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

Gene ID: 64345, updated on 3-Jun-2026
Official Symbol
Hif3aprovided by RGD
Official Full Name
hypoxia inducible factor 3 subunit alphaprovided by RGD
Primary source
RGD:70332
See related
Ensembl: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, Apr 2025]
Expression
Biased expression in Adrenal (RPKM 9.8), Uterus (RPKM 5.3) and 7 other tissues See more
Orthologs
all
Try the new Gene page
Try the new Transcripts and proteins table
See Hif3a in Genome Data Viewer
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_086019.1Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 8 subunit of 3M complex Neighboring gene protein phosphatase 5, catalytic subunit Neighboring gene carcinoembryonic antigen gene family 4 Neighboring gene pregnancy specific glycoprotein 16

Go to nucleotide: Graphics FASTA GenBank

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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].
  9. 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.
  10. 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)

Homology

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 IEA
Inferred from Electronic Annotation
more info
  
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 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 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 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 intracellular oxygen homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within response to hypoxia ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrion ISS
Inferred from Sequence or Structural Similarity
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 nuclear speck ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
part_of transcription regulator complex IBA
Inferred from Biological aspect of Ancestor
more info
  
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

NEW Try the new Transcript table

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)

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

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000001
    UniProtKB/TrEMBL
    A0A8I6A5W6, 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

  2. 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

  1. NC_086019.1 Reference GRCr8

    Range
    86846196..86878527 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A8I6A5W6
    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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9JHS2.1 GenPept UniProtKB/Swiss-Prot:Q9JHS2

Gene LinkOut

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