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

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: mouse all
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Genomic context

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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pilot Study on the Effect of Patient Condition and Clinical Parameters on Hypoxia-Induced Factor Expression: HIF1A, EPAS1 and HIF3A in Human Colostrum Cells.
Title: Pilot Study on the Effect of Patient Condition and Clinical Parameters on Hypoxia-Induced Factor Expression: HIF1A, EPAS1 and HIF3A in Human Colostrum Cells.
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.
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.
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.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (60)

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

D12S1977 (e-PCR)
- UniSTS:71990

D4S2902 (e-PCR)
- UniSTS:154217

STS-AA027108 (e-PCR)
- UniSTS:63863

D11S3114 (e-PCR)
- UniSTS:152207

G44334 (e-PCR)
- UniSTS:95121

D17S610 (e-PCR)
- UniSTS:46230

L17877 (e-PCR)
- UniSTS:61334

L17809 (e-PCR)
- UniSTS:39087

RH68490 (e-PCR)
- UniSTS:41180

RH80031 (e-PCR)
- UniSTS:91103

D19S666E (e-PCR)
- UniSTS:4856

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 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	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

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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

NG_029679.1 RefSeqGene

Range

4995..51386

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

46297042..46343433

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B2RBI6
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
XM_047439216.1 → XP_047295172.1 hypoxia-inducible factor 3-alpha isoform X11

UniProtKB/TrEMBL

B4DSD9
XM_017027134.2 → XP_016882623.1 hypoxia-inducible factor 3-alpha isoform X4

UniProtKB/TrEMBL

B2RBI6
XM_017027140.2 → XP_016882629.1 hypoxia-inducible factor 3-alpha isoform X11

UniProtKB/TrEMBL

B4DSD9
XM_047439217.1 → XP_047295173.1 hypoxia-inducible factor 3-alpha isoform X13

UniProtKB/TrEMBL

B4DSD9
XM_017027133.2 → XP_016882622.1 hypoxia-inducible factor 3-alpha isoform X2

UniProtKB/TrEMBL

B2RBI6
XM_017027136.2 → XP_016882625.1 hypoxia-inducible factor 3-alpha isoform X6

UniProtKB/TrEMBL

B2RBI6
XM_047439214.1 → XP_047295170.1 hypoxia-inducible factor 3-alpha isoform X7

UniProtKB/TrEMBL

B2RBI6
XM_017027138.2 → XP_016882627.1 hypoxia-inducible factor 3-alpha isoform X9

UniProtKB/TrEMBL

B2RBI6
XM_047439218.1 → XP_047295174.1 hypoxia-inducible factor 3-alpha isoform X14

UniProtKB/TrEMBL

B4DSD9, M0R104
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
XM_047439219.1 → XP_047295175.1 hypoxia-inducible factor 3-alpha isoform X16
XM_017027135.2 → XP_016882624.1 hypoxia-inducible factor 3-alpha isoform X5

UniProtKB/TrEMBL

B2RBI6
XM_017027141.2 → XP_016882630.1 hypoxia-inducible factor 3-alpha isoform X11

UniProtKB/TrEMBL

B4DSD9
XM_005259153.4 → XP_005259210.3 hypoxia-inducible factor 3-alpha isoform X12

UniProtKB/TrEMBL

B4DSD9

Related

ENSP00000471560.1, ENST00000600383.1
XM_017027137.2 → XP_016882626.1 hypoxia-inducible factor 3-alpha isoform X8

UniProtKB/TrEMBL

B2RBI6
XM_047439215.1 → XP_047295171.1 hypoxia-inducible factor 3-alpha isoform X10

UniProtKB/TrEMBL

B2RBI6

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

49124507..49170893

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B2RBI6
XM_054321745.1 → XP_054177720.1 hypoxia-inducible factor 3-alpha isoform X3

UniProtKB/TrEMBL

B2RBI6
XM_054321753.1 → XP_054177728.1 hypoxia-inducible factor 3-alpha isoform X11

UniProtKB/TrEMBL

B4DSD9
XM_054321746.1 → XP_054177721.1 hypoxia-inducible factor 3-alpha isoform X4

UniProtKB/TrEMBL

B2RBI6
XM_054321752.1 → XP_054177727.1 hypoxia-inducible factor 3-alpha isoform X11

UniProtKB/TrEMBL

B4DSD9
XM_054321756.1 → XP_054177731.1 hypoxia-inducible factor 3-alpha isoform X13

UniProtKB/TrEMBL

B4DSD9
XM_054321744.1 → XP_054177719.1 hypoxia-inducible factor 3-alpha isoform X2

UniProtKB/TrEMBL

B2RBI6
XM_054321748.1 → XP_054177723.1 hypoxia-inducible factor 3-alpha isoform X6

UniProtKB/TrEMBL

B2RBI6
XM_054321749.1 → XP_054177724.1 hypoxia-inducible factor 3-alpha isoform X7

UniProtKB/TrEMBL

B2RBI6
XM_054321750.1 → XP_054177725.1 hypoxia-inducible factor 3-alpha isoform X9

UniProtKB/TrEMBL

B2RBI6
XM_054321757.1 → XP_054177732.1 hypoxia-inducible factor 3-alpha isoform X14

UniProtKB/TrEMBL

B4DSD9, M0R104
XM_054321758.1 → XP_054177733.1 hypoxia-inducible factor 3-alpha isoform X15
XM_054321759.1 → XP_054177734.1 hypoxia-inducible factor 3-alpha isoform X16
XM_054321747.1 → XP_054177722.1 hypoxia-inducible factor 3-alpha isoform X5

UniProtKB/TrEMBL

B2RBI6
XM_054321754.1 → XP_054177729.1 hypoxia-inducible factor 3-alpha isoform X11

UniProtKB/TrEMBL

B4DSD9
XM_054321751.1 → XP_054177726.1 hypoxia-inducible factor 3-alpha isoform X10

UniProtKB/TrEMBL

B2RBI6
XM_054321755.1 → XP_054177730.1 hypoxia-inducible factor 3-alpha isoform X17

UniProtKB/TrEMBL

B4DSD9