BARX1 Gene (Protein Coding)

BARX Homeobox 1

GC09M093951
GIFtS:
38
This gene encodes a member of the Bar subclass of homeobox transcription factors. Studies of the mouse and chick homolog suggest the encoded protein may play a role in developing teeth and craniofacial mesenchyme of neural crest origin. The protein may also be associated with differentiation of stomach epithelia. [provided by RefSeq, Jul 2008] See more...

Aliases for BARX1 Gene

Aliases for BARX1 Gene

  • BARX Homeobox 1 2 3 5
  • Homeobox Protein BarH-Like 1 3 4
  • BarH-Like Homeobox 1 2 3
  • BARX1 5

External Ids for BARX1 Gene

Previous GeneCards Identifiers for BARX1 Gene

  • GC09M087540
  • GC09M088441
  • GC09M090013
  • GC09M092055
  • GC09M093793
  • GC09M095753
  • GC09M096713
  • GC09M066390

Summaries for BARX1 Gene

Entrez Gene Summary for BARX1 Gene

  • This gene encodes a member of the Bar subclass of homeobox transcription factors. Studies of the mouse and chick homolog suggest the encoded protein may play a role in developing teeth and craniofacial mesenchyme of neural crest origin. The protein may also be associated with differentiation of stomach epithelia. [provided by RefSeq, Jul 2008]

GeneCards Summary for BARX1 Gene

BARX1 (BARX Homeobox 1) is a Protein Coding gene. Diseases associated with BARX1 include Hernia, Hiatus and Hypertrophic Pyloric Stenosis. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is BARX2.

UniProtKB/Swiss-Prot Summary for BARX1 Gene

  • Transcription factor, which is involved in craniofacial development, in odontogenesis and in stomach organogenesis. May have a role in the differentiation of molars from incisors. Plays a role in suppressing endodermal Wnt activity (By similarity). Binds to a regulatory module of the NCAM promoter.

Additional gene information for BARX1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for BARX1 Gene

Genomics for BARX1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for BARX1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH09J093954 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 +0.1 56 2.6 ZEB1 ZNF341 KLF9 SP2 KLF16 CBX8 ZBTB21 SP7 PRDM4 L3MBTL2 BARX1-DT PTPDC1 BARX1 HSALNG0072871 HSALNG0072869 PHF2
GH09J094029 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 4.4 -75.7 -75746 3 TBP ZBTB10 SP1 MXD4 MNT SMAD5 MBD2 ZNF217 POLR2A BHLHE40 PTPDC1 HSALNG0072877-001 HSALNG0072877-002 ENSG00000232063 PHF2 BARX1 CYCSP24 LOC107987099
GH09J093685 Enhancer 0.4 Ensembl 17.5 +270.3 270254 1 REST CTCF RAD21 BARX1 BARX1-DT HSALNG0072858 RF00017-7720 PHF2
GH09J093869 Enhancer 0.6 Ensembl CraniofacialAtlas 11.1 +85.7 85695 1.1 PAX8 KDM1A MNT BARX1 BARX1-DT HSALNG0072863 piR-53063-266 PHF2
GH09J093949 Promoter/Enhancer 1.2 Ensembl ENCODE dbSUPER 4.9 +4.8 4846 2.6 IKZF1 ZNF217 ELF1 GABPB1 FOSL1 TCF7L2 JUND ZBTB40 MAX EGR1 HSALNG0072869 PTPDC1 BARX1-DT BARX1 HSALNG0072868 PHF2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BARX1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for BARX1

Top Transcription factor binding sites by QIAGEN in the BARX1 gene promoter:
  • AP-2gamma
  • AREB6
  • c-Myc
  • IRF-1
  • Max1
  • NF-1
  • NF-1/L
  • Nkx2-5
  • RP58
  • STAT5A

Genomic Locations for BARX1 Gene

Latest Assembly
chr9:93,951,627-93,955,355
(GRCh38/hg38)
Size:
3,729 bases
Orientation:
Minus strand

