Mouse Gene Barhl1 (ENSMUST00000050776.8) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus BarH like homeobox 1 (Barhl1), transcript variant 1, mRNA. (from RefSeq NM_019446)
Gencode Transcript: ENSMUST00000050776.8
Gencode Gene: ENSMUSG00000026805.14
Transcript (Including UTRs)
   Position: mm10 chr2:28,907,679-28,916,412 Size: 8,734 Total Exon Count: 3 Strand: -
Coding Region
   Position: mm10 chr2:28,909,628-28,915,679 Size: 6,052 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:28,907,679-28,916,412)mRNA (may differ from genome)Protein (327 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: BARH1_MOUSE
DESCRIPTION: RecName: Full=BarH-like 1 homeobox protein; AltName: Full=Bar-class homeodomain protein MBH2; AltName: Full=BarH-related homeobox protein 1;
SUBCELLULAR LOCATION: Nucleus (Probable).
DEVELOPMENTAL STAGE: Exclusively expressed in restricted domains of the developing central nervous system, in particular the diencephalon and rhombencephalon, where it is expressed in migrating cells giving rise to the cerebellar external granular layer and to specific populations of dorsal sensory interneurons of the spinal cord.
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           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -328.40733-0.448 Picture PostScript Text
3' UTR -750.701949-0.385 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 P63157
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  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:0043565 sequence-specific DNA binding

Biological Process:
GO:0001764 neuron migration
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007605 sensory perception of sound
GO:0030901 midbrain development
GO:0043524 negative regulation of neuron apoptotic process
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK036312 - Mus musculus 16 days neonate cerebellum cDNA, RIKEN full-length enriched library, clone:9630055M08 product:BARHL1 PROTEIN (BAR-CLASS HOMEODOMAIN PROTEIN MBH2) (BARH-RELATED HOMEOBOX PROTEIN 1 BHX1) homolog [Mus musculus], full insert sequence.
AK048063 - Mus musculus 16 days embryo head cDNA, RIKEN full-length enriched library, clone:C130032L02 product:BARHL1 PROTEIN (FRAGMENT) homolog [Homo sapiens], full insert sequence.
AB043980 - Mus musculus mbh2 mRNA for Bar-class homeodomain protein MBH2, complete cds.
BC055731 - Mus musculus BarH-like 1 (Drosophila), mRNA (cDNA clone MGC:66954 IMAGE:6413504), complete cds.
AF264026 - Mus musculus barH-related homeobox protein 1 BHX1 (Bhx1) mRNA, complete cds.
AK082610 - Mus musculus 0 day neonate cerebellum cDNA, RIKEN full-length enriched library, clone:C230069A10 product:Mus musculus barH-related homeobox protein 1 BHX1 (Bhx1) mRNA, full insert sequence.
AJ237590 - Mus musculus mRNA for BARHL1 protein.

-  Other Names for This Gene
  Alternate Gene Symbols: BARH1_MOUSE, Bhx1, Mbh2, NM_019446, P63157, Q9JK26, uc008izh.1, uc008izh.2, uc008izh.3
UCSC ID: uc008izh.3
RefSeq Accession: NM_019446
Protein: P63157 (aka BARH1_MOUSE or BRH1_MOUSE)
CCDS: CCDS15849.1

-  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.