Human Gene LHX2 (ENST00000373615.9) from GENCODE V44
  Description: Homo sapiens LIM homeobox 2 (LHX2), mRNA. (from RefSeq NM_004789)
RefSeq Summary (NM_004789): This gene encodes a protein belonging to a large protein family, members of which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein may function as a transcriptional regulator. The protein can recapitulate or rescue phenotypes in Drosophila caused by a related protein, suggesting conservation of function during evolution. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000373615.9
Gencode Gene: ENSG00000106689.11
Transcript (Including UTRs)
   Position: hg38 chr9:124,011,768-124,033,301 Size: 21,534 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg38 chr9:124,012,349-124,032,707 Size: 20,359 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:124,011,768-124,033,301)mRNA (may differ from genome)Protein (406 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LHX2_HUMAN
DESCRIPTION: RecName: Full=LIM/homeobox protein Lhx2; Short=Homeobox protein LH-2; Short=LIM homeobox protein 2;
FUNCTION: Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types (By similarity).
SUBUNIT: interacts (via LIM domains) with CITED2 (By similarity).
SUBCELLULAR LOCATION: Nucleus (Probable).
DOMAIN: LIM domains are necessary for transcription activation (By similarity).
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SIMILARITY: Contains 2 LIM zinc-binding domains.
SEQUENCE CAUTION: Sequence=BAC04371.1; Type=Erroneous initiation;

-  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: LHX2
Diseases sorted by gene-association score: schizencephaly (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.58 RPKM in Brain - Anterior cingulate cortex (BA24)
Total median expression: 198.25 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 -336.50581-0.579 Picture PostScript Text
3' UTR -117.00594-0.197 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

ModBase Predicted Comparative 3D Structure on P50458
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001076 transcription factor activity, RNA polymerase II transcription factor binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0001843 neural tube closure
GO:0001942 hair follicle development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007399 nervous system development
GO:0007411 axon guidance
GO:0007420 brain development
GO:0007498 mesoderm development
GO:0009953 dorsal/ventral pattern formation
GO:0021537 telencephalon development
GO:0021772 olfactory bulb development
GO:0021978 telencephalon regionalization
GO:0021987 cerebral cortex development
GO:0022008 neurogenesis
GO:0030182 neuron differentiation
GO:0045199 maintenance of epithelial cell apical/basal polarity
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048646 anatomical structure formation involved in morphogenesis
GO:0048675 axon extension
GO:0060041 retina development in camera-type eye
GO:2000678 negative regulation of transcription regulatory region DNA binding

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK027597 - Homo sapiens cDNA FLJ14691 fis, clone NT2RP2005325, highly similar to LIM/homeobox protein Lhx2.
JD133411 - Sequence 114435 from Patent EP1572962.
BC034458 - Homo sapiens LIM homeobox 2, mRNA (cDNA clone IMAGE:5180630).
U11701 - Human LIM-homeobox domain protein (hLH-2) mRNA, complete cds.
JD191327 - Sequence 172351 from Patent EP1572962.
JD125112 - Sequence 106136 from Patent EP1572962.
JD406213 - Sequence 387237 from Patent EP1572962.
BC112185 - Homo sapiens LIM homeobox 2, mRNA (cDNA clone MGC:138390 IMAGE:8327653), complete cds.
BC093662 - Homo sapiens LIM homeobox 2, mRNA (cDNA clone MGC:120697 IMAGE:7939507), complete cds.
AB527955 - Synthetic construct DNA, clone: pF1KB7676, Homo sapiens LHX2 gene for LIM homeobox 2, without stop codon, in Flexi system.
EU446687 - Synthetic construct Homo sapiens clone IMAGE:100069986; IMAGE:100011896; FLH257175.01L LIM homeobox 2 (LHX2) gene, encodes complete protein.
AK094511 - Homo sapiens cDNA FLJ37192 fis, clone BRALZ2003525, highly similar to LIM/HOMEOBOX PROTEIN LHX2.
AF124735 - Homo sapiens LIM-homeodomain protein HLHX2 (LHX2) mRNA, complete cds.
JD174240 - Sequence 155264 from Patent EP1572962.
JD564610 - Sequence 545634 from Patent EP1572962.
JD048876 - Sequence 29900 from Patent EP1572962.
JD137338 - Sequence 118362 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P50458 (Reactome details) participates in the following event(s):

R-HSA-9011074 LHX2 binds to ROBO1 gene locus
R-HSA-9011077 LHX2 binds to ROBO2 gene locus
R-HSA-9011145 LHX2,(LHX9) binds the ROBO3 gene promoter
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-376176 Signaling by ROBO receptors
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000373615.1, ENST00000373615.2, ENST00000373615.3, ENST00000373615.4, ENST00000373615.5, ENST00000373615.6, ENST00000373615.7, ENST00000373615.8, LH2, LHX2_HUMAN, NM_004789, O95860, P50458, Q52M57, Q8N1Z3, uc004boe.1, uc004boe.2, uc004boe.3
UCSC ID: ENST00000373615.9
RefSeq Accession: NM_004789
Protein: P50458 (aka LHX2_HUMAN)
CCDS: CCDS6853.1

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