HIF3A

hypoxia inducible factor 3 subunit alpha | IPAS, MOP7, PASD7, bHLHe17

The protein encoded by this gene is the alpha-3 subunit of one of several alpha/beta-subunit heterodimeric transcription factors that regulate many adaptive responses to low oxygen tension (hypoxia). The alpha-3 subunit lacks the transactivation domain found in factors containing either the alpha-1 or alpha-2 subunits. It is thought that factors containing the alpha-3 subunit are negative regulators of hypoxia-inducible gene expression. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2011]

Member of: DE-8 Developmental clusters: GC6

Biological processes 26 terms

DNA binding (GO:0003677)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 activity, RNA polymerase II-specific (GO:0000981)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)cellular response to hypoxia (GO:0071456)chromatin (GO:0000785)chromatin (GO:0000785)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)intracellular oxygen homeostasis (GO:0032364)mitochondrion (GO:0005739)nuclear speck (GO:0016607)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)protein dimerization activity (GO:0046983)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)transcription regulator complex (GO:0005667)

Expression (TPM)

TFs regulating HIF3A 0 TFs

Transcription factors with Perturb-seq knockdown data for HIF3A. 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 = HIF3A 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 HIF3A

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of HIF3A, 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
chr19:46,014,941–46,015,784	281.7 kb	Distal (>10kb) Multiome	220
chr19:46,016,414–46,017,078	280.1 kb	Distal (>10kb) Multiome	364
chr19:46,076,819–46,077,882	219.4 kb	Distal (>10kb) Multiome	516
chr19:46,133,049–46,133,620	163.5 kb	Distal (>10kb) Multiome	189
chr19:46,186,238–46,186,877	110.5 kb	Distal (>10kb) Multiome	83
chr19:46,240,361–46,242,067	56.2 kb	Distal (>10kb) Multiome	199
chr19:46,264,949–46,266,023	31.6 kb	Distal (>10kb) Multiome	189
chr19:46,270,338–46,270,840	26.4 kb	Distal (>10kb) Multiome	63
chr19:46,278,494–46,279,057	18.4 kb	Distal (>10kb) Multiome	15
chr19:46,296,572–46,297,359	90 bp	At TSS Multiome	158
chr19:46,300,632–46,301,183	4.0 kb	Proximal (<10kb) Multiome	282
chr19:46,303,439–46,304,504	7.1 kb	Proximal (<10kb) Multiome	300
chr19:46,346,454–46,347,599	50.0 kb	Distal (>10kb) Multiome	835
chr19:46,373,466–46,374,149	76.7 kb	Distal (>10kb) Multiome	293
chr19:46,413,092–46,414,029	116.6 kb	Distal (>10kb) Multiome	530
chr19:46,416,168–46,416,925	119.5 kb	Distal (>10kb) Multiome	522
chr19:46,426,339–46,427,101	129.7 kb	Distal (>10kb) Multiome	220
chr19:46,471,149–46,471,898	174.5 kb	Distal (>10kb) Multiome	339
chr19:46,495,489–46,496,206	198.9 kb	Distal (>10kb) Multiome	177
chr19:46,587,845–46,588,467	291.1 kb	Distal (>10kb) Multiome	21

Genome Browser

Genomic view of the HIF3A 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.