U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 64344, updated on 3-Dec-2024

    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; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HIF3A in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (46297042..46343433)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (49124507..49170893)
    RS_2024_09 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

    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

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in 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

    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)

    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.

    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/TrEMBL
      B4DSD9
      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/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
      B0M185, B4DNA2, I6L988, Q58A43, Q66K72, Q8WXA1, Q96K34, Q9H7Z9, Q9HAI2, Q9Y2N7
      UniProtKB/TrEMBL
      B2RBI6
      Related
      ENSP00000366898.3, ENST00000377670.9
      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: GCF_000001405.40-RS_2024_08

    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_017027132.2XP_016882621.1  hypoxia-inducible factor 3-alpha isoform X1

      UniProtKB/TrEMBL
      B2RBI6
    2. XM_005259152.5XP_005259209.1  hypoxia-inducible factor 3-alpha isoform X3

      UniProtKB/TrEMBL
      B2RBI6
      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
    3. XM_047439216.1XP_047295172.1  hypoxia-inducible factor 3-alpha isoform X11

      UniProtKB/TrEMBL
      B4DSD9
    4. XM_017027134.2XP_016882623.1  hypoxia-inducible factor 3-alpha isoform X4

      UniProtKB/TrEMBL
      B2RBI6
    5. XM_017027140.2XP_016882629.1  hypoxia-inducible factor 3-alpha isoform X11

      UniProtKB/TrEMBL
      B4DSD9
    6. XM_047439217.1XP_047295173.1  hypoxia-inducible factor 3-alpha isoform X13

      UniProtKB/TrEMBL
      B4DSD9
    7. XM_017027133.2XP_016882622.1  hypoxia-inducible factor 3-alpha isoform X2

      UniProtKB/TrEMBL
      B2RBI6
    8. XM_017027136.2XP_016882625.1  hypoxia-inducible factor 3-alpha isoform X6

      UniProtKB/TrEMBL
      B2RBI6
    9. XM_047439214.1XP_047295170.1  hypoxia-inducible factor 3-alpha isoform X7

      UniProtKB/TrEMBL
      B2RBI6
    10. XM_017027138.2XP_016882627.1  hypoxia-inducible factor 3-alpha isoform X9

      UniProtKB/TrEMBL
      B2RBI6
    11. XM_047439218.1XP_047295174.1  hypoxia-inducible factor 3-alpha isoform X14

      UniProtKB/TrEMBL
      B4DSD9, M0R104
    12. XM_005259156.5XP_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:139214
      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:56118
      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:285390
      PAS_11; PAS domain
    13. XM_047439219.1XP_047295175.1  hypoxia-inducible factor 3-alpha isoform X16

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

      UniProtKB/TrEMBL
      B2RBI6
    15. XM_017027141.2XP_016882630.1  hypoxia-inducible factor 3-alpha isoform X11

      UniProtKB/TrEMBL
      B4DSD9
    16. XM_005259153.4XP_005259210.3  hypoxia-inducible factor 3-alpha isoform X12

      UniProtKB/TrEMBL
      B4DSD9
      Related
      ENSP00000471560.1, ENST00000600383.1
    17. XM_017027137.2XP_016882626.1  hypoxia-inducible factor 3-alpha isoform X8

      UniProtKB/TrEMBL
      B2RBI6
    18. XM_047439215.1XP_047295171.1  hypoxia-inducible factor 3-alpha isoform X10

      UniProtKB/TrEMBL
      B2RBI6

    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_054321743.1XP_054177718.1  hypoxia-inducible factor 3-alpha isoform X1

      UniProtKB/TrEMBL
      B2RBI6
    2. XM_054321745.1XP_054177720.1  hypoxia-inducible factor 3-alpha isoform X3

      UniProtKB/TrEMBL
      B2RBI6
    3. XM_054321753.1XP_054177728.1  hypoxia-inducible factor 3-alpha isoform X11

      UniProtKB/TrEMBL
      B4DSD9
    4. XM_054321746.1XP_054177721.1  hypoxia-inducible factor 3-alpha isoform X4

      UniProtKB/TrEMBL
      B2RBI6
    5. XM_054321752.1XP_054177727.1  hypoxia-inducible factor 3-alpha isoform X11

      UniProtKB/TrEMBL
      B4DSD9
    6. XM_054321756.1XP_054177731.1  hypoxia-inducible factor 3-alpha isoform X13

      UniProtKB/TrEMBL
      B4DSD9
    7. XM_054321744.1XP_054177719.1  hypoxia-inducible factor 3-alpha isoform X2

      UniProtKB/TrEMBL
      B2RBI6
    8. XM_054321748.1XP_054177723.1  hypoxia-inducible factor 3-alpha isoform X6

      UniProtKB/TrEMBL
      B2RBI6
    9. XM_054321749.1XP_054177724.1  hypoxia-inducible factor 3-alpha isoform X7

      UniProtKB/TrEMBL
      B2RBI6
    10. XM_054321750.1XP_054177725.1  hypoxia-inducible factor 3-alpha isoform X9

      UniProtKB/TrEMBL
      B2RBI6
    11. XM_054321757.1XP_054177732.1  hypoxia-inducible factor 3-alpha isoform X14

      UniProtKB/TrEMBL
      B4DSD9, M0R104
    12. XM_054321758.1XP_054177733.1  hypoxia-inducible factor 3-alpha isoform X15

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

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

      UniProtKB/TrEMBL
      B2RBI6
    15. XM_054321754.1XP_054177729.1  hypoxia-inducible factor 3-alpha isoform X11

      UniProtKB/TrEMBL
      B4DSD9
    16. XM_054321751.1XP_054177726.1  hypoxia-inducible factor 3-alpha isoform X10

      UniProtKB/TrEMBL
      B2RBI6
    17. XM_054321755.1XP_054177730.1  hypoxia-inducible factor 3-alpha isoform X17

      UniProtKB/TrEMBL
      B4DSD9