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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 TCF3 |
 Gene summary |
| Gene information | Gene symbol | TCF3 | Gene ID | 6929 |
| Gene name | transcription factor 3 | |
| Synonyms | AGM8|E2A|E47|ITF1|TCF-3|VDIR|bHLHb21|p75 | |
| Cytomap | 19p13.3 | |
| Type of gene | protein-coding | |
| Description | transcription factor E2-alphaNOL1-TCF3 fusionVDR interacting repressorclass B basic helix-loop-helix protein 21helix-loop-helix protein HE47immunoglobulin transcription factor 1kappa-E2-binding factornegative vitamin D response element-binding prot | |
| Modification date | 20200313 | |
| UniProtAcc | A0A0A0MRB7, A0A0A0MTS0, A0A494C1R3, K7EJN4, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| TCF3 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 14576336 |
| TCF3 | GO:0006351 | transcription, DNA-templated | 10775504 |
| TCF3 | GO:0033152 | immunoglobulin V(D)J recombination | 16428437 |
| TCF3 | GO:0045893 | positive regulation of transcription, DNA-templated | 2105528 |
| TCF3 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 16428437|19362560 |
| TCF3 | GO:0051091 | positive regulation of DNA-binding transcription factor activity | 14752053 |
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Gene structures and expression levels for TCF3 |
| 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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ENSG00000071564
| 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 |
| PCC | UP | ENST00000593064.5 | TCF3-218:protein_coding:TCF3 | 2.290903e+01 | 8.017732e-01 | 1.651792e-03 | 3.474901e-02 |
| PG | UP | ENST00000262965.11 | TCF3-201:protein_coding:TCF3 | 1.943881e+01 | 1.455882e+00 | 4.628987e-03 | 4.330929e-02 |
| CB | DOWN | ENST00000592628.5 | TCF3-217:protein_coding:TCF3 | 7.483116e+01 | -8.019701e-01 | 1.976313e-06 | 2.674615e-05 |
| CB | DOWN | ENST00000592395.5 | TCF3-216:nonsense_mediated_decay:TCF3 | 9.768495e+00 | -8.048858e-01 | 3.346793e-04 | 2.055207e-03 |
| CB | DOWN | ENST00000587425.5 | TCF3-211:protein_coding:TCF3 | 1.699013e+00 | -1.510207e+00 | 9.505075e-03 | 3.334576e-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 TCF3 |
| 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_105226 | chr19 | 1621838:1621970:1622054:1622223:1622313:1622415 | 1622054:1622223 |
| exon_skip_155137 | chr19 | 1619111:1619234:1619316:1619471:1619780:1619853 | 1619316:1619471 |
| exon_skip_159961 | chr19 | 1619111:1619234:1619316:1619474:1619780:1619853 | 1619316:1619474 |
| exon_skip_169136 | chr19 | 1612207:1612433:1615285:1615520:1615686:1615798 | 1615285:1615520 |
| exon_skip_17281 | chr19 | 1612207:1612433:1615285:1615515:1615686:1615798 | 1615285:1615515 |
| exon_skip_175644 | chr19 | 1620968:1621046:1621133:1621191:1621838:1621970 | 1621133:1621191 |
| exon_skip_177500 | chr19 | 1612207:1612433:1615285:1615515:1615686:1615821 | 1615285:1615515 |
| exon_skip_18440 | chr19 | 1627359:1627426:1632038:1632116:1632332:1632405 | 1632038:1632116 |
| exon_skip_188658 | chr19 | 1611755:1611849:1612207:1612433:1615285:1615485 | 1612207:1612433 |
| exon_skip_21751 | chr19 | 1612421:1612433:1615285:1615515:1615686:1615798 | 1615285:1615515 |
| exon_skip_248741 | chr19 | 1612421:1612433:1615285:1615485:1615686:1615798 | 1615285:1615485 |
| exon_skip_277014 | chr19 | 1612207:1612433:1615285:1615485:1615686:1615798 | 1615285:1615485 |
| exon_skip_280155 | chr19 | 1611755:1611849:1612207:1612433:1615285:1615480 | 1612207:1612433 |
| exon_skip_280889 | chr19 | 1612207:1612433:1615285:1615485:1615686:1615711 | 1615285:1615485 |
