
| LEF1 | GO:0043923 | positive regulation by host of viral transcription | 7657162 |
| LEF1 | GO:0045892 | negative regulation of transcription, DNA-templated | 18794125 |
| LEF1 | GO:0045893 | positive regulation of transcription, DNA-templated | 7657162|10644691|17063141|19620402|20128911 |
| LEF1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 11751639 |
| LEF1 | GO:0060070 | canonical Wnt signaling pathway | 20123964 |
| LEF1 | GO:0060326 | cell chemotaxis | 19576624 |
| LEF1 | GO:0071353 | cellular response to interleukin-4 | 18579517 |
| LEF1 | GO:0071899 | negative regulation of estrogen receptor binding | 18794125 |
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Exon skipping events across known transcript of Ensembl for LEF1 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 LEF1 |
| 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 LEF1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_431762 | 4 | 108969794:108969907:108984778:108984813:108985491:108985540 | 108984778:108984813 | ENSG00000138795.5 | ENST00000509428.1 |
| exon_skip_431763 | 4 | 108969794:108969907:108984778:108984819:108985491:108985540 | 108984778:108984819 | ENSG00000138795.5 | ENST00000504426.1,ENST00000507470.1,ENST00000514444.1,ENST00000265165.1,ENST00000510624.1,ENST00000505297.1,ENST00000512407.1,ENST00000438313.2,ENST00000510135.1 |
| exon_skip_431765 | 4 | 108969794:108969907:108985491:108985540:108991818:108991926 | 108985491:108985540 | ENSG00000138795.5 | ENST00000379951.2,ENST00000505379.1 |
| exon_skip_431776 | 4 | 108985491:108985540:108991818:108991926:108999375:108999508 | 108991818:108991926 | ENSG00000138795.5 | ENST00000379951.2,ENST00000503879.1,ENST00000505379.1,ENST00000265165.1,ENST00000510624.1,ENST00000506680.1,ENST00000509428.1,ENST00000438313.2,ENST00000510135.1 |
| exon_skip_431782 | 4 | 108991818:108991926:108996530:108996633:108999375:108999528 | 108996530:108996633 | ENSG00000138795.5 | ENST00000514444.1 |
| exon_skip_431783 | 4 | 109000647:109000770:109002741:109002825:109004511:109004569 | 109002741:109002825 | ENSG00000138795.5 | ENST00000265165.1,ENST00000506680.1,ENST00000504950.1 |
| exon_skip_431784 | 4 | 109004511:109004602:109010280:109010413:109084723:109084852 | 109010280:109010413 | ENSG00000138795.5 | ENST00000379951.2,ENST00000504775.1,ENST00000265165.1,ENST00000510624.1,ENST00000506680.1,ENST00000515500.1,ENST00000509428.1,ENST00000505293.1,ENST00000438313.2,ENST00000510717.1,ENST00000512172.1,ENST00000510135.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LEF1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_431762 | 4 | 108969794:108969907:108984778:108984813:108985491:108985540 | 108984778:108984813 | ENSG00000138795.5 | ENST00000509428.1 |
| exon_skip_431763 | 4 | 108969794:108969907:108984778:108984819:108985491:108985540 | 108984778:108984819 | ENSG00000138795.5 | ENST00000265165.1,ENST00000504426.1,ENST00000514444.1,ENST00000505297.1,ENST00000510135.1,ENST00000438313.2,ENST00000507470.1,ENST00000512407.1,ENST00000510624.1 |
| exon_skip_431765 | 4 | 108969794:108969907:108985491:108985540:108991818:108991926 | 108985491:108985540 | ENSG00000138795.5 | ENST00000379951.2,ENST00000505379.1 |
| exon_skip_431776 | 4 | 108985491:108985540:108991818:108991926:108999375:108999508 | 108991818:108991926 | ENSG00000138795.5 | ENST00000265165.1,ENST00000379951.2,ENST00000503879.1,ENST00000505379.1,ENST00000510135.1,ENST00000438313.2,ENST00000509428.1,ENST00000510624.1,ENST00000506680.1 |
| exon_skip_431778 | 4 | 108991818:108991926:108992813:108992899:108993158:108993407 | 108992813:108992899 | ENSG00000138795.5 | ENST00000505297.1 |
