U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

BARHL2 BarH like homeobox 2 [ Homo sapiens (human) ]

Gene ID: 343472, updated on 19-Aug-2025
Official Symbol
BARHL2provided by HGNC
Official Full Name
BarH like homeobox 2provided by HGNC
Primary source
HGNC:HGNC:954
See related
Ensembl:ENSG00000143032 MIM:605212; AllianceGenome:HGNC:954
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including generation of neurons; positive regulation of macromolecule biosynthetic process; and regulation of axon extension. Predicted to be located in chromatin. Predicted to be active in nucleus. Implicated in oral squamous cell carcinoma. Biomarker of colorectal cancer; oral squamous cell carcinoma; and stomach cancer. [provided by Alliance of Genome Resources, Jul 2025]
Expression
Restricted expression toward testis (RPKM 1.8) See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table
See BARHL2 in Genome Data Viewer
Location:
1p22.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (90711539..90717302, complement)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (90555903..90561666, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (91177096..91182859, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2787 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:91027459-91027961 Neighboring gene small nucleolar RNA, C/D box 3G Neighboring gene NANOG hESC enhancer GRCh37_chr1:91149838-91150358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:91171602-91172396 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:91176541-91177109 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:91190371-91190926 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:91190927-91191482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:91192039-91192594 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:91193268-91194089 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:91227242-91228098 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:91253233-91253482 Neighboring gene long intergenic non-protein coding RNA 2609 Neighboring gene uncharacterized LOC124904217 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:91275093-91275704 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:91277119-91277260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:91300317-91300956 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:91304224-91304748 Neighboring gene VISTA enhancer hs612 Neighboring gene long intergenic non-protein coding RNA 2788

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Barhl1, a gene belonging to a new subfamily of mammalian homeobox genes, is expressed in migrating neurons of the CNS. Bulfone A, et al. Hum Mol Genet, 2000 May 22. PMID 10814725
  2. Role of the Barhl2 homeobox gene in the specification of glycinergic amacrine cells. Mo Z, et al. Development, 2004 Apr. PMID 14998930
  3. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Yin Y, et al. Science, 2017 May 5. PMID 28473536, Free PMC Article
  4. A census of human transcription factors: function, expression and evolution. Vaquerizas JM, et al. Nat Rev Genet, 2009 Apr. PMID 19274049
  5. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific 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 DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
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 sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within amacrine cell differentiation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cell fate commitment IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cell fate determination IEA
Inferred from Electronic Annotation
more info
  
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within neuron migration IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within positive regulation of translation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within regulation of axon extension 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
  
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
barH-like 2 homeobox protein

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.

mRNA and Protein(s)

  1. NM_020063.2 → NP_064447.1  barH-like 2 homeobox protein

    See identical proteins and their annotated locations for NP_064447.1

    Status: VALIDATED

    Source sequence(s)
    AC092805, AY338397
    Consensus CDS
    CCDS730.1
    UniProtKB/Swiss-Prot
    A0AVP2, Q7Z4N7, Q9NY43
    Related
    ENSP00000359474.3, ENST00000370445.5
    Conserved Domains (1) summary
    pfam00046
    Location:236 → 288
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    90711539..90717302 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419616.1 → XP_047275572.1  barH-like 2 homeobox protein isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    90555903..90561666 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336367.1 → XP_054192342.1  barH-like 2 homeobox protein isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NY43.2 GenPept UniProtKB/Swiss-Prot:Q9NY43

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools