TCF3
transcription factor 3 | E2A, E47, ITF1, MGC129647, MGC129648, VDIR, bHLHb21, p75

This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Sep 2011]

Member of: DE-6
Biological processes 59 terms
B cell differentiation (GO:0030183)B cell lineage commitment (GO:0002326)B cell lineage commitment (GO:0002326)DNA binding (GO:0003677)DNA binding (GO:0003677)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor binding (GO:0140297)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)E-box binding (GO:0070888)E-box binding (GO:0070888)E-box binding (GO:0070888)E-box binding (GO:0070888)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II transcription regulator complex (GO:0090575)RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629)bHLH transcription factor binding (GO:0043425)chromatin (GO:0000785)chromatin (GO:0000785)chromatin (GO:0000785)cis-regulatory region sequence-specific DNA binding (GO:0000987)cytoplasm (GO:0005737)euchromatin (GO:0000791)immunoglobulin V(D)J recombination (GO:0033152)immunoglobulin V(D)J recombination (GO:0033152)mitogen-activated protein kinase kinase kinase binding (GO:0031435)negative regulation of transcription by RNA polymerase II (GO:0000122)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of B cell proliferation (GO:0030890)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of cell cycle (GO:0045787)positive regulation of neuron differentiation (GO:0045666)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)protein dimerization activity (GO:0046983)protein heterodimerization activity (GO:0046982)protein heterodimerization activity (GO:0046982)protein homodimerization activity (GO:0042803)protein homodimerization activity (GO:0042803)protein-containing complex (GO:0032991)regulation of DNA-templated transcription (GO:0006355)regulation of G1/S transition of mitotic cell cycle (GO:2000045)regulation of transcription by RNA polymerase II (GO:0006357)transcription cis-regulatory region binding (GO:0000976)transcription regulator complex (GO:0005667)transcription regulator complex (GO:0005667)vitamin D response element binding (GO:0070644)
Expression (TPM)
TCF3 — as a Regulated Gene

TFs regulating TCF3 0 TFs

Transcription factors with Perturb-seq knockdown data for TCF3. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = TCF3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to TCF3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of TCF3, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr19:1,354,303–1,355,411 297.7 kb Distal (>10kb) Multiome 688
chr19:1,383,122–1,384,333 269.0 kb Distal (>10kb) Multiome 1228
chr19:1,401,101–1,401,839 251.1 kb Distal (>10kb) Multiome 540
chr19:1,406,589–1,408,783 245.2 kb Distal (>10kb) Multiome 911
chr19:1,415,008–1,415,721 237.1 kb Distal (>10kb) Multiome 597
chr19:1,437,988–1,438,998 214.2 kb Distal (>10kb) Multiome 1076
chr19:1,444,785–1,447,383 207.4 kb Distal (>10kb) Multiome 797
chr19:1,455,191–1,456,421 196.8 kb Distal (>10kb) Multiome 491
chr19:1,468,941–1,469,903 183.3 kb Distal (>10kb) Multiome 242
chr19:1,470,088–1,471,597 181.8 kb Distal (>10kb) Multiome 544
chr19:1,478,772–1,479,848 173.3 kb Distal (>10kb) Multiome 857
chr19:1,489,566–1,491,829 161.7 kb Distal (>10kb) Multiome 836
chr19:1,507,230–1,508,699 144.5 kb Distal (>10kb) Multiome 596
chr19:1,512,960–1,513,686 139.4 kb Distal (>10kb) Multiome 541
chr19:1,523,798–1,524,624 128.6 kb Distal (>10kb) Multiome 263
chr19:1,566,277–1,568,916 85.9 kb Distal (>10kb) Multiome 748
chr19:1,592,085–1,593,444 59.9 kb Distal (>10kb) Multiome 883
chr19:1,604,859–1,606,501 47.0 kb Distal (>10kb) Multiome 902
chr19:1,651,519–1,653,514 332 bp At TSS Multiome 909
chr19:1,725,307–1,726,101 73.1 kb Distal (>10kb) Multiome 455
chr19:1,811,638–1,813,347 160.0 kb Distal (>10kb) Multiome 782
chr19:1,826,853–1,827,379 174.6 kb Distal (>10kb) Multiome 193
chr19:1,848,048–1,848,953 196.1 kb Distal (>10kb) Multiome 819
chr19:1,851,701–1,852,216 199.3 kb Distal (>10kb) Multiome 115
chr19:1,855,082–1,856,620 202.9 kb Distal (>10kb) Multiome 476
chr19:1,861,439–1,865,723 211.3 kb Distal (>10kb) Multiome 891
chr19:1,875,645–1,876,693 223.6 kb Distal (>10kb) Multiome 887
chr19:1,885,058–1,885,861 232.9 kb Distal (>10kb) Multiome 495
chr19:1,904,556–1,906,084 252.8 kb Distal (>10kb) Multiome 907
chr19:1,940,240–1,942,987 288.4 kb Distal (>10kb) Multiome 901

Genome Browser

Genomic view of the TCF3 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr19:1,344,303 – 1,952,987
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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