Mouse Gene Lhx8 (ENSMUST00000205251.2) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Nucleus (By similarity). (from UniProt H3BJ54)
Gencode Transcript: ENSMUST00000205251.2
Gencode Gene: ENSMUSG00000096225.7
Transcript (Including UTRs)
   Position: mm10 chr3:154,306,296-154,330,059 Size: 23,764 Total Exon Count: 9 Strand: -
Coding Region
   Position: mm10 chr3:154,306,933-154,328,429 Size: 21,497 Coding Exon Count: 8 

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 (chr3:154,306,296-154,330,059)mRNA (may differ from genome)Protein (346 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsMGIPubMed
SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: H3BJ54_MOUSE
DESCRIPTION: SubName: Full=LIM/homeobox protein Lhx8;
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SIMILARITY: Contains 2 LIM zinc-binding domains.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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 -17.9051-0.351 Picture PostScript Text
3' UTR -143.10637-0.225 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
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR001781 - Znf_LIM

Pfam Domains:
PF00046 - Homeobox domain
PF00412 - LIM domain
PF05920 - Homeobox KN domain

SCOP Domains:
46689 - Homeodomain-like
57716 - Glucocorticoid receptor-like (DNA-binding domain)

ModBase Predicted Comparative 3D Structure on H3BJ54
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
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
 RGDEnsembl   
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0007611 learning or memory
GO:0008585 female gonad development
GO:0021879 forebrain neuron differentiation
GO:0021884 forebrain neuron development
GO:0042475 odontogenesis of dentin-containing tooth

Cellular Component:
GO:0001674 female germ cell nucleus
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK165733 - Mus musculus adult male accessory axillary lymph node cDNA, RIKEN full-length enriched library, clone:G630032N03 product:LIM homeobox protein 8, full insert sequence.
AK160121 - Mus musculus whole joints cDNA, RIKEN full-length enriched library, clone:L230001B22 product:LIM homeobox protein 8, full insert sequence.
D49658 - Mus musculus mRNA for LIM-homeodomain protein, partial cds.
AJ000338 - Mus musculus mRNA for putative transcriptional regulator Lhx7.
BC125281 - Mus musculus LIM homeobox protein 8, mRNA (cDNA clone MGC:158984 IMAGE:40129796), complete cds.
BC144768 - Mus musculus LIM homeobox protein 8, mRNA (cDNA clone MGC:178324 IMAGE:9053316), complete cds.
BC125283 - Mus musculus LIM homeobox protein 8, mRNA (cDNA clone MGC:158986 IMAGE:40129798), complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: AK165733, H3BJ54, H3BJ54_MOUSE, uc290kta.1
UCSC ID: uc290kta.1
RefSeq Accession: NM_010713
Protein: H3BJ54

-  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.