| exon_skip_431783 | 4 | 109000647:109000770:109002741:109002825:109004511:109004569 | 109002741:109002825 | ENSG00000138795.5 | ENST00000265165.1,ENST00000506680.1,ENST00000504950.1 |
| 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 LEF1 |
| 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 |
| ENST00000265165 | 108984778 | 108984819 | 5CDS-5UTR |
| ENST00000265165 | 109010280 | 109010413 | Frame-shift |
| ENST00000265165 | 108991818 | 108991926 | In-frame |
| ENST00000265165 | 109002741 | 109002825 | 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 |
| ENST00000265165 | 108984778 | 108984819 | 5CDS-5UTR |
| ENST00000265165 | 108991818 | 108991926 | In-frame |
| ENST00000265165 | 109002741 | 109002825 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LEF1 |
| 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 |
| ENST00000265165 | 3085 | 399 | 109002741 | 109002825 | 1294 | 1377 | 213 | 240 |
| ENST00000265165 | 3085 | 399 | 108991818 | 108991926 | 1664 | 1771 | 336 | 372 |
| 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 |
| ENST00000265165 | 3085 | 399 | 109002741 | 109002825 | 1294 | 1377 | 213 | 240 |
| ENST00000265165 | 3085 | 399 | 108991818 | 108991926 | 1664 | 1771 | 336 | 372 |
| 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 |
| Q9UJU2 | 213 | 240 | 214 | 241 | Alternative sequence | ID=VSP_040068;Note=In isoform 5%2C isoform 6 and isoform 7. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:19653274;Dbxref=PMID:14702039,PMID:15489334,PMID:1965 |
| Q9UJU2 | 213 | 240 | 1 | 399 | Chain | ID=PRO_0000048595;Note=Lymphoid enhancer-binding factor 1 |
| Q9UJU2 | 213 | 240 | 77 | 273 | Compositional bias | Note=Pro-rich |
| Q9UJU2 | 336 | 372 | 283 | 399 | Alternative sequence | ID=VSP_002188;Note=In isoform 2 and isoform 4. KPQHEQRKEQEPKRPHIKKPLNAFMLYMKEMRANVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREKLQESASGTGPRMTAAYI->CSAFLLPHPFLIPSTPSPNHHHHHLLGSLSMNRERSRSQKDLTLRSL;Ontology_term=ECO:0000303;evidence=ECO:00 |
| Q9UJU2 | 336 | 372 | 1 | 399 | Chain | ID=PRO_0000048595;Note=Lymphoid enhancer-binding factor 1 |
| Q9UJU2 | 336 | 372 | 299 | 367 | DNA binding | Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00267 |
| 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 |
| Q9UJU2 | 213 | 240 | 214 | 241 | Alternative sequence | ID=VSP_040068;Note=In isoform 5%2C isoform 6 and isoform 7. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:19653274;Dbxref=PMID:14702039,PMID:15489334,PMID:1965 |
| Q9UJU2 | 213 | 240 | 1 | 399 | Chain | ID=PRO_0000048595;Note=Lymphoid enhancer-binding factor 1 |
| Q9UJU2 | 213 | 240 | 77 | 273 | Compositional bias | Note=Pro-rich |
| Q9UJU2 | 336 | 372 | 283 | 399 | Alternative sequence | ID=VSP_002188;Note=In isoform 2 and isoform 4. KPQHEQRKEQEPKRPHIKKPLNAFMLYMKEMRANVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREKLQESASGTGPRMTAAYI->CSAFLLPHPFLIPSTPSPNHHHHHLLGSLSMNRERSRSQKDLTLRSL;Ontology_term=ECO:0000303;evidence=ECO:00 |
| Q9UJU2 | 336 | 372 | 1 | 399 | Chain | ID=PRO_0000048595;Note=Lymphoid enhancer-binding factor 1 |
| Q9UJU2 | 336 | 372 | 299 | 367 | DNA binding | Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00267 |
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SNVs in the skipped exons for LEF1 |
| - 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. |
LEF1_SKCM_exon_skip_431783_psi_boxplot.png |
| - 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 |
| SKCM | TCGA-BF-AAP7-01 | exon_skip_431776 | 108991819 | 108991926 | 108991871 | 108991877 | Frame_Shift_Del | TCTTTCC | - | p.RKE325fs |
