Hif3a hypoxia inducible factor 3 subunit alpha [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hif3aprovided by RGD
Official Full Name: hypoxia inducible factor 3 subunit alphaprovided by RGD
Primary source: RGD:70332
See related: EnsemblRapid:ENSRNOG00000017198 AllianceGenome:RGD:70332
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Ipas; Mop7
Summary: Enables DNA-binding transcription factor activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in several cellular components, including chromatin; mitochondrion; and nuclear speck. Biomarker of pulmonary hypertension. Orthologous to human HIF3A (hypoxia inducible factor 3 subunit alpha). [provided by Alliance of Genome Resources, Jan 2025]
Expression: Biased expression in Adrenal (RPKM 9.8), Uterus (RPKM 5.3) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q21

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (86846196..86878527, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (77718110..77750448, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (78976318..78997869, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

miR-485-5p alleviates obstructive sleep apnea syndrome with hypertension by inhibiting PI3K/AKT signaling pathway via downregulating HIF3A expression.
Title: miR-485-5p alleviates obstructive sleep apnea syndrome with hypertension by inhibiting PI3K/AKT signaling pathway via downregulating HIF3A expression.
MicroRNA-210-3p Promotes Chondrogenic Differentiation and Inhibits Adipogenic Differentiation Correlated with HIF-3alpha Signalling in Bone Marrow Mesenchymal Stem Cells.
Title: MicroRNA-210-3p Promotes Chondrogenic Differentiation and Inhibits Adipogenic Differentiation Correlated with HIF-3α Signalling in Bone Marrow Mesenchymal Stem Cells.
Study in human mesenchymal stromal/stem cells revealed robust hypermethylation of histone H3 across HIF3A locus driven by pro-inflammatory cytokines. Experiments in a murine model of arteriotomy highlighted the activation of Hif3alpha expression in infiltrated inflammatory cells, suggesting a new role for Hif3alpha in inflammation in vivo.
Title: Pro-inflammatory cytokines activate hypoxia-inducible factor 3α via epigenetic changes in mesenchymal stromal/stem cells.
Hif3a RNA interference and HIF-prolyl hydroxylase inhibition protect cardiomyocytes against anoxia-reoxygenation injury via the HIF signaling pathway
Title: The protective effect of Hif3a RNA interference and HIF-prolyl hydroxylase inhibition on cardiomyocytes under anoxia-reoxygenation.
ZnCl2 (10 mg/kg) significantly lowered the creatinine and urea concentrations compared to saline-treated control rats following a clinically relevant 60 minutes of ischemia. Zn2+ induced expression of HIF1a and HIF2a but not HIF3a.ZnCl2 preconditioning protects against renal Ischemia-reperfusion injury in a dose-dependent manner
Title: Protective effect of zinc preconditioning against renal ischemia reperfusion injury is dose dependent.
The association of IPAS with Bcl-x(L) was also observed in living cells by the FLIM-based FRET analysis, indicating direct binding between the two proteins.
Title: Pro-apoptotic activity of inhibitory PAS domain protein (IPAS), a negative regulator of HIF-1, through binding to pro-survival Bcl-2 family proteins.
NF-kB activation in PC12 cells upregulates IPAS gene expression without activating HIF-1a and HIF-2a.
Title: Tumour necrosis factor-α suppresses the hypoxic response by NF-κB-dependent induction of inhibitory PAS domain protein in PC12 cells.
The differential expression of HIF1a, HIF2a, and HIF3a may play a role in the development of hypoxia-induced pulmonary hypertension.
Title: [Differential expression of the three hypoxia-inducible factor alpha subunits in pulmonary artery of rats with hypoxia-induced pulmonary hypertension].
There were increased carotid body expressions of HIF-2alpha and -3alpha, and also endothelin-1 and tyrosine hydroxylase in both intermittent hypoxia and chronic hypoxia groups.
Title: Differential expressions and roles of hypoxia-inducible factor-1alpha, -2alpha and -3alpha in the rat carotid body during chronic and intermittent hypoxia.
HIF-1alpha, HIF-2alpha and HIF-3alpha may not only confer different target genes, but also play key pathogenetic roles in hypoxic-induced pulmonary hypertension.
Title: Differential expression of three hypoxia-inducible factor-alpha subunits in pulmonary arteries of rat with hypoxia-induced hypertension.

Submit: New GeneRIF Correction See all GeneRIFs (13)

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hypoxia	IBA Inferred from Biological aspect of Ancestor more info
NOT involved_in cellular response to hypoxia	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to hypoxia	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to hypoxia	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: hypoxia-inducible factor 3-alpha

Names: HIF-3-alpha; HIF3-alpha; HIF3-alpha-1; Inhibitory PAS (Per/Arnt/Sim) domain protein; hypoxia inducible factor 3, alpha subunit; hypoxia inducible factor 3a

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001388512.1 → NP_001375441.1 hypoxia-inducible factor 3-alpha isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

Q9JHS2

UniProtKB/TrEMBL

A0A8I6GMD1

Related

ENSRNOP00000097060.1, ENSRNOT00000099745.2

Conserved Domains (5) summary

smart00091
Location:90 → 145

PAS; PAS domain

PHA03247
Location:360 → 633

PHA03247; large tegument protein UL36; Provisional

pfam08447
Location:251 → 338

PAS_3; PAS fold

cd19729
Location:12 → 74

bHLH-PAS_HIF3a_PASD7; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 3-alpha (HIF3a) and similar proteins

pfam11413
Location:477 → 506

HIF-1; Hypoxia-inducible factor-1
NM_022528.3 → NP_071973.2 hypoxia-inducible factor 3-alpha isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

Q9JHS2

UniProtKB/TrEMBL

F1LRL5

Related

ENSRNOP00000023490.2, ENSRNOT00000023490.5

Conserved Domains (5) summary

smart00091
Location:88 → 143

PAS; PAS domain

PHA03247
Location:358 → 631

PHA03247; large tegument protein UL36; Provisional

pfam08447
Location:249 → 336

PAS_3; PAS fold

cd19729
Location:10 → 72

bHLH-PAS_HIF3a_PASD7; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 3-alpha (HIF3a) and similar proteins

pfam11413
Location:475 → 504

HIF-1; Hypoxia-inducible factor-1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

86846196..86878527 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039089538.2 → XP_038945466.1 hypoxia-inducible factor 3-alpha isoform X1

UniProtKB/Swiss-Prot

Q9JHS2

Related

ENSRNOP00000087469.2, ENSRNOT00000101762.2

Conserved Domains (5) summary

smart00091
Location:34 → 89

PAS; PAS domain

PHA03247
Location:304 → 577

PHA03247; large tegument protein UL36; Provisional

pfam08447
Location:195 → 282

PAS_3; PAS fold

pfam11413
Location:421 → 450

HIF-1; Hypoxia-inducible factor-1

cl00081
Location:1 → 18

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily