Human Gene LBX1 (ENST00000370193.4_6) from GENCODE V47lift37
  Description: ladybird homeobox 1 (from RefSeq NM_006562.5)
Gencode Transcript: ENST00000370193.4_6
Gencode Gene: ENSG00000138136.7_8
Transcript (Including UTRs)
   Position: hg19 chr10:102,986,751-102,989,220 Size: 2,470 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr10:102,987,027-102,988,572 Size: 1,546 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:102,986,751-102,989,220)mRNA (may differ from genome)Protein (281 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LBX1_HUMAN
DESCRIPTION: RecName: Full=Transcription factor LBX1; AltName: Full=Ladybird homeobox protein homolog 1;
FUNCTION: Transcription factor required for the development of GABAergic interneurons in the dorsal horn of the spinal cord and migration and further development of hypaxial muscle precursor cells for limb muscles, diaphragm and hypoglossal cord (By similarity).
SUBUNIT: Interacts with SKOR1 which acts as a transcriptional corepressor (By similarity).
SUBCELLULAR LOCATION: Nucleus (Probable).
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


-  MalaCards Disease Associations
  MalaCards Gene Search: LBX1
Diseases sorted by gene-association score: idiopathic scoliosis (10), adolescent idiopathic scoliosis (9), split-hand/foot malformation 3 (7), split hand-split foot malformation (6), cryptorchidism (6), split foot (6), agnathia-otocephaly complex (4), bone structure disease (4), scoliosis (3)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.29 RPKM in Muscle - Skeletal
Total median expression: 4.64 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 -272.67648-0.421 Picture PostScript Text
3' UTR -109.40276-0.396 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
IPR000047 - HTH_motif

Pfam Domains:
PF00046 - Homeodomain

SCOP Domains:
46689 - Homeodomain-like
88659 - Sigma3 and sigma4 domains of RNA polymerase sigma factors

ModBase Predicted Comparative 3D Structure on P52954
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0001947 heart looping
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0007517 muscle organ development
GO:0008285 negative regulation of cell proliferation
GO:0009653 anatomical structure morphogenesis
GO:0021522 spinal cord motor neuron differentiation
GO:0021920 regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification
GO:0030154 cell differentiation
GO:0045665 negative regulation of neuron differentiation
GO:0048663 neuron fate commitment
GO:0048664 neuron fate determination

Cellular Component:
GO:0005634 nucleus
GO:0005667 transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  LF211347 - JP 2014500723-A/18850: Polycomb-Associated Non-Coding RNAs.
LF212793 - JP 2014500723-A/20296: Polycomb-Associated Non-Coding RNAs.
BC069156 - Homo sapiens ladybird homeobox 1, mRNA (cDNA clone MGC:95442 IMAGE:7217017), complete cds.
X90828 - H.sapiens mRNA for transcription factor, Lbx1.
JD405085 - Sequence 386109 from Patent EP1572962.
BC136321 - Homo sapiens ladybird homeobox 1, mRNA (cDNA clone MGC:167931 IMAGE:9020308), complete cds.
JD255500 - Sequence 236524 from Patent EP1572962.
JD071897 - Sequence 52921 from Patent EP1572962.
JD139042 - Sequence 120066 from Patent EP1572962.
LF345789 - JP 2014500723-A/153292: Polycomb-Associated Non-Coding RNAs.
AJ004949 - Homo sapiens mRNA for homeobox protein, partial, clone h5.
X74863 - H.sapiens HPX-6 mRNA.
LF345790 - JP 2014500723-A/153293: Polycomb-Associated Non-Coding RNAs.
JD406817 - Sequence 387841 from Patent EP1572962.
MA581366 - JP 2018138019-A/153292: Polycomb-Associated Non-Coding RNAs.
MA581367 - JP 2018138019-A/153293: Polycomb-Associated Non-Coding RNAs.
MA446924 - JP 2018138019-A/18850: Polycomb-Associated Non-Coding RNAs.
MA448370 - JP 2018138019-A/20296: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B9EGA2, ENST00000370193.1, ENST00000370193.2, ENST00000370193.3, LBX1H, LBX1_HUMAN, NM_006562, P52954, Q05BB2, uc318iei.1, uc318iei.2
UCSC ID: ENST00000370193.4_6
RefSeq Accession: NM_006562.5
Protein: P52954 (aka LBX1_HUMAN)

-  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.