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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 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 | 20200322 | |
| 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 |
| 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: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 | 10644691|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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Gene structures and expression levels for LEF1 |
| 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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ENSG00000138795
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| STG | UP | 6.979913e+01 | 9.842808e-01 | 2.985332e-05 | 3.128914e-03 |
| PG | UP | 9.352272e+01 | 8.160925e-01 | 1.667498e-08 | 8.939395e-07 |
| 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 |
| PCC | UP | ENST00000504426.5 | LEF1-205:lncRNA:LEF1 | 2.277485e+01 | 1.344168e+00 | 1.326646e-03 | 3.023010e-02 |
| PG | UP | ENST00000379951.6 | LEF1-202:protein_coding:LEF1 | 2.963594e+01 | 1.233161e+00 | 8.132730e-04 | 1.255667e-02 |
| PG | UP | ENST00000515500.5 | LEF1-221:protein_coding:LEF1 | 2.599597e+00 | 1.364574e+00 | 1.673999e-03 | 2.103881e-02 |
| PG | UP | ENST00000505328.1 | LEF1-210:retained_intron:LEF1 | 1.038371e+00 | 1.149135e+00 | 2.731947e-03 | 2.980380e-02 |
| CB | DOWN | ENST00000659790.1 | LEF1-AS1-208:lncRNA:LEF1 | 6.918497e-01 | -1.330464e+00 | 5.663691e-04 | 3.201661e-03 |
| CB | UP | ENST00000379951.6 | LEF1-202:protein_coding:LEF1 | 3.397088e+01 | 9.031169e-01 | 6.713004e-04 | 3.696658e-03 |
| CB | UP | ENST00000515500.5 | LEF1-221:protein_coding:LEF1 | 1.098441e+00 | 1.318996e+00 | 1.135086e-02 | 3.857800e-02 |
| TC | UP | ENST00000510624.5 | LEF1-216:protein_coding:LEF1 | 5.075258e+00 | 9.840232e-01 | 3.749037e-03 | 2.696041e-02 |
| TC | DOWN | ENST00000503879.5 | LEF1-204:lncRNA:LEF1 | 2.731321e+01 | -1.112165e+00 | 6.686335e-03 | 4.157605e-02 |
| TC | UP | ENST00000504775.5 | LEF1-206:lncRNA:LEF1 | 9.558367e+00 | 9.237181e-01 | 7.072499e-03 | 4.337961e-02 |
| 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 LEF1 |
| 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_119358 | chr4 | 108048639:108048751:108063623:108063663:108064336:108064384 | 108063623:108063663 |
| exon_skip_194797 | chr4 | 108048639:108048751:108063623:108063657:108064336:108064384 | 108063623:108063657 |
| exon_skip_201681 | chr4 | 108048639:108048751:108064336:108064384:108070663:108070770 | 108064336:108064384 |
| exon_skip_264006 | chr4 | 108064336:108064384:108070663:108070770:108078220:108078352 | 108070663:108070770 |
| exon_skip_286063 | chr4 | 108079492:108079614:108081586:108081669:108083356:108083413 | 108081586:108081669 |
| 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 LEF1 |
| 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 |
| ENST00000265165 | 108063623 | 108063663 | 5CDS-5UTR |
| ENST00000265165 | 108081586 | 108081669 | 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 |
| ENST00000265165 | 108063623 | 108063663 | 5CDS-5UTR |
| ENST00000265165 | 108081586 | 108081669 | 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 |
| ENST00000265165 | 108063623 | 108063663 | 5CDS-5UTR |
| ENST00000265165 | 108070663 | 108070770 | In-frame |
| ENST00000265165 | 108081586 | 108081669 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LEF1 |
p-ENSG00000138795_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 |
| ENST00000265165 | 3085 | 399 | 108081586 | 108081669 | 1294 | 1376 | 213 | 240 |
| 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 |
| ENST00000265165 | 3085 | 399 | 108081586 | 108081669 | 1294 | 1376 | 213 | 240 |
| 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 |
| ENST00000265165 | 3085 | 399 | 108081586 | 108081669 | 1294 | 1376 | 213 | 240 |
| ENST00000265165 | 3085 | 399 | 108070663 | 108070770 | 1664 | 1770 | 336 | 371 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | 371 | 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 | 371 | 1 | 399 | Chain | ID=PRO_0000048595;Note=Lymphoid enhancer-binding factor 1 |
| Q9UJU2 | 336 | 371 | 299 | 367 | DNA binding | Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00267 |
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3'-UTR located exon skipping events that lost miRNA binding sites in LEF1 |
| 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 LEF1 |
| - 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 LEF1 |
| 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 LEF1 |
| 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 LEF1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for LEF1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Q9UJU2 | approved|investigational | DB00903 | Etacrynic acid | small molecule | Q9UJU2 |
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RelatedDiseases for LEF1 |
| 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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