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

Gene ID: 64344, updated on 20-Sep-2020

Summary

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
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

Genomic context

See HIF3A in Genome Data Viewer
Location:
19q13.32
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (46297042..46343433)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (46800303..46846690)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene IGF like family member 1 Neighboring gene IGF like family member 1 pseudogene 2 Neighboring gene RNA, U6 small nuclear 924, pseudogene Neighboring gene protein phosphatase 5 catalytic subunit Neighboring gene uncharacterized LOC105372426 Neighboring gene coiled-coil domain containing 8

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
angiogenesis IEA
Inferred from Electronic Annotation
more info
 
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
post-translational protein modification TAS
Traceable Author Statement
more info
 
protein ubiquitination TAS
Traceable Author Statement
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription from RNA polymerase II promoter in response to hypoxia TAS
Traceable Author Statement
more info
 
transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

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)

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_022462.4NP_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/Swiss-Prot
    Q9Y2N7
    Related
    ENSP00000244303.6, ENST00000244303.10
    Conserved Domains (3) summary
    cd00130
    Location:172269
    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:411440
    HIF-1; Hypoxia-inducible factor-1
    pfam14598
    Location:172279
    PAS_11; PAS domain
  2. NM_152794.4NP_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/Swiss-Prot
    Q9Y2N7
    UniProtKB/TrEMBL
    B2RBI6
    Related
    ENSP00000300862.3, ENST00000300862.7
    Conserved Domains (4) summary
    cd00083
    Location:1166
    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:239336
    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:478507
    HIF-1; Hypoxia-inducible factor-1
    pfam14598
    Location:239346
    PAS_11; PAS domain
  3. NM_152795.4NP_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
    Q9Y2N7
    Related
    ENSP00000366898.3, ENST00000377670.8
    Conserved Domains (4) summary
    cd00083
    Location:1368
    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:241338
    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:480509
    HIF-1; Hypoxia-inducible factor-1
    pfam14598
    Location:241348
    PAS_11; PAS domain
  4. NM_152796.2NP_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:172269
    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:429450
    GVQW; Putative domain of unknown function
    pfam14598
    Location:172279
    PAS_11; PAS domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

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

  2. XM_017027140.1XP_016882629.1  hypoxia-inducible factor 3-alpha isoform X9

  3. XM_017027138.1XP_016882627.1  hypoxia-inducible factor 3-alpha isoform X8

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

  5. XM_005259152.4XP_005259209.1  hypoxia-inducible factor 3-alpha isoform X3

    Conserved Domains (4) summary
    cd00083
    Location:57112
    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:285382
    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:524553
    HIF-1; Hypoxia-inducible factor-1
    pfam14598
    Location:285392
    PAS_11; PAS domain
  6. XM_005259155.4XP_005259212.1  hypoxia-inducible factor 3-alpha isoform X11

    See identical proteins and their annotated locations for XP_005259212.1

    Conserved Domains (3) summary
    cd00083
    Location:57112
    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:285382
    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 ...
    pfam14598
    Location:285392
    PAS_11; PAS domain
  7. XM_017027133.1XP_016882622.1  hypoxia-inducible factor 3-alpha isoform X2

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

  9. XM_005259156.4XP_005259213.1  hypoxia-inducible factor 3-alpha isoform X11

    See identical proteins and their annotated locations for XP_005259213.1

    Conserved Domains (3) summary
    cd00083
    Location:57112
    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:285382
    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 ...
    pfam14598
    Location:285392
    PAS_11; PAS domain
  10. XM_017027139.1XP_016882628.1  hypoxia-inducible factor 3-alpha isoform X9

  11. XM_017027142.1XP_016882631.1  hypoxia-inducible factor 3-alpha isoform X13

  12. XM_024451649.1XP_024307417.1  hypoxia-inducible factor 3-alpha isoform X12

    Conserved Domains (3) summary
    cd00130
    Location:173
    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:383412
    HIF-1; Hypoxia-inducible factor-1
    cl25986
    Location:144251
    PAS_3; PAS fold
  13. XM_017027141.1XP_016882630.1  hypoxia-inducible factor 3-alpha isoform X9

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

  15. XM_017027137.1XP_016882626.1  hypoxia-inducible factor 3-alpha isoform X7

  16. XM_005259153.3XP_005259210.2  hypoxia-inducible factor 3-alpha isoform X10

    UniProtKB/TrEMBL
    M0R104
    Related
    ENSP00000471560.1, ENST00000600383.1
    Conserved Domains (4) summary
    cd00130
    Location:172269
    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:411440
    HIF-1; Hypoxia-inducible factor-1
    pfam13900
    Location:573594
    GVQW; Putative domain of unknown function
    pfam14598
    Location:172279
    PAS_11; PAS domain

RNA

  1. XR_001753736.1 RNA Sequence

  2. XR_935849.2 RNA Sequence

  3. XR_002958343.1 RNA Sequence

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