Mouse Gene Barhl2 (ENSMUST00000086795.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus BarH like homeobox 2 (Barhl2), mRNA. (from RefSeq NM_001005477)
Gencode Transcript: ENSMUST00000086795.7
Gencode Gene: ENSMUSG00000034384.11
Transcript (Including UTRs)
   Position: mm10 chr5:106,452,523-106,458,166 Size: 5,644 Total Exon Count: 3 Strand: -
Coding Region
   Position: mm10 chr5:106,453,357-106,457,841 Size: 4,485 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr5:106,452,523-106,458,166)mRNA (may differ from genome)Protein (384 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=BarH-like 2 homeobox protein; AltName: Full=Bar-class homeodomain protein MBH1; AltName: Full=Homeobox protein B-H1;
FUNCTION: Potential regulator of neural basic helix-loop-helix genes. It may down-regulate expression of ASCL1 and, within the thalamus, up-regulate NGN2, thereby regulating distinct patterns of neuronal differentiation (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Belongs to the BAR homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.

-  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

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -114.80325-0.353 Picture PostScript Text
3' UTR -235.00834-0.282 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

Pfam Domains:
PF00046 - Homeobox domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on Q8VIB5
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0001709 cell fate determination
GO:0001764 neuron migration
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0030182 neuron differentiation
GO:0030516 regulation of axon extension
GO:0045165 cell fate commitment
GO:0045727 positive regulation of translation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  BC078444 - Mus musculus BarH-like 2 (Drosophila), mRNA (cDNA clone MGC:90874 IMAGE:5688311), complete cds.
AK053799 - Mus musculus 0 day neonate eyeball cDNA, RIKEN full-length enriched library, clone:E130309B19 product:HOMEOBOX PROTEIN B-H1 (HOMEOBOX PROTEIN MBH1) homolog [Rattus norvegicus], full insert sequence.
BC055789 - Mus musculus BarH-like 2 (Drosophila), mRNA (cDNA clone IMAGE:6409990), partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: Barh1, BARH2_MOUSE, Mbh1, NM_001005477, Q66L43, Q8VIB5, uc008ylm.1
UCSC ID: uc008ylm.1
RefSeq Accession: NM_001005477
Protein: Q8VIB5 (aka BARH2_MOUSE or BRH2_MOUSE)
CCDS: CCDS19497.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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