Mouse Gene Lhx1 (ENSMUST00000018842.13) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus LIM homeobox protein 1 (Lhx1), mRNA. (from RefSeq NM_008498)
Gencode Transcript: ENSMUST00000018842.13
Gencode Gene: ENSMUSG00000018698.15
Transcript (Including UTRs)
   Position: mm10 chr11:84,518,284-84,525,535 Size: 7,252 Total Exon Count: 5 Strand: -
Coding Region
   Position: mm10 chr11:84,519,549-84,524,175 Size: 4,627 Coding Exon Count: 5 

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 (chr11:84,518,284-84,525,535)mRNA (may differ from genome)Protein (406 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI

-  Comments and Description Text from UniProtKB
  ID: Q569N5_MOUSE
DESCRIPTION: SubName: Full=LIM homeobox protein 1; SubName: Full=Lhx1 protein;
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SIMILARITY: Contains 2 LIM zinc-binding domains.

-  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 -507.881360-0.373 Picture PostScript Text
3' UTR -314.701265-0.249 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 Q569N5
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 orthologGenome BrowserGenome BrowserNo ortholog
 Protein Sequence Protein SequenceProtein Sequence 
 Alignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0001655 urogenital system development
GO:0001656 metanephros development
GO:0001657 ureteric bud development
GO:0001658 branching involved in ureteric bud morphogenesis
GO:0001702 gastrulation with mouth forming second
GO:0001705 ectoderm formation
GO:0001706 endoderm formation
GO:0001822 kidney development
GO:0001823 mesonephros development
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007267 cell-cell signaling
GO:0007389 pattern specification process
GO:0008045 motor neuron axon guidance
GO:0009653 anatomical structure morphogenesis
GO:0009791 post-embryonic development
GO:0009880 embryonic pattern specification
GO:0009948 anterior/posterior axis specification
GO:0009952 anterior/posterior pattern specification
GO:0009953 dorsal/ventral pattern formation
GO:0010468 regulation of gene expression
GO:0010842 retina layer formation
GO:0021510 spinal cord development
GO:0021517 ventral spinal cord development
GO:0021527 spinal cord association neuron differentiation
GO:0021537 telencephalon development
GO:0021549 cerebellum development
GO:0021702 cerebellar Purkinje cell differentiation
GO:0021871 forebrain regionalization
GO:0021937 cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation
GO:0032525 somite rostral/caudal axis specification
GO:0035502 metanephric part of ureteric bud development
GO:0035846 oviduct epithelium development
GO:0035847 uterine epithelium development
GO:0035849 nephric duct elongation
GO:0035852 horizontal cell localization
GO:0040019 positive regulation of embryonic development
GO:0044344 cellular response to fibroblast growth factor stimulus
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0048646 anatomical structure formation involved in morphogenesis
GO:0048703 embryonic viscerocranium morphogenesis
GO:0048793 pronephros development
GO:0060041 retina development in camera-type eye
GO:0060059 embryonic retina morphogenesis in camera-type eye
GO:0060065 uterus development
GO:0060066 oviduct development
GO:0060067 cervix development
GO:0060068 vagina development
GO:0060322 head development
GO:0060429 epithelium development
GO:0061205 paramesonephric duct development
GO:0072001 renal system development
GO:0072049 comma-shaped body morphogenesis
GO:0072050 S-shaped body morphogenesis
GO:0072077 renal vesicle morphogenesis
GO:0072164 mesonephric tubule development
GO:0072177 mesonephric duct development
GO:0072178 nephric duct morphogenesis
GO:0072224 metanephric glomerulus development
GO:0072278 metanephric comma-shaped body morphogenesis
GO:0072283 metanephric renal vesicle morphogenesis
GO:0072284 metanephric S-shaped body morphogenesis
GO:0090009 primitive streak formation
GO:0090190 positive regulation of branching involved in ureteric bud morphogenesis
GO:0097477 lateral motor column neuron migration
GO:2000543 positive regulation of gastrulation
GO:2000744 positive regulation of anterior head development
GO:2000768 positive regulation of nephron tubule epithelial cell differentiation

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0032991 macromolecular complex

-  Descriptions from all associated GenBank mRNAs
  LF198743 - JP 2014500723-A/6246: Polycomb-Associated Non-Coding RNAs.
AK141086 - Mus musculus 0 day neonate cerebellum cDNA, RIKEN full-length enriched library, clone:C230045C03 product:LIM homeobox protein 1, full insert sequence.
AK032067 - Mus musculus adult male medulla oblongata cDNA, RIKEN full-length enriched library, clone:6330569O10 product:LIM homeobox protein 1, full insert sequence.
AK049786 - Mus musculus 12 days embryo spinal cord cDNA, RIKEN full-length enriched library, clone:C530049N19 product:hypothetical protein, full insert sequence.
AK080848 - Mus musculus adult male corpora quadrigemina cDNA, RIKEN full-length enriched library, clone:B230369I01 product:LIM homeobox protein 1, full insert sequence.
Z27410 - M.musculus lim1 mRNA for putative transcription regulator.
LF203897 - JP 2014500723-A/11400: Polycomb-Associated Non-Coding RNAs.
BC092374 - Mus musculus LIM homeobox protein 1, mRNA (cDNA clone MGC:90731 IMAGE:30363447), complete cds.
S68107 - Mus sp. lateral and intermediate mesoderm differentiation and neurogenesis protein (Lim-1) mRNA, complete cds.
LF229497 - JP 2014500723-A/37000: Polycomb-Associated Non-Coding RNAs.
LF203045 - JP 2014500723-A/10548: Polycomb-Associated Non-Coding RNAs.
MA434320 - JP 2018138019-A/6246: Polycomb-Associated Non-Coding RNAs.
MA439474 - JP 2018138019-A/11400: Polycomb-Associated Non-Coding RNAs.
MA465074 - JP 2018138019-A/37000: Polycomb-Associated Non-Coding RNAs.
MA438622 - JP 2018138019-A/10548: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: mCG_11270, NM_008498, Q569N5, Q569N5_MOUSE, RP23-381C21.1-001, uc007kqo.1, uc007kqo.2
UCSC ID: uc007kqo.2
RefSeq Accession: NM_008498
Protein: Q569N5 CCDS: CCDS25187.1

-  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.