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HIF3A hypoxia inducible factor 3 subunit alpha [ Homo sapiens (human) ]

Gene ID: 64344, updated on 11-Apr-2024

Summary

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Official Symbol
HIF3Aprovided by HGNC
Official Full Name
hypoxia inducible factor 3 subunit alphaprovided by HGNC
Primary source
HGNC:HGNC:15825
See related
Ensembl:ENSG00000124440 MIM:609976; AllianceGenome:HGNC:15825
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IPAS; MOP7; PASD7; HIF-3A; bHLHe17; HIF3-alpha-1
Summary
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]
Expression
Broad expression in placenta (RPKM 8.3), spleen (RPKM 6.6) and 17 other tissues See more
Orthologs
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Genomic context

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See HIF3A in Genome Data Viewer
Location:
19q13.32
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (46297042..46343433)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (49124507..49170893)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (46800299..46846690)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46763899-46764398 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:46765735-46766934 Neighboring gene Sharpr-MPRA regulatory region 13463 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46774457-46775170 Neighboring gene IGF like family member 1 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46806397-46806980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46806981-46807564 Neighboring gene RNA, U6 small nuclear 924, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46823333-46823834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46823835-46824334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46854004-46854805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10810 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10811 Neighboring gene protein phosphatase 5 catalytic subunit Neighboring gene uncharacterized LOC105372426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46886025-46886926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46896972-46897472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46906697-46907404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46911937-46912461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46915195-46916028 Neighboring gene coiled-coil domain containing 8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Association between the Extent of Peripheral Blood DNA Methylation of HIF3A and Accumulation of Adiposity in community-dwelling Women: The Yakumo Study. Mizuno G, et al. Endocr Res, 2022 Aug-Nov. PMID 36104828
  2. Aberrant expression of HIF3A in plasma of patients with non-small cell lung cancer and its clinical significance. Wei L, et al. J Clin Lab Anal, 2021 Aug. PMID 34245041, Free PMC Article
  3. Short-chain fatty acids combined with intronic DNA methylation of HIF3A: Potential predictors for diabetic cardiomyopathy. Guo Y, et al. Clin Nutr, 2021 Jun. PMID 34130016
  4. A Functional Polymorphism in HIF-3α Is Related to an Increased Risk of Ischemic Stroke. Gu XX, et al. J Mol Neurosci, 2021 May. PMID 33226577, Free PMC Article
  5. HIF‑3α affects preeclampsia development by regulating EVT growth via activation of the Flt‑1/JAK/STAT signaling pathway in hypoxia. Qu H, et al. Mol Med Rep, 2021 Jan. PMID 33215219, Free PMC Article

See all (73) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Hypoxia Inducible Factors (HIF1alpha and HIF3alpha) are differentially methylated in preeclampsia placentae and are associated with birth outcomes.
    Title: Hypoxia Inducible Factors (HIF1α and HIF3α) are differentially methylated in preeclampsia placentae and are associated with birth outcomes.
  2. DUXAP8 Promotes LPS-Induced Cell Injury in Pulpitis by Regulating miR-18b-5p/HIF3A.
    Title: DUXAP8 Promotes LPS-Induced Cell Injury in Pulpitis by Regulating miR-18b-5p/HIF3A.
  3. HIF-3alpha-Induced miR-630 Expression Promotes Cancer Hallmarks in Cervical Cancer Cells by Forming a Positive Feedback Loop.
    Title: HIF-3α-Induced miR-630 Expression Promotes Cancer Hallmarks in Cervical Cancer Cells by Forming a Positive Feedback Loop.
  4. Association between the Extent of Peripheral Blood DNA Methylation of HIF3A and Accumulation of Adiposity in community-dwelling Women: The Yakumo Study.
    Title: Association between the Extent of Peripheral Blood DNA Methylation of HIF3A and Accumulation of Adiposity in community-dwelling Women: The Yakumo Study.
  5. Short-chain fatty acids combined with intronic DNA methylation of HIF3A: Potential predictors for diabetic cardiomyopathy.
    Title: Short-chain fatty acids combined with intronic DNA methylation of HIF3A: Potential predictors for diabetic cardiomyopathy.
  6. Hypoxia inducible factor-3alpha promotes osteosarcoma progression by activating KDM3A-mediated demethylation of SOX9.
    Title: Hypoxia inducible factor-3α promotes osteosarcoma progression by activating KDM3A-mediated demethylation of SOX9.
  7. Aberrant expression of HIF3A in plasma of patients with non-small cell lung cancer and its clinical significance.
    Title: Aberrant expression of HIF3A in plasma of patients with non-small cell lung cancer and its clinical significance.
  8. A Functional Polymorphism in HIF-3alpha Is Related to an Increased Risk of Ischemic Stroke.
    Title: A Functional Polymorphism in HIF-3α Is Related to an Increased Risk of Ischemic Stroke.
  9. HIF3A DNA methylation, obesity and weight gain, and breast cancer risk among Mexican American women.
    Title: HIF3A DNA methylation, obesity and weight gain, and breast cancer risk among Mexican American women.
  10. HIF3A cord blood methylation and systolic blood pressure at 4 years - a population-based cohort study.
    Title: HIF3A cord blood methylation and systolic blood pressure at 4 years - a population-based cohort study.
Submit: New GeneRIF Correction See all GeneRIFs (59)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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 regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
hypoxia-inducible factor 3-alpha
Names
PAS domain-containing protein 7
basic-helix-loop-helix-PAS protein MOP7
class E basic helix-loop-helix protein 17
hypoxia inducible factor 3 alpha subunit
inhibitory PAS domain protein
member of PAS protein 7