| exon_skip_42076 | chr19 | 1612207:1612433:1615285:1615520:1615686:1615711 | 1615285:1615520 |
| exon_skip_43865 | chr19 | 1612421:1612433:1615285:1615520:1615686:1615798 | 1615285:1615520 |
| exon_skip_5884 | chr19 | 1627359:1627426:1631951:1632116:1632332:1632405 | 1631951:1632116 |
| exon_skip_85922 | chr19 | 1627359:1627426:1646355:1646427:1650177:1650287 | 1646355:1646427 |
| 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 TCF3 |
| 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 |
| ENST00000262965 | 1619316 | 1619474 | In-frame |
| ENST00000611869 | 1619316 | 1619474 | 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 |
| 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 |
| ENST00000262965 | 1621133 | 1621191 | Frame-shift |
| ENST00000611869 | 1621133 | 1621191 | Frame-shift |
| ENST00000262965 | 1622054 | 1622223 | Frame-shift |
| ENST00000611869 | 1622054 | 1622223 | Frame-shift |
| ENST00000262965 | 1632038 | 1632116 | Frame-shift |
| ENST00000611869 | 1632038 | 1632116 | Frame-shift |
| ENST00000262965 | 1619316 | 1619474 | In-frame |
| ENST00000611869 | 1619316 | 1619474 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TCF3 |
p-ENSG00000071564_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 |
| ENST00000262965 | 4468 | 654 | 1619316 | 1619474 | 1237 | 1394 | 389 | 441 |
| ENST00000611869 | 4426 | 654 | 1619316 | 1619474 | 1198 | 1355 | 389 | 441 |
| 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 |
| 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 |
| ENST00000262965 | 4468 | 654 | 1619316 | 1619474 | 1237 | 1394 | 389 | 441 |
| ENST00000611869 | 4426 | 654 | 1619316 | 1619474 | 1198 | 1355 | 389 | 441 |
| 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 |
| P15923 | 389 | 441 | 1 | 654 | Chain | ID=PRO_0000127466;Note=Transcription factor E2-alpha |
| P15923 | 389 | 441 | 1 | 654 | Chain | ID=PRO_0000127466;Note=Transcription factor E2-alpha |
| P15923 | 389 | 441 | 431 | 431 | Natural variant | ID=VAR_049554;Note=G->S;Dbxref=dbSNP:rs1052692 |
| P15923 | 389 | 441 | 431 | 431 | Natural variant | ID=VAR_049554;Note=G->S;Dbxref=dbSNP:rs1052692 |
| P15923 | 389 | 441 | 389 | 425 | Region | Note=Leucine-zipper |
| P15923 | 389 | 441 | 389 | 425 | Region | Note=Leucine-zipper |
| P15923 | 389 | 441 | 390 | 390 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P15923 | 389 | 441 | 390 | 390 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| 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 |
| P15923 | 389 | 441 | 1 | 654 | Chain | ID=PRO_0000127466;Note=Transcription factor E2-alpha |
| P15923 | 389 | 441 | 1 | 654 | Chain | ID=PRO_0000127466;Note=Transcription factor E2-alpha |
| P15923 | 389 | 441 | 431 | 431 | Natural variant | ID=VAR_049554;Note=G->S;Dbxref=dbSNP:rs1052692 |
| P15923 | 389 | 441 | 431 | 431 | Natural variant | ID=VAR_049554;Note=G->S;Dbxref=dbSNP:rs1052692 |
| P15923 | 389 | 441 | 389 | 425 | Region | Note=Leucine-zipper |
| P15923 | 389 | 441 | 389 | 425 | Region | Note=Leucine-zipper |
| P15923 | 389 | 441 | 390 | 390 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P15923 | 389 | 441 | 390 | 390 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in TCF3 |
| 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 TCF3 |
| - 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 TCF3 |
| 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 TCF3 |
| 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 TCF3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for TCF3 |
| 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 TCF3 |
| 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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