Aliases for BARHL1 Gene

Aliases for BARHL1 Gene

  • BarH Like Homeobox 1 2 3 5
  • BarH-Like 1 Homeobox Protein 3 4
  • BarH (Drosophila)-Like 1 2
  • BarH-Like Homeobox 1 2
  • BARHL1 5

External Ids for BARHL1 Gene

Previous GeneCards Identifiers for BARHL1 Gene

  • GC09P126482
  • GC09P127014
  • GC09P128811
  • GC09P130734
  • GC09P132487
  • GC09P134447
  • GC09P135457
  • GC09P104951

Summaries for BARHL1 Gene

GeneCards Summary for BARHL1 Gene

BARHL1 (BarH Like Homeobox 1) is a Protein Coding gene. Diseases associated with BARHL1 include Cataract 34, Multiple Types and Medulloblastoma. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific. An important paralog of this gene is BARHL2.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for BARHL1 Gene

Genomics for BARHL1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for BARHL1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J132582 Promoter/Enhancer 1.4 EPDnew ENCODE 250.7 -0.4 -424 0.2 MYC ZNF600 ATF2 KLF9 CEBPA ZIC2 ZBTB10 MXD4 REST KLF11 BARHL1 lnc-CFAP77-1 CFAP77
GH09J132561 Enhancer 0.8 FANTOM5 Ensembl 15.9 -21.2 -21205 2.4 KLF9 ZBTB48 SCRT1 ZBTB21 GLIS1 ZNF398 SP7 ZSCAN4 ZNF629 GLIS2 BARHL1 RNU5D-2P TTF1 DDX31 HSALNG0074936 lnc-CFAP77-1 CFAP77
GH09J132650 Enhancer 0.7 Ensembl ENCODE 10.8 +68.9 68880 1.1 CTCF RAD21 SMARCE1 PKNOX1 BHLHE40 CEBPB TRIM22 FOS NONHSAG053670.2 DDX31 BARHL1 RNU5D-2P ENSG00000234907 RNU7-21P GTF3C4 lnc-DDX31-2
GH09J132630 Enhancer 0.6 Ensembl ENCODE 11.3 +48.8 48776 1.7 RAD21 ZSCAN4 RFX1 FOS CEBPB SCRT2 DDX31 BARHL1 RNU5D-2P ENSG00000234907 RNU7-21P lnc-DDX31-2 NONHSAG053670.2 GTF3C4
GH09J132474 Enhancer 0.6 Ensembl CraniofacialAtlas 10.9 -107.9 -107892 1 TEAD3 BCL6 NR2F6 ZNF24 TCF7 SOX13 piR-57134-121 RNU5D-2P BARHL1 CFAP77 HSALNG0074935
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BARHL1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for BARHL1

Top Transcription factor binding sites by QIAGEN in the BARHL1 gene promoter:
  • C/EBPbeta
  • CUTL1
  • E4BP4
  • NRSF form 1
  • NRSF form 2
  • Spz1

Genomic Locations for BARHL1 Gene

Latest Assembly
7,647 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
7,647 bases
Plus strand

(GRCh37/hg19 by Ensembl)
8,082 bases
Plus strand

Genomic View for BARHL1 Gene

Genes around BARHL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BARHL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BARHL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BARHL1 Gene

Proteins for BARHL1 Gene

  • Protein details for BARHL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    BarH-like 1 homeobox protein
    Protein Accession:
    Secondary Accessions:
    • Q5T6V2
    • Q9NY88

    Protein attributes for BARHL1 Gene

    327 amino acids
    Molecular mass:
    35074 Da
    Quaternary structure:
    No Data Available

neXtProt entry for BARHL1 Gene

Post-translational modifications for BARHL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BARHL1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for BARHL1 Gene

Domains & Families for BARHL1 Gene

Gene Families for BARHL1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for BARHL1 Gene

  • Lambda and other repressor helix-turn-helix signature

Suggested Antigen Peptide Sequences for BARHL1 Gene

GenScript: Design optimal peptide antigens:
  • BarH-like homeobox 1 (B7ZMC8_HUMAN)
  • BarH-like 1 homeobox protein (BARH1_HUMAN)
  • BarH-like homeobox 1 (Q5T6V2_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the BAR homeobox family.
  • Belongs to the BAR homeobox family.
genes like me logo Genes that share domains with BARHL1: view

Function for BARHL1 Gene

Phenotypes From GWAS Catalog for BARHL1 Gene

Gene Ontology (GO) - Molecular Function for BARHL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IEA --
GO:0003677 DNA binding IEA --
GO:1990837 sequence-specific double-stranded DNA binding IDA 28473536
genes like me logo Genes that share ontologies with BARHL1: view
genes like me logo Genes that share phenotypes with BARHL1: view