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.

Genomic

  1. NG_029679.1 RefSeqGene

    Range
    4995..51386
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_022462.4 → NP_071907.4  hypoxia-inducible factor 3-alpha isoform b

    See identical proteins and their annotated locations for NP_071907.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 3. The resulting isoform (b) has a distinct and shorter N-terminus, compared to isoform c.
    Source sequence(s)
    AC007193, AK297828, BM971722, DC423791
    Consensus CDS
    CCDS42580.2
    UniProtKB/TrEMBL
    B4DSD9
    Related
    ENSP00000244303.6, ENST00000244303.10
    Conserved Domains (3) summary
    cd00130
    Location:172 → 269
    PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
    pfam11413
    Location:411 → 440
    HIF-1; Hypoxia-inducible factor-1
    pfam14598
    Location:172 → 279
    PAS_11; PAS domain

  2. NM_152794.4 → NP_690007.1  hypoxia-inducible factor 3-alpha isoform a

    See identical proteins and their annotated locations for NP_690007.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and 5' coding region, compared to variant 3. The resulting isoform (a) has a distinct and shorter N-terminus, compared to isoform c.
    Source sequence(s)
    AB054067, AC007193, AK314680, BM971722
    Consensus CDS
    CCDS12682.1
    UniProtKB/TrEMBL
    B2RBI6
    Related
    ENSP00000300862.3, ENST00000300862.7
    Conserved Domains (4) summary
    cd00083
    Location:11 → 66
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    cd00130
    Location:239 → 336
    PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
    pfam11413
    Location:478 → 507
    HIF-1; Hypoxia-inducible factor-1
    pfam14598
    Location:239 → 346
    PAS_11; PAS domain

  3. NM_152795.4 → NP_690008.2  hypoxia-inducible factor 3-alpha isoform c

    See identical proteins and their annotated locations for NP_690008.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes the longest isoform (c).
    Source sequence(s)
    AC007193, BC080551, BM971722, DR001068
    Consensus CDS
    CCDS12681.2
    UniProtKB/Swiss-Prot
    B0M185, B4DNA2, I6L988, Q58A43, Q66K72, Q8WXA1, Q96K34, Q9H7Z9, Q9HAI2, Q9Y2N7
    UniProtKB/TrEMBL
    B2RBI6
    Related
    ENSP00000366898.3, ENST00000377670.9
    Conserved Domains (4) summary
    cd00083
    Location:13 → 68
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    cd00130
    Location:241 → 338
    PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
    pfam11413
    Location:480 → 509
    HIF-1; Hypoxia-inducible factor-1
    pfam14598
    Location:241 → 348
    PAS_11; PAS domain

  4. NM_152796.2 → NP_690009.1  hypoxia-inducible factor 3-alpha isoform d

    See identical proteins and their annotated locations for NP_690009.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, uses an alternate start codon, and differs in the 3' coding region and 3' UTR, compared to variant 3. The resulting isoform (d) has distinct N- and C-termini, and is shorter than isoform c.
    Source sequence(s)
    AC007193, AU143858, BE250295, CA437428, CF593418, DA559979, DC423791
    UniProtKB/TrEMBL
    H0YDZ5
    Related
    ENSP00000434653.2, ENST00000472815.5
    Conserved Domains (3) summary
    cd00130
    Location:172 → 269
    PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
    pfam13900
    Location:429 → 450
    GVQW; Putative domain of unknown function
    pfam14598
    Location:172 → 279
    PAS_11; PAS domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    46297042..46343433
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017027132.2 → XP_016882621.1  hypoxia-inducible factor 3-alpha isoform X1

    UniProtKB/TrEMBL
    B2RBI6

  2. XM_005259152.5 → XP_005259209.1  hypoxia-inducible factor 3-alpha isoform X3

    UniProtKB/TrEMBL
    B2RBI6
    Conserved Domains (4) summary
    cd00083
    Location:57 → 112
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    cd00130
    Location:285 → 382
    PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
    pfam11413
    Location:524 → 553
    HIF-1; Hypoxia-inducible factor-1
    pfam14598
    Location:285 → 392
    PAS_11; PAS domain