| UCEC | TCGA-AP-A0LM-01 | exon_skip_431783 | 109002742 | 109002825 | 109002824 | 109002824 | Nonsense_Mutation | G | A | p.Q214* |
| HNSC | TCGA-P3-A6T7-01 | exon_skip_431765 | 108985492 | 108985540 | 108985490 | 108985500 | Splice_Site | ACCTGATGCAG | - | p.358_splice |
| SKCM | TCGA-EE-A29M-06 | exon_skip_431783 | 109002742 | 109002825 | 109002741 | 109002741 | Splice_Site | C | T | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-EE-A29M-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_431783 | |
| Skipped exon start: 109002742 | |
| Skipped exon end: 109002825 | |
| Mutation start: 109002741 | |
| Mutation end: 109002741 | |
| Mutation type: Splice_Site | |
| Reference seq: C | |
| Mutation seq: T | |
| AAchange: . | |
exon_skip_370579_SKCM_TCGA-EE-A29M-06.png | |
exon_skip_431783_SKCM_TCGA-EE-A29M-06.png | |
exon_skip_516534_SKCM_TCGA-EE-A29M-06.png | |
exon_skip_516535_SKCM_TCGA-EE-A29M-06.png | |
exon_skip_62987_SKCM_TCGA-EE-A29M-06.png | |
| - 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 |
| PANC0403_PANCREAS | 108985492 | 108985540 | 108985517 | 108985517 | Frame_Shift_Del | T | - | p.R380fs |
| YD38_UPPER_AERODIGESTIVE_TRACT | 108984779 | 108984813 | 108984788 | 108984788 | Missense_Mutation | G | C | p.I399M |
| YD38_UPPER_AERODIGESTIVE_TRACT | 108984779 | 108984819 | 108984788 | 108984788 | Missense_Mutation | G | C | p.I399M |
| HCC2998_LARGE_INTESTINE | 108984779 | 108984813 | 108984790 | 108984790 | Missense_Mutation | T | G | p.I399L |
| HCC2998_LARGE_INTESTINE | 108984779 | 108984819 | 108984790 | 108984790 | Missense_Mutation | T | G | p.I399L |
| MDAMB436_BREAST | 108991819 | 108991926 | 108991865 | 108991865 | Missense_Mutation | T | C | p.Q357R |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 109002742 | 109002825 | 109002760 | 109002760 | Missense_Mutation | A | C | p.V235G |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 109002742 | 109002825 | 109002760 | 109002760 | Missense_Mutation | A | C | p.V235G |
| MEWO_SKIN | 109002742 | 109002825 | 109002772 | 109002772 | Missense_Mutation | G | A | p.S231F |
| ME1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 109010281 | 109010413 | 109010298 | 109010298 | Missense_Mutation | T | C | p.D177G |
| CORL23_LUNG | 109010281 | 109010413 | 109010326 | 109010326 | Missense_Mutation | C | T | p.G168R |
| NCIH2172_LUNG | 109010281 | 109010413 | 109010362 | 109010362 | Missense_Mutation | G | A | p.P156S |
| HEC59_ENDOMETRIUM | 109010281 | 109010413 | 109010404 | 109010404 | Missense_Mutation | C | T | p.V142M |
| EB3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 108984779 | 108984813 | 108984819 | 108984819 | Splice_Site | C | T | p.G389D |
| EB3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 108984779 | 108984819 | 108984819 | 108984819 | Splice_Site | C | T | p.G389D |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LEF1 |
| 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 LEF1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LEF1 |
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RelatedDrugs for LEF1 |
| 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 |
| Q9UJU2 | DB00903 | Etacrynic acid | Lymphoid enhancer-binding factor 1 | small molecule | approved|investigational |
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RelatedDiseases for LEF1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| LEF1 | C0009375 | Colonic Neoplasms | 1 | CTD_human |
| LEF1 | C0023434 | Chronic Lymphocytic Leukemia | 1 | CTD_human |
| LEF1 | C0036503 | Sebaceous Gland Neoplasms | 1 | CTD_human |
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