U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Lhx9 LIM homeobox protein 9 [ Mus musculus (house mouse) ]

Gene ID: 16876, updated on 21-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
Lhx9provided by MGI
Official Full Name
LIM homeobox protein 9provided by MGI
Primary source
MGI:MGI:1316721
See related
Ensembl:ENSMUSG00000019230 AllianceGenome:MGI:1316721
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
LH2B; 3110009O07Rik
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within cell population proliferation and gonad development. Predicted to be active in nucleus. Is expressed in several structures, including brain; genitourinary system; heart and pericardium; limb; and sensory organ. Orthologous to human LHX9 (LIM homeobox 9). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in whole brain E14.5 (RPKM 7.8), CNS E14 (RPKM 6.5) and 4 other tissues See more
Orthologs
human all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
1 E4; 1 60.82 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (138752924..138776577, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (138825186..138848839, complement)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene predicted gene 5833 Neighboring gene predicted gene 8790 Neighboring gene STARR-seq mESC enhancer starr_02466 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:140682812-140682921 Neighboring gene STARR-seq mESC enhancer starr_02467 Neighboring gene RIKEN cDNA 2310009B15 gene Neighboring gene STARR-positive B cell enhancer mm9_chr1:140753241-140753541 Neighboring gene STARR-seq mESC enhancer starr_02468 Neighboring gene RIKEN cDNA 1700019P21 gene

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. RNA sequencing and expression analysis reveal a role for Lhx9 in the haploinsufficient adult mouse ovary. Workman S, et al. Mol Reprod Dev, 2023 May. PMID 37084273
  2. Development of the mouse anterior amygdalar radial unit marked by Lhx9-expression. Garcia-Calero E, et al. Brain Struct Funct, 2021 Mar. PMID 33515280, Free PMC Article
  3. Lhx9 Is Required for the Development of Retinal Nitric Oxide-Synthesizing Amacrine Cell Subtype. Balasubramanian R, et al. Mol Neurobiol, 2018 Apr. PMID 28456934, Free PMC Article
  4. The Lhx9 homeobox gene controls pineal gland development and prevents postnatal hydrocephalus. Yamazaki F, et al. Brain Struct Funct, 2015. PMID 24647753, Free PMC Article
  5. Translational profiling of hypocretin neurons identifies candidate molecules for sleep regulation. Dalal J, et al. Genes Dev, 2013 Mar 1. PMID 23431030, Free PMC Article

See all (182) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RNA sequencing and expression analysis reveal a role for Lhx9 in the haploinsufficient adult mouse ovary.
    Title: RNA sequencing and expression analysis reveal a role for Lhx9 in the haploinsufficient adult mouse ovary.
  2. Alternative LIM homeodomain splice variants are dynamically regulated at key developmental steps in vertebrates.
    Title: Alternative LIM homeodomain splice variants are dynamically regulated at key developmental steps in vertebrates.
  3. Development of the mouse anterior amygdalar radial unit marked by Lhx9-expression.
    Title: Development of the mouse anterior amygdalar radial unit marked by Lhx9-expression.
  4. that Smurf1 promotes Lhx9 ubiquitylation and is involved in testosterone production in Leydig cells directly
    Title: Smad ubiquitylation regulatory factor 1 promotes LIM-homeobox gene 9 degradation and represses testosterone production in Leydig cells.
  5. Lhx9 is a new molecular marker that defines a subset of amacrine cells and show that it is necessary for the development of the Nitric Oxide-Synthesizing Amacrine Cell subtype of amacrine cells.
    Title: Lhx9 Is Required for the Development of Retinal Nitric Oxide-Synthesizing Amacrine Cell Subtype.
  6. Authors examined the expression pattern for the three alternative splice forms of Lhx9; Lhx9alpha, Lhx9beta and Lhx9c during early limb development.
    Title: Lhx9 gene expression during early limb development in mice requires the FGF signalling pathway.
  7. Study has revealed that Lhx9 plays a role in the development of the pineal gland and in maintenance of the brain structure.
    Title: The Lhx9 homeobox gene controls pineal gland development and prevents postnatal hydrocephalus.
  8. Lhx9-GCE mouse line could serve as a beneficial tool for lineage tracing and gene manipulation experiments.
    Title: Generation and characterization of Lhx9-GFPCreER(T2) knock-in mouse line.
  9. Gbx2 regulates thalamocortical axon guidance by modifying the LIM and Robo codes.
    Title: Gbx2 regulates thalamocortical axon guidance by modifying the LIM and Robo codes.
  10. The second wave of expression at E12.5 includes Lhx3, 5, 9, Isl2, and Lmx1b in the differentiating sensory epithelia with cellular specificities.
    Title: Diverse expression patterns of LIM-homeodomain transcription factors (LIM-HDs) in mammalian inner ear development.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4)  1 citation
  • Endonuclease-mediated (1) 

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within female gonad development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within gonad morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within male gonad development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

Go to the top of the page Help
Preferred Names
LIM/homeobox protein Lhx9

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

mRNA and Protein(s)

