FOXA3

forkhead box A3 | HNF3G

This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. The crystal structure of a similar protein in rat has been resolved. [provided by RefSeq, Jul 2008]

Member of: DE-7 DE-7.1 Developmental clusters: GC7

Biological processes 27 terms

DNA binding (GO:0003677)DNA-binding transcription factor activity (GO:0003700)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)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)anatomical structure morphogenesis (GO:0009653)cell differentiation (GO:0030154)chromatin (GO:0000785)intracellular glucose homeostasis (GO:0001678)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)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 domain specific binding (GO:0019904)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)spermatogenesis (GO:0007283)transcription cis-regulatory region binding (GO:0000976)transcription cis-regulatory region binding (GO:0000976)

Expression (TPM)

TFs regulating FOXA3 0 TFs

Transcription factors with Perturb-seq knockdown data for FOXA3. 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 = FOXA3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to FOXA3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of FOXA3, 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.

Element	Dist. to TSS	Link type	TFs
chr19:45,584,026–45,585,251	279.7 kb	Distal (>10kb) Multiome	907
chr19:45,607,096–45,607,695	256.9 kb	Distal (>10kb) Multiome	526
chr19:45,615,654–45,616,944	248.2 kb	Distal (>10kb) Multiome	480
chr19:45,632,406–45,633,148	231.6 kb	Distal (>10kb) Multiome	358
chr19:45,638,965–45,639,696	225.0 kb	Distal (>10kb) Multiome	477
chr19:45,640,813–45,642,557	222.0 kb	Distal (>10kb) Multiome	865
chr19:45,643,187–45,644,012	220.7 kb	Distal (>10kb) Multiome	542
chr19:45,645,389–45,646,343	218.4 kb	Distal (>10kb) Multiome	566
chr19:45,667,856–45,668,417	196.3 kb	Distal (>10kb) Multiome	386
chr19:45,668,914–45,669,719	195.0 kb	Distal (>10kb) Multiome	611
chr19:45,670,481–45,671,446	193.3 kb	Distal (>10kb) Multiome	361
chr19:45,676,875–45,678,209	186.8 kb	Distal (>10kb) Multiome	418
chr19:45,681,530–45,682,004	182.6 kb	Distal (>10kb) Multiome	648
chr19:45,691,622–45,693,062	171.9 kb	Distal (>10kb) Multiome	943
chr19:45,716,851–45,718,343	146.8 kb	Distal (>10kb) Multiome	895
chr19:45,730,200–45,731,219	133.3 kb	Distal (>10kb) Multiome	740
chr19:45,767,223–45,771,892	94.9 kb	Distal (>10kb) Multiome	1161
chr19:45,779,258–45,780,150	84.7 kb	Distal (>10kb) Multiome	445
chr19:45,792,338–45,793,273	71.4 kb	Distal (>10kb) Multiome	609
chr19:45,815,484–45,818,073	48.4 kb	Distal (>10kb) Multiome	623
chr19:45,862,559–45,864,765	97 bp	At TSS Multiome	976
chr19:45,881,480–45,883,645	17.8 kb	Distal (>10kb) Multiome	990
chr19:45,885,092–45,887,294	22.4 kb	Distal (>10kb) Multiome	913
chr19:45,901,212–45,903,471	38.5 kb	Distal (>10kb) Multiome	780
chr19:45,952,967–45,953,485	88.7 kb	Distal (>10kb) Multiome	329
chr19:45,973,761–45,974,227	109.7 kb	Distal (>10kb) Multiome	201
chr19:45,994,774–45,995,740	131.0 kb	Distal (>10kb) Multiome	660
chr19:46,014,941–46,015,784	151.1 kb	Distal (>10kb) Multiome	220
chr19:46,016,414–46,017,078	152.6 kb	Distal (>10kb) Multiome	364
chr19:46,076,819–46,077,882	213.3 kb	Distal (>10kb) Multiome	516
chr19:46,133,049–46,133,620	269.2 kb	Distal (>10kb) Multiome	189

Genome Browser

Genomic view of the FOXA3 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.