hif1al hypoxia inducible factor 1 subunit alpha, like [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hif1alprovided by ZNC
Official Full Name: hypoxia inducible factor 1 subunit alpha, likeprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-1315
See related: Ensembl:ENSDARG00000100826 AllianceGenome:ZFIN:ZDB-GENE-040426-1315
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: zgc:63965; Hif-3alpha
Summary: Enables beta-catenin binding activity and transcription cis-regulatory region binding activity. Acts upstream of or within several processes, including neuron apoptotic process; response to activity; and response to hypoxia. Part of beta-catenin-TCF complex. Is active in nucleus. Is expressed in several structures, including digestive system; head; heart; inner ear; and pleuroperitoneal region. Orthologous to human HIF3A (hypoxia inducible factor 3 subunit alpha). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 15

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	15	NC_007126.7 (25503955..25527622, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	15	NC_007126.6 (25568697..25592349, complement)

Chromosome 15 - NC_007126.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mechanistically, Hif-3alpha2 binds to beta-catenin and destabilizes the nuclear beta-catenin complex.
Title: An oxygen-insensitive Hif-3α isoform inhibits Wnt signaling by destabilizing the nuclear β-catenin complex.
Zebrafish Hif3alpha modulates erythropoiesis via regulation of gata1 to facilitate hypoxia tolerance.
Title: Zebrafish Hif3α modulates erythropoiesis via regulation of gata1 to facilitate hypoxia tolerance.
These results provide new information about the structural and functional conservation, spatial and temporal expression, and physiological regulation of hypoxia-inducible factor-3alpha (HIF-3alpha) in a teleost model organism.
Title: Molecular, functional, and gene expression analysis of zebrafish hypoxia-inducible factor-3α.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables beta-catenin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular response to hypoxia	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within erythrocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within 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
acts_upstream_of_or_within response to activity	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within response to hypoxia	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of beta-catenin-TCF complex	IPI Inferred from Physical Interaction more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: hypoxia inducible factor 1 subunit alpha, like; hypoxia-inducible factor 3-alpha

Names: Hif-3 alpha; Hif3a; hif-3; hypoxia-inducible factor 1, alpha subunit, like; hypoxia-inducible factor 3 alpha subunit

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.

mRNA and Protein(s)

NM_200405.1 → NP_956699.1 hypoxia inducible factor 1 subunit alpha, like

See identical proteins and their annotated locations for NP_956699.1

Status: PROVISIONAL

Source sequence(s)

BC054582

UniProtKB/TrEMBL

Q7T2E4

Conserved Domains (4) summary

smart00091
Location:36 → 92

PAS; PAS domain

cd00130
Location:173 → 272

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:424 → 455

HIF-1; Hypoxia-inducible factor-1

pfam14598
Location:176 → 277

PAS_11; PAS domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007126.7 Reference GRCz11 Primary Assembly

Range

25503955..25527622 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005157571.4 → XP_005157628.2 hypoxia-inducible factor 3-alpha isoform X1

UniProtKB/TrEMBL

A0A0R4IBR4, A0A8M2B4E3

Related

ENSDARP00000132400.1, ENSDART00000167005.2

Conserved Domains (5) summary

smart00091
Location:91 → 147

PAS; PAS domain

cd00083
Location:12 → 65

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:228 → 327

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:479 → 510

HIF-1; Hypoxia-inducible factor-1

pfam14598
Location:231 → 332

PAS_11; PAS domain
XM_005157572.4 → XP_005157629.2 hypoxia-inducible factor 3-alpha isoform X2

UniProtKB/TrEMBL

A0A0R4IB28, A0A8M2B3Q6

Related

ENSDARP00000129996.2, ENSDART00000158594.2

Conserved Domains (5) summary

smart00091
Location:84 → 140

PAS; PAS domain

cd00083
Location:5 → 58

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:221 → 320

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:472 → 503

HIF-1; Hypoxia-inducible factor-1

pfam14598
Location:224 → 325

PAS_11; PAS domain
XM_021481358.1 → XP_021337033.1 hypoxia-inducible factor 3-alpha isoform X3

UniProtKB/TrEMBL

A0A8M9QBW4

Conserved Domains (2) summary

pfam11413
Location:419 → 448

HIF-1; Hypoxia-inducible factor-1

cl25986
Location:169 → 270

PAS_3; PAS fold