Human Gene BARX2 (ENST00000281437.6) from GENCODE V44
  Description: Homo sapiens BARX homeobox 2 (BARX2), mRNA. (from RefSeq NM_003658)
RefSeq Summary (NM_003658): This gene encodes a member of the homeobox transcription factor family. A highly related protein in mouse has been shown to influence cellular processes that control cell adhesion and remodeling of the actin cytoskeleton in myoblast fusion and chondrogenesis. The encoded protein may also play a role in cancer progression. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000281437.6
Gencode Gene: ENSG00000043039.7
Transcript (Including UTRs)
   Position: hg38 chr11:129,375,848-129,452,279 Size: 76,432 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr11:129,376,036-129,451,402 Size: 75,367 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:129,375,848-129,452,279)mRNA (may differ from genome)Protein (279 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BARX2_HUMAN
DESCRIPTION: RecName: Full=Homeobox protein BarH-like 2;
FUNCTION: Transcription factor. Binds optimally to the DNA consensus sequence 5'-YYTAATGRTTTTY-3'. May control the expression of neural adhesion molecules such as L1 or Ng-CAM during embryonic development of both the central and peripherical nervous system. May be involved in controlling adhesive processes in keratinizing epithelia (By similarity).
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Highly expressed in adult salivary gland and at much lower levels in mammary gland, kidney and placenta.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the BAR homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAC04705.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAC04705.1; Type=Frameshift; Positions=11; Sequence=AAF09453.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAF09453.1; Type=Frameshift; Positions=11;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 55.23 RPKM in Esophagus - Mucosa
Total median expression: 166.10 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -104.70188-0.557 Picture PostScript Text
3' UTR -292.70877-0.334 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017970 - Homeobox_CS
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR000047 - HTH_motif

Pfam Domains:
PF00046 - Homeobox domain

ModBase Predicted Comparative 3D Structure on Q9UMQ3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001502 cartilage condensation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0014902 myotube differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0007399 nervous system development

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AF031924 - Homo sapiens homeobox transcription factor barx2 (BARX2) mRNA, complete cds.
JD117452 - Sequence 98476 from Patent EP1572962.
BC069378 - Homo sapiens BARX homeobox 2, mRNA (cDNA clone MGC:96985 IMAGE:7262194), complete cds.
BC111432 - Homo sapiens BARX homeobox 2, mRNA (cDNA clone MGC:133368 IMAGE:40069348), complete cds.
BC111572 - Homo sapiens BARX homeobox 2, mRNA (cDNA clone MGC:133369 IMAGE:40069358), complete cds.
JD464925 - Sequence 445949 from Patent EP1572962.
JD151872 - Sequence 132896 from Patent EP1572962.
AJ243512 - Homo sapiens mRNA for Barx2 protein (Barx2 gene).
AB527829 - Synthetic construct DNA, clone: pF1KB7570, Homo sapiens BARX2 gene for BARX homeobox 2, without stop codon, in Flexi system.
DQ577116 - Homo sapiens piRNA piR-45228, complete sequence.
AK022187 - Homo sapiens cDNA FLJ12125 fis, clone MAMMA1000155.
JD214164 - Sequence 195188 from Patent EP1572962.
JD068328 - Sequence 49352 from Patent EP1572962.
JD217298 - Sequence 198322 from Patent EP1572962.
JD139662 - Sequence 120686 from Patent EP1572962.
JD037997 - Sequence 19021 from Patent EP1572962.
JD165495 - Sequence 146519 from Patent EP1572962.
JD477566 - Sequence 458590 from Patent EP1572962.
JD346795 - Sequence 327819 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BARX2_HUMAN, ENST00000281437.1, ENST00000281437.2, ENST00000281437.3, ENST00000281437.4, ENST00000281437.5, NM_003658, O43518, Q6NT51, Q9UMQ3, uc001qfc.1, uc001qfc.2, uc001qfc.3, uc001qfc.4, uc001qfc.5, uc001qfc.6
UCSC ID: ENST00000281437.6
RefSeq Accession: NM_003658
Protein: Q9UMQ3 (aka BARX2_HUMAN or BRX2_HUMAN)
CCDS: CCDS8481.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.