  1. NM_001025565.2 → NP_001020736.1  LIM/homeobox protein Lhx9 isoform a

    See identical proteins and their annotated locations for NP_001020736.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1), also known as Lhx9alpha, represents the longest transcript.
    Source sequence(s)
    AC154398
    Consensus CDS
    CCDS15334.1
    UniProtKB/Swiss-Prot
    Q9WUH2
    Related
    ENSMUSP00000019374.8, ENSMUST00000019374.14
    Conserved Domains (3) summary
    cd09377
    Location:129 → 187
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61 → 124
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:271 → 312
    Homeobox; Homeobox domain

  2. NM_001042577.1 → NP_001036042.1  LIM/homeobox protein Lhx9 isoform c

    See identical proteins and their annotated locations for NP_001036042.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, compared to variant 1. The resulting isoform (c) has a longer, distinct C-terminus that encodes an intact LIM homeodomain, compared to isoform a.
    Source sequence(s)
    AC154398, BC072623
    Consensus CDS
    CCDS35726.1
    UniProtKB/Swiss-Prot
    Q6GQU4, Q9QYQ5, Q9QYQ6, Q9QZ00, Q9WU44, Q9WUH2
    Related
    ENSMUSP00000107657.3, ENSMUST00000112026.4
    Conserved Domains (3) summary
    cd09377
    Location:129 → 187
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61 → 124
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:271 → 323
    Homeobox; Homeobox domain

  3. NM_010714.3 → NP_034844.1  LIM/homeobox protein Lhx9 isoform b

    See identical proteins and their annotated locations for NP_034844.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR, and coding region, compared to variant 1. The resulting isoform (b) maintains the reading frame but is shorter at both the N- and C-termini, compared to isoform a.
    Source sequence(s)
    AB221560, AC144921, AC154398, AJ243851
    Consensus CDS
    CCDS15333.1
    UniProtKB/Swiss-Prot
    Q9WUH2
    Related
    ENSMUSP00000091198.4, ENSMUST00000093486.10
    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258 → 303
    HOX; Homeodomain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    138752924..138776577 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036162372.1 → XP_036018265.1  LIM/homeobox protein Lhx9 isoform X5

    Conserved Domains (3) summary
    cd09377
    Location:119 → 177
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:257 → 302
    HOX; Homeodomain

  2. XM_036162371.1 → XP_036018264.1  LIM/homeobox protein Lhx9 isoform X5

    Conserved Domains (3) summary
    cd09377
    Location:119 → 177
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:257 → 302
    HOX; Homeodomain

  3. XM_030251728.2 → XP_030107588.1  LIM/homeobox protein Lhx9 isoform X5

    Conserved Domains (3) summary
    cd09377
    Location:119 → 177
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:257 → 302
    HOX; Homeodomain

  4. XM_036162374.1 → XP_036018267.1  LIM/homeobox protein Lhx9 isoform X6

    Conserved Domains (3) summary
    cd09377
    Location:110 → 168
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:42 → 105
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:248 → 293
    HOX; Homeodomain

  5. XM_030251703.2 → XP_030107563.1  LIM/homeobox protein Lhx9 isoform X7

    Conserved Domains (3) summary
    cd09377
    Location:128 → 186
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61 → 124
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:266 → 311
    HOX; Homeodomain

  6. XM_030251723.1 → XP_030107583.1  LIM/homeobox protein Lhx9 isoform X4

    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258 → 303
    HOX; Homeodomain

  7. XM_030251724.1 → XP_030107584.1  LIM/homeobox protein Lhx9 isoform X4

    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258 → 303
    HOX; Homeodomain

  8. XM_030251726.2 → XP_030107586.1  LIM/homeobox protein Lhx9 isoform X4

    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258 → 303
    HOX; Homeodomain

  9. XM_017318637.2 → XP_017174126.1  LIM/homeobox protein Lhx9 isoform X4

    UniProtKB/Swiss-Prot
    Q9WUH2
    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258 → 303
    HOX; Homeodomain

  10. XM_006529173.4 → XP_006529236.1  LIM/homeobox protein Lhx9 isoform X2

    See identical proteins and their annotated locations for XP_006529236.1

    UniProtKB/Swiss-Prot
    Q9WUH2
    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262 → 315
    Homeobox; Homeobox domain

  11. XM_030251701.2 → XP_030107561.1  LIM/homeobox protein Lhx9 isoform X3

    Conserved Domains (3) summary
    cd09377
    Location:119 → 177
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:261 → 314
    Homeobox; Homeobox domain

  12. XM_006529172.5 → XP_006529235.1  LIM/homeobox protein Lhx9 isoform X2

    See identical proteins and their annotated locations for XP_006529235.1

    UniProtKB/Swiss-Prot
    Q9WUH2
    Related
    ENSMUSP00000036480.7, ENSMUST00000046870.13
    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262 → 315
    Homeobox; Homeobox domain

  13. XM_006529171.3 → XP_006529234.1  LIM/homeobox protein Lhx9 isoform X2

    See identical proteins and their annotated locations for XP_006529234.1

    UniProtKB/Swiss-Prot
    Q9WUH2
    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262 → 315
    Homeobox; Homeobox domain

  14. XM_030251696.1 → XP_030107556.1  LIM/homeobox protein Lhx9 isoform X2

    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262 → 315
    Homeobox; Homeobox domain

  15. XM_006529170.4 → XP_006529233.1  LIM/homeobox protein Lhx9 isoform X1

    Conserved Domains (