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LHX3 LIM homeobox 3 [ Homo sapiens (human) ]

Gene ID: 8022, updated on 13-Feb-2019

Summary

Official Symbol
LHX3provided by HGNC
Official Full Name
LIM homeobox 3provided by HGNC
Primary source
HGNC:HGNC:6595
See related
Ensembl:ENSG00000107187 MIM:600577
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LIM3; CPHD3; M2-LHX3
Summary
This gene encodes a member of a large family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutations in this gene cause combined pituitary hormone deficiency 3. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See LHX3 in Genome Data Viewer
Location:
9q34.3
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (136196250..136205129, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139088096..139096955, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376323 Neighboring gene uncharacterized LOC107987142 Neighboring gene transmembrane protein 250 Neighboring gene quiescin sulfhydryl oxidase 2 Neighboring gene 9q34.3 QSOX2 distal recombination region Neighboring gene nascent polypeptide-associated complex subunit alpha, muscle-specific form-like

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Pituitary hormone deficiency, combined 3
MedGen: C3489787 OMIM: 221750 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
NHGRI GWA Catalog
A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp762A2013

Gene Ontology Provided by GOA

Process Evidence Code Pubs
animal organ morphogenesis TAS
Traceable Author Statement
more info
PubMed 
inner ear development IEP
Inferred from Expression Pattern
more info
PubMed 
lung development IEA
Inferred from Electronic Annotation
more info
 
medial motor column neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
motor neuron axon guidance IEA
Inferred from Electronic Annotation
more info
 
negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pituitary gland development IEA
Inferred from Electronic Annotation
more info
 
placenta development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
spinal cord association neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
spinal cord motor neuron cell fate specification IEA
Inferred from Electronic Annotation
more info
 
ventral spinal cord interneuron specification IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
LIM/homeobox protein Lhx3
Names
LIM homeobox protein 3
LIM/homeodomain protein LHX3

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008097.1 RefSeqGene

    Range
    4981..13860
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001363746.1NP_001350675.1  LIM/homeobox protein Lhx3 isoform c

    Status: REVIEWED

    Source sequence(s)
    AB593064, AL138781
    Consensus CDS
    CCDS87713.1
    Conserved Domains (4) summary
    cd09376
    Location:79134
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    cd09467
    Location:1771
    LIM1_Lhx3b; The first LIM domain of Lhx3b
    pfam00046
    Location:149202
    Homeobox; Homeobox domain
    pfam04503
    Location:247368
    SSDP; Single-stranded DNA binding protein, SSDP
  2. NM_014564.4NP_055379.1  LIM/homeobox protein Lhx3 isoform b

    See identical proteins and their annotated locations for NP_055379.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate exon in the 5' UTR and coding sequence, compared to variant 1. The resulting isoform (b) has a longer and distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AB593066, AL138781, CK300529
    Consensus CDS
    CCDS6995.1
    UniProtKB/Swiss-Prot
    Q9UBR4
    UniProtKB/TrEMBL
    F1T0D9
    Related
    ENSP00000360811.3, ENST00000371746.8
    Conserved Domains (3) summary
    cd09376
    Location:95150
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    cd09467
    Location:3387
    LIM1_Lhx3b; The first LIM domain of Lhx3b
    pfam00046
    Location:165218
    Homeobox; Homeobox domain
  3. NM_178138.6NP_835258.1  LIM/homeobox protein Lhx3 isoform a

    See identical proteins and their annotated locations for NP_835258.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript. This transcript encodes two proteins; isoform a and M2-LHX3, which is generated by an internal translation initiation codon.
    Source sequence(s)
    AB593062, AL138781, CK300529
    Consensus CDS
    CCDS6994.1
    UniProtKB/Swiss-Prot
    Q9UBR4
    UniProtKB/TrEMBL
    F1T0D5
    Related
    ENSP00000360813.4, ENST00000371748.10
    Conserved Domains (3) summary
    cd09376
    Location:90145
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    cd09467
    Location:2882
    LIM1_Lhx3b; The first LIM domain of Lhx3b
    pfam00046
    Location:160213
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    136196250..136205129 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017015168.1XP_016870657.1  LIM/homeobox protein Lhx3 isoform X2

  2. XM_005263410.1XP_005263467.1  LIM/homeobox protein Lhx3 isoform X1

    UniProtKB/TrEMBL
    F1T0D7
    Related
    ENSP00000483080.1, ENST00000619587.1
    Conserved Domains (4) summary
    cd09376
    Location:79134
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    cd09467
    Location:1771
    LIM1_Lhx3b; The first LIM domain of Lhx3b
    pfam00046
    Location:149202
    Homeobox; Homeobox domain
    pfam04503
    Location:247368
    SSDP; Single-stranded DNA binding protein, SSDP
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