Human Gene LHX3 (ENST00000371748.10_9) from GENCODE V47lift37

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Description: LIM homeobox 3, transcript variant 1 (from RefSeq NM_178138.6)
Gencode Transcript: ENST00000371748.10_9
Gencode Gene: ENSG00000107187.17_12
Transcript (Including UTRs)
Position: hg19 chr9:139,088,096-139,096,974 Size: 8,879 Total Exon Count: 6 Strand: -
Coding Region
Position: hg19 chr9:139,089,171-139,096,858 Size: 7,688 Coding Exon Count: 6

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr9:139,088,096-139,096,974)			mRNA (may differ from genome)		Protein (397 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: LHX3_HUMAN DESCRIPTION: RecName: Full=LIM/homeobox protein Lhx3; Short=LIM homeobox protein 3; FUNCTION: Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with Pit-1 (By similarity). SUBCELLULAR LOCATION: Nucleus (Probable). DOMAIN: The LIM domain specifically interacts with the Pit-1 POU domain and is required for synergistic interactions with Pit-1, but not for basal transcriptional activation events (By similarity). DISEASE: Defects in LHX3 are the cause of pituitary hormone deficiency combined type 3 (CPHD3) [MIM:221750]; also known as combined pituitary hormone deficiency with rigid cervical spine or sensorineural deafness with pituitary dwarfism. CPHD is characterized by a complete deficit in all but one (adrenocorticotropin) anterior pituitary hormone and a rigid cervical spine leading to limited head rotation. SIMILARITY: Contains 1 homeobox DNA-binding domain. SIMILARITY: Contains 2 LIM zinc-binding domains. WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LHX3";

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: LHX3 Diseases sorted by gene-association score: pituitary hormone deficiency, combined, 3* (1580), lhx3-related combined pituitary hormone deficiency* (500), hypothyroidism due to deficient transcription factors involved in pituitary development or function* (175), combined pituitary hormone deficiency (23), septooptic dysplasia (17), hypopituitarism (17), neonatal thyrotoxicosis (11), pituitary hypoplasia (11), pituitary hormone deficiency, combined, 2 (11), pituitary gland disease (9), borjeson-forssman-lehmann syndrome (8), isolated growth hormone deficiency (7), deafness, autosomal dominant 15 (6), acth deficiency (5), kallmann syndrome (3) * = Manually curated disease association

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D001564 Benzo(a)pyrene C009505 4,4'-diaminodiphenylmethane C547126 AZM551248 D002509 Cephaloridine D002794 Choline D019327 Copper Sulfate D005492 Folic Acid D005839 Gentamicins D008715 Methionine D013749 Tetrachlorodibenzodioxin more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 53.26 RPKM in Pituitary Total median expression: 53.57 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-62.00	116	-0.534	Picture	PostScript	Text
3' UTR	-433.00	1075	-0.403	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 - Homeodomain
PF00412 - LIM domain

SCOP Domains:
48695 - Multiheme cytochromes
46689 - Homeodomain-like
57716 - Glucocorticoid receptor-like (DNA-binding domain)

ModBase Predicted Comparative 3D Structure on Q9UBR4


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

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:0001085 RNA polymerase II transcription factor binding GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding GO:0003677 DNA binding GO:0043565 sequence-specific DNA binding GO:0046872 metal ion binding Biological Process: GO:0001890 placenta development GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0006366 transcription from RNA polymerase II promoter GO:0008045 motor neuron axon guidance GO:0009887 animal organ morphogenesis GO:0009953 dorsal/ventral pattern formation GO:0021520 spinal cord motor neuron cell fate specification GO:0021521 ventral spinal cord interneuron specification GO:0021526 medial motor column neuron differentiation GO:0021527 spinal cord association neuron differentiation GO:0021983 pituitary gland development GO:0030154 cell differentiation GO:0030324 lung development GO:0043066 negative regulation of apoptotic process GO:0045893 positive regulation of transcription, DNA-templated GO:0045944 positive regulation of transcription from RNA polymerase II promoter GO:0048839 inner ear development Cellular Component: GO:0005622 intracellular GO:0005634 nucleus GO:0005667 transcription factor complex

Descriptions from all associated GenBank mRNAs


	AB593064 - Homo sapiens LHX3 mRNA for LIM/homeobox protein Lhx3, complete cds, clone: HP05297-RBd31E04. AB593065 - Homo sapiens LHX3 mRNA for LIM/homeobox protein Lhx3, complete cds, clone: HP05297-RBd40E03. AB593066 - Homo sapiens LHX3 mRNA for LIM/homeobox protein Lhx3, complete cds, clone: HP05297-RBd68D07. AB593067 - Homo sapiens LHX3 mRNA for LIM/homeobox protein Lhx3, complete cds, clone: HP05297-RBd88E01. AB593063 - Homo sapiens LHX3 mRNA for LIM/homeobox protein Lhx3, complete cds, clone: HP05297-RBd23B02. AB593062 - Homo sapiens LHX3 mRNA for LIM/homeobox protein Lhx3, complete cds, clone: HP05297-RBb10F05. AF156889 - Homo sapiens LIM homeobox protein 3 isoform b (LHX3) mRNA, complete cds. AF156888 - Homo sapiens LIM homeobox protein 3 isoform a (LHX3) mRNA, complete cds. JD325005 - Sequence 306029 from Patent EP1572962. JD399642 - Sequence 380666 from Patent EP1572962. JD070927 - Sequence 51951 from Patent EP1572962. JD260339 - Sequence 241363 from Patent EP1572962. JD394439 - Sequence 375463 from Patent EP1572962. JD515451 - Sequence 496475 from Patent EP1572962. JD195782 - Sequence 176806 from Patent EP1572962. JD418284 - Sequence 399308 from Patent EP1572962. JD252921 - Sequence 233945 from Patent EP1572962. JD311078 - Sequence 292102 from Patent EP1572962. JD259534 - Sequence 240558 from Patent EP1572962. JD132876 - Sequence 113900 from Patent EP1572962. JD075696 - Sequence 56720 from Patent EP1572962. JD076541 - Sequence 57565 from Patent EP1572962. JD431722 - Sequence 412746 from Patent EP1572962. JD084876 - Sequence 65900 from Patent EP1572962. JD304833 - Sequence 285857 from Patent EP1572962. JD431913 - Sequence 412937 from Patent EP1572962. JD439397 - Sequence 420421 from Patent EP1572962. JD259659 - Sequence 240683 from Patent EP1572962. JD451065 - Sequence 432089 from Patent EP1572962. JD415439 - Sequence 396463 from Patent EP1572962. AF096169 - Homo sapiens LHX3 protein mRNA, partial cds. JD260882 - Sequence 241906 from Patent EP1572962. JD057411 - Sequence 38435 from Patent EP1572962. JD088393 - Sequence 69417 from Patent EP1572962. BC152818 - Synthetic construct Homo sapiens clone IMAGE:100016058, MGC:184146 LIM homeobox 3 (LHX3) mRNA, encodes complete protein. BC156735 - Synthetic construct Homo sapiens clone IMAGE:100062248, MGC:190219 LIM homeobox 3 (LHX3) mRNA, encodes complete protein. AB590758 - Synthetic construct DNA, clone: pFN21AB9719, Homo sapiens LHX3 gene for LIM homeobox 3, without stop codon, in Flexi system.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q9UBR4 (Reactome details) participates in the following event(s): R-HSA-9010541 ISL1 binds the SLIT2 gene enhancer 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: ENST00000371748.1, ENST00000371748.2, ENST00000371748.3, ENST00000371748.4, ENST00000371748.5, ENST00000371748.6, ENST00000371748.7, ENST00000371748.8, ENST00000371748.9, LHX3_HUMAN, NM_178138, Q5TB39, Q5TB40, Q9NZB5, Q9P0I8, Q9P0I9, Q9UBR4, uc318jjl.1, uc318jjl.2 UCSC ID: ENST00000371748.10_9 RefSeq Accession: NM_178138.6 Protein: Q9UBR4 (aka LHX3_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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