  3. XM_047439216.1 → XP_047295172.1  hypoxia-inducible factor 3-alpha isoform X11

  4. XM_017027134.2 → XP_016882623.1  hypoxia-inducible factor 3-alpha isoform X4

    UniProtKB/TrEMBL
    B2RBI6

  5. XM_017027140.2 → XP_016882629.1  hypoxia-inducible factor 3-alpha isoform X11

    UniProtKB/TrEMBL
    B4DSD9

  6. XM_047439217.1 → XP_047295173.1  hypoxia-inducible factor 3-alpha isoform X13

  7. XM_017027133.2 → XP_016882622.1  hypoxia-inducible factor 3-alpha isoform X2

    UniProtKB/TrEMBL
    B2RBI6

  8. XM_017027136.2 → XP_016882625.1  hypoxia-inducible factor 3-alpha isoform X6

    UniProtKB/TrEMBL
    B2RBI6

  9. XM_047439214.1 → XP_047295170.1  hypoxia-inducible factor 3-alpha isoform X7

  10. XM_017027138.2 → XP_016882627.1  hypoxia-inducible factor 3-alpha isoform X9

    UniProtKB/TrEMBL
    B2RBI6

  11. XM_047439218.1 → XP_047295174.1  hypoxia-inducible factor 3-alpha isoform X14

    UniProtKB/TrEMBL
    M0R104

  12. XM_005259156.5 → XP_005259213.1  hypoxia-inducible factor 3-alpha isoform X15

    See identical proteins and their annotated locations for XP_005259213.1

    Conserved Domains (3) summary
    cd00130
    Location:139 → 214
    PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
    cd19729
    Location:56 → 118
    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
    pfam14598
    Location:285 → 390
    PAS_11; PAS domain

  13. XM_047439219.1 → XP_047295175.1  hypoxia-inducible factor 3-alpha isoform X16

  14. XM_017027135.2 → XP_016882624.1  hypoxia-inducible factor 3-alpha isoform X5

    UniProtKB/TrEMBL
    B2RBI6

  15. XM_017027141.2 → XP_016882630.1  hypoxia-inducible factor 3-alpha isoform X11

    UniProtKB/TrEMBL
    B4DSD9

  16. XM_005259153.4 → XP_005259210.3  hypoxia-inducible factor 3-alpha isoform X12

    Related
    ENSP00000471560.1, ENST00000600383.1

  17. XM_017027137.2 → XP_016882626.1  hypoxia-inducible factor 3-alpha isoform X8

    UniProtKB/TrEMBL
    B2RBI6

  18. XM_047439215.1 → XP_047295171.1  hypoxia-inducible factor 3-alpha isoform X10

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    49124507..49170893
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321743.1 → XP_054177718.1  hypoxia-inducible factor 3-alpha isoform X1

  2. XM_054321745.1 → XP_054177720.1  hypoxia-inducible factor 3-alpha isoform X3

  3. XM_054321753.1 → XP_054177728.1  hypoxia-inducible factor 3-alpha isoform X11

  4. XM_054321746.1 → XP_054177721.1  hypoxia-inducible factor 3-alpha isoform X4

  5. XM_054321752.1 → XP_054177727.1  hypoxia-inducible factor 3-alpha isoform X11

  6. XM_054321756.1 → XP_054177731.1  hypoxia-inducible factor 3-alpha isoform X13

  7. XM_054321744.1 → XP_054177719.1  hypoxia-inducible factor 3-alpha isoform X2

  8. XM_054321748.1 → XP_054177723.1  hypoxia-inducible factor 3-alpha isoform X6

  9. XM_054321749.1 → XP_054177724.1  hypoxia-inducible factor 3-alpha isoform X7

  10. XM_054321750.1 → XP_054177725.1  hypoxia-inducible factor 3-alpha isoform X9

  11. XM_054321757.1 → XP_054177732.1  hypoxia-inducible factor 3-alpha isoform X14

    UniProtKB/TrEMBL
    M0R104

  12. XM_054321758.1 → XP_054177733.1  hypoxia-inducible factor 3-alpha isoform X15

  13. XM_054321759.1 → XP_054177734.1  hypoxia-inducible factor 3-alpha isoform X16

  14. XM_054321747.1 → XP_054177722.1  hypoxia-inducible factor 3-alpha isoform X5

  15. XM_054321754.1 → XP_054177729.1  hypoxia-inducible factor 3-alpha isoform X11

  16. XM_054321751.1 → XP_054177726.1  hypoxia-inducible factor 3-alpha isoform X10

  17. XM_054321755.1 → XP_054177730.1  hypoxia-inducible factor 3-alpha isoform X17

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2N7.2 GenPept UniProtKB/Swiss-Prot:Q9Y2N7

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