FOXD3

forkhead box D3 | Genesis, HFH2

This gene belongs to the forkhead family of transcription factors which is characterized by a distinct forkhead domain. Mutations in this gene cause autoimmune susceptibility 1. [provided by RefSeq, Nov 2008]

Developmental clusters: GC4

Biological processes 23 terms

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 repressor activity, RNA polymerase II-specific (GO:0001227)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)anatomical structure morphogenesis (GO:0009653)cell differentiation (GO:0030154)chromatin (GO:0000785)chromatin (GO:0000785)in utero embryonic development (GO:0001701)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription by RNA polymerase II (GO:0000122)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)

Expression (TPM)

TFs regulating FOXD3 0 TFs

Transcription factors with Perturb-seq knockdown data for FOXD3. 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 = FOXD3 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 FOXD3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of FOXD3, 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
chr1:63,189,665–63,190,489	132.7 kb	Distal (>10kb) Multiome	215
chr1:63,316,605–63,317,949	5.3 kb	Proximal (<10kb) Multiome	584
chr1:63,319,478–63,320,003	2.6 kb	Proximal (<10kb)	118
chr1:63,320,118–63,320,808	1.8 kb	Proximal (<10kb)	76
chr1:63,321,080–63,321,448	1.1 kb	Proximal (<10kb)	51
chr1:63,321,551–63,321,712	853 bp	At TSS	44
chr1:63,321,880–63,324,736	133 bp	At TSS Multiome	684
chr1:63,326,144–63,327,160	3.6 kb	Proximal (<10kb)	213
chr1:63,327,552–63,328,285	5.2 kb	Proximal (<10kb) Multiome	328
chr1:63,329,526–63,330,869	8.1 kb	Proximal (<10kb) Multiome	128
chr1:63,367,059–63,368,178	45.0 kb	Distal (>10kb) Multiome	818
chr1:63,522,907–63,524,033	200.8 kb	Distal (>10kb) Multiome	1049
chr1:63,574,025–63,574,937	251.9 kb	Distal (>10kb) Multiome	44
chr1:63,592,855–63,594,596	271.0 kb	Distal (>10kb) Multiome	842

Genome Browser

Genomic view of the FOXD3 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.