Animal Models for BARHL1 Gene

MGI Knock Outs for BARHL1:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for BARHL1

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for BARHL1 Gene

Localization for BARHL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BARHL1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for BARHL1 gene
Compartment Confidence
nucleus 4
plasma membrane 1
extracellular 1
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for BARHL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with BARHL1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for BARHL1 Gene

Pathways & Interactions for BARHL1 Gene

PathCards logo

SuperPathways for BARHL1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for BARHL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001764 neuron migration IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0007605 sensory perception of sound IEA --
GO:0030901 midbrain development IEA --
genes like me logo Genes that share ontologies with BARHL1: view

No data available for Pathways by source and SIGNOR curated interactions for BARHL1 Gene

Drugs & Compounds for BARHL1 Gene

No Compound Related Data Available

Transcripts for BARHL1 Gene

mRNA/cDNA for BARHL1 Gene

6 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for BARHL1

Alternative Splicing Database (ASD) splice patterns (SP) for BARHL1 Gene

No ASD Table

Relevant External Links for BARHL1 Gene

GeneLoc Exon Structure for

Expression for BARHL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for BARHL1 Gene

mRNA differential expression in normal tissues according to GTEx for BARHL1 Gene

This gene is overexpressed in Brain - Cerebellum (x24.9) and Brain - Cerebellar Hemisphere (x24.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for BARHL1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for BARHL1

SOURCE GeneReport for Unigene cluster for BARHL1 Gene:


Evidence on tissue expression from TISSUES for BARHL1 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with BARHL1: view

Primer products for research

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for BARHL1 Gene

Orthologs for BARHL1 Gene

This gene was present in the common ancestor of animals.

Orthologs for BARHL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BARHL1 29 30
  • 99.69 (n)
(Canis familiaris)
Mammalia BARHL1 29 30
  • 95.62 (n)
(Bos Taurus)
Mammalia BARHL1 29 30
  • 94.39 (n)
(Mus musculus)
Mammalia Barhl1 29 16 30
  • 93.17 (n)
(Rattus norvegicus)
Mammalia Barhl1 29
  • 92.46 (n)
(Monodelphis domestica)
Mammalia BARHL1 30
  • 71 (a)
(Gallus gallus)
Aves BARHL1 29
  • 79.63 (n)
(Anolis carolinensis)
Reptilia -- 30
  • 71 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia barhl1 29
  • 76.23 (n)
African clawed frog
(Xenopus laevis)
Amphibia barh2-A-prov 29
(Danio rerio)
Actinopterygii barhl1a 30
  • 79 (a)
barhl1b 29 30
  • 73.23 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta B-H1 31
  • 68 (a)
B-H2 31
  • 62 (a)
CG11085 30
  • 24 (a)
(Caenorhabditis elegans)
Secernentea ceh-30 30
  • 35 (a)
ceh-31 30
  • 30 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 40 (a)
Species where no ortholog for BARHL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for BARHL1 Gene

Gene Tree for BARHL1 (if available)
Gene Tree for BARHL1 (if available)
Evolutionary constrained regions (ECRs) for BARHL1: view image
Alliance of Genome Resources:
Additional Orthologs for BARHL1

Paralogs for BARHL1 Gene

Paralogs for BARHL1 Gene

(7) SIMAP similar genes for BARHL1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with BARHL1: view

Variants for BARHL1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for BARHL1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Variation tolerance for BARHL1 Gene

Residual Variation Intolerance Score: 19.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.46; 9.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BARHL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Structural Variations from Database of Genomic Variants (DGV) for BARHL1 Gene

Disorders for BARHL1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for BARHL1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
cataract 34, multiple types
  • ctrct34
  • mdb
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for BARHL1

genes like me logo Genes that share disorders with BARHL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BARHL1 Gene

Publications for BARHL1 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  2. Barhl1, a gene belonging to a new subfamily of mammalian homeobox genes, is expressed in migrating neurons of the CNS. (PMID: 10814725) Bulfone A … Banfi S (Human molecular genetics 2000) 3 4
  3. Impact of cytosine methylation on DNA binding specificities of human transcription factors. (PMID: 28473536) Yin Y … Taipale J (Science (New York, N.Y.) 2017) 3
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3
  5. Expression of BARHL1 in medulloblastoma is associated with prolonged survival in mice and humans. (PMID: 21602885) Pöschl J … Schüller U (Oncogene 2011) 3

Products for BARHL1 Gene

Sources for BARHL1 Gene