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FOXA2 forkhead box A2 [ Homo sapiens (human) ]

Gene ID: 3170, updated on 26-Sep-2021

Summary

Official Symbol
FOXA2provided by HGNC
Official Full Name
forkhead box A2provided by HGNC
Primary source
HGNC:HGNC:5022
See related
Ensembl:ENSG00000125798 MIM:600288
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
HNF3B; TCF3B; HNF-3-beta
Summary
This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific genes such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. This gene has been linked to sporadic cases of maturity-onset diabetes of the young. Transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]
Expression
Biased expression in stomach (RPKM 15.2), lung (RPKM 9.0) and 8 other tissues See more
Orthologs
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Genomic context

See FOXA2 in Genome Data Viewer
Location:
20p11.21
Exon count:
3
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (22580998..22585490, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (22561636..22566128, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372564 Neighboring gene long intergenic non-protein coding RNA 261 Neighboring gene lncRNA neighboring enhancer of FOXA2 Neighboring gene long intergenic non-protein coding RNA 1747

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
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
GeneReviews: Not available
A weighted false discovery rate control procedure reveals alleles at FOXA2 that influence fasting glucose levels.
GeneReviews: Not available
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
GeneReviews: Not available
Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC19807

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in adult locomotory behavior ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in anatomical structure morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell fate specification ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in dopaminergic neuron differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in dopaminergic neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in dopaminergic neuron differentiation TAS
Traceable Author Statement
more info
PubMed 
involved_in endocrine pancreas development IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of detection of glucose ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of epithelial to mesenchymal transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of glucokinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of transcription from RNA polymerase II promoter by glucose ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of cell-cell adhesion mediated by cadherin IC
Inferred by Curator
more info
PubMed 
involved_in positive regulation of embryonic development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of gastrulation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
involved_in positive regulation of transcription from RNA polymerase II promoter by glucose ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in primitive streak formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of blood coagulation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to interleukin-6 TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in cell junction IDA
Inferred from Direct Assay
more info
 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
hepatocyte nuclear factor 3-beta
Names
forkhead box protein A2
hepatic nuclear factor-3-beta
transcription factor 3B

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)

  1. NM_021784.5NP_068556.2  hepatocyte nuclear factor 3-beta isoform 1

    See identical proteins and their annotated locations for NP_068556.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL121722
    Consensus CDS
    CCDS46585.1
    UniProtKB/Swiss-Prot
    Q9Y261
    UniProtKB/TrEMBL
    B0ZTD4
    Related
    ENSP00000400341.3, ENST00000419308.7
    Conserved Domains (3) summary
    pfam08430
    Location:23164
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:380452
    HNF_C; HNF3 C-terminal domain
    cd20039
    Location:163264
    FH_FOXA2; Forkhead (FH) domain found in Forkhead box protein A2 (FOXA2) and similar proteins
  2. NM_153675.3NP_710141.1  hepatocyte nuclear factor 3-beta isoform 2

    See identical proteins and their annotated locations for NP_710141.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has a different splice pattern at the 5' end compared to transcript variant 1, resulting in translation initiation from a downstream AUG, and a shorter isoform (2) missing 6 aa from the N-terminus compared to isoform 1.
    Source sequence(s)
    AA469087, AB028021, AI268650, AL121722
    Consensus CDS
    CCDS13147.1
    UniProtKB/Swiss-Prot
    Q9Y261
    Related
    ENSP00000366319.4, ENST00000377115.4
    Conserved Domains (3) summary
    pfam08430
    Location:17158
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:374446
    HNF_C; HNF3 C-terminal domain
    cd20039
    Location:157258
    FH_FOXA2; Forkhead (FH) domain found in Forkhead box protein A2 (FOXA2) and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    22580998..22585490 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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