Previous Assembly
chr9:96,713,909-96,717,637
(GRCh37/hg19 by Entrez Gene)
Size:
3,729 bases
Orientation:
Minus strand

chr9:96,713,905-96,717,654
(GRCh37/hg19 by Ensembl)
Size:
3,750 bases
Orientation:
Minus strand

Genomic View for BARX1 Gene

Genes around BARX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BARX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BARX1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for BARX1 Gene

Proteins for BARX1 Gene

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  1. Antibodies for research
  2. Protein products for research
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  • Protein details for BARX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBU1-BARX1_HUMAN
    Recommended name:
    Homeobox protein BarH-like 1
    Protein Accession:
    Q9HBU1
    Secondary Accessions:
    • Q6P2R4
    • Q96GH8

    Protein attributes for BARX1 Gene

    Size:
    254 amino acids
    Molecular mass:
    27298 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAG23738.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for BARX1 Gene

    Alternative splice isoforms for BARX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for BARX1 Gene

Protein Expression for BARX1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for BARX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BARX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for BARX1 Gene

Domains & Families for BARX1 Gene

Gene Families for BARX1 Gene

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

Protein Domains for BARX1 Gene

InterPro:
Blocks:
  • Lambda and other repressor helix-turn-helix signature
ProtoNet:

Suggested Antigen Peptide Sequences for BARX1 Gene

GenScript: Design optimal peptide antigens:
  • Homeobox protein BarH-like 1 (BARX1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9HBU1

UniProtKB/Swiss-Prot:

BARX1_HUMAN :
  • Belongs to the BAR homeobox family.
Family:
  • Belongs to the BAR homeobox family.
genes like me logo Genes that share domains with BARX1: view

Function for BARX1 Gene

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  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for BARX1 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor, which is involved in craniofacial development, in odontogenesis and in stomach organogenesis. May have a role in the differentiation of molars from incisors. Plays a role in suppressing endodermal Wnt activity (By similarity). Binds to a regulatory module of the NCAM promoter.

Phenotypes From GWAS Catalog for BARX1 Gene

Gene Ontology (GO) - Molecular Function for BARX1 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:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity NAS 10995576
genes like me logo Genes that share ontologies with BARX1: view
genes like me logo Genes that share phenotypes with BARX1: view

Animal Models for BARX1 Gene

MGI Knock Outs for BARX1:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for BARX1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for BARX1 Gene

Localization for BARX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BARX1 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
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 BARX1 gene
Compartment Confidence
nucleus 4
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for BARX1 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 BARX1: view

Pathways & Interactions for BARX1 Gene

PathCards logo

SuperPathways for BARX1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for BARX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0007267 cell-cell signaling IEA --
GO:0009888 tissue development IEA --
GO:0009952 anterior/posterior pattern specification IEA --
genes like me logo Genes that share ontologies with BARX1: view

No data available for Pathways by source and SIGNOR curated interactions for BARX1 Gene

Drugs & Compounds for BARX1 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for BARX1 Gene

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  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
  4. Clone products for research

mRNA/cDNA for BARX1 Gene

1 REFSEQ mRNAs :
3 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 BARX1

Alternative Splicing Database (ASD) splice patterns (SP) for BARX1 Gene

No ASD Table

Relevant External Links for BARX1 Gene

GeneLoc Exon Structure for
BARX1

Expression for BARX1 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for BARX1 Gene

mRNA expression in normal human tissues for BARX1 Gene
mRNA expression by GTEx for BARX1 GenemRNA expression by BioGPS for BARX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for BARX1 Gene

This gene is overexpressed in Stomach (x27.6) and Esophagus - Gastroesophageal Junction (x18.3).

Protein differential expression in normal tissues from HIPED for BARX1 Gene

This gene is overexpressed in Heart (42.1) and Fetal gut (26.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for BARX1 Gene



Protein tissue co-expression partners for BARX1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for BARX1

SOURCE GeneReport for Unigene cluster for BARX1 Gene:

Hs.164960

mRNA Expression by UniProt/SwissProt for BARX1 Gene:

Q9HBU1-BARX1_HUMAN
Tissue specificity: Widely expressed. Expressed at higher levels in testis and heart. Detected in craniofacial tissue and adult iris, but not in lymphocytes, fibroblasts, choroid retina, retinal pigment epithelium, kidney, or fetal liver.

Evidence on tissue expression from TISSUES for BARX1 Gene

  • Lung(4.2)
  • Stomach(2.4)
genes like me logo Genes that share expression patterns with BARX1: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for BARX1 Gene

Orthologs for BARX1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for BARX1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia BARX1 30 31
  • 99.44 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia BARX1 30 31
  • 90.16 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia BARX1 30 31
  • 89.76 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Barx1 30
  • 88.58 (n)
Mouse
(Mus musculus)
 Mammalia Barx1 30 17 31
  • 88.06 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia BARX1 31
  • 84 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia BARX1 31
  • 82 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves BARX1 30 31
  • 80.43 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia BARX1 31
  • 73 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia LOC100491751 30
  • 69.1 (n)
Zebrafish
(Danio rerio)
 Actinopterygii barx1 30 31
  • 65.8 (n)
 OneToOne
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 30 (a)
 OneToMany
Species where no ortholog for BARX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for BARX1 Gene

ENSEMBL:
Gene Tree for BARX1 (if available)
TreeFam:
Gene Tree for BARX1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for BARX1: view image

Paralogs for BARX1 Gene

Paralogs for BARX1 Gene

(8) SIMAP similar genes for BARX1 Gene using alignment to 1 proteins:

  • BARX1_HUMAN
genes like me logo Genes that share paralogs with BARX1: view

Variants for BARX1 Gene

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Polymorphic Variants from UniProtKB/Swiss-Prot for BARX1 Gene

BARX1_HUMAN-Q9HBU1
The polymorphism is not associated with Axenfeld-Reiger syndrome (ARS), iridogoniodysgenesis syndrome (IGDS) or related ocular malformations.

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for BARX1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs191789925 - p.Ala48Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for BARX1 Gene

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

Structural Variations from Database of Genomic Variants (DGV) for BARX1 Gene

Variant ID Type Subtype PubMed ID
esv3621110 CNV gain 21293372
nsv1113011 CNV deletion 24896259
nsv509312 CNV insertion 20534489
nsv824993 CNV gain 20364138

Variation tolerance for BARX1 Gene

Gene Damage Index Score: 4.65; 65.75% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BARX1 Gene

Human Gene Mutation Database (HGMD)
BARX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
BARX1

SNP Genotyping and Copy Number Assays for research

Disorders for BARX1 Gene

MalaCards: The human disease database

(13) MalaCards diseases for BARX1 Gene - From: CVR, COP, and GCD

Disorder Aliases PubMed IDs
hernia, hiatus
  • hiatal hernia
hypertrophic pyloric stenosis
  • congenital hypertrophic pyloric stenosis
syngnathia
  • cleft palate-lateral synechia syndrome
pyloric stenosis
witkop syndrome
  • ectodermal dysplasia 3, witkop type; ectd3
- elite association - COSMIC cancer census association via MalaCards
Search BARX1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for BARX1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with BARX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BARX1 Gene

Publications for BARX1 Gene

  1. Cloning, characterization, localization, and mutational screening of the human BARX1 gene. (PMID: 10995576) Gould DB … Walter MA (Genomics 2000) 3 4 23
  2. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 41
  3. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. (PMID: 18978678) Vieira AR … Marazita ML (Genetics in medicine : official journal of the American College of Medical Genetics 2008) 3 41
  4. Genome-wide meta-analysis identifies BARX1 and EML4-MTA3 as new loci associated with infantile hypertrophic pyloric stenosis. (PMID: 30281099) Fadista J … Feenstra B (Human molecular genetics 2019) 3
  5. Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS. (PMID: 29478914) Yamauchi T … Maeda T (Cancer cell 2018) 3

ExternalLinks

View latest publications for BARX1 gene in Mastermind

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Sources for BARX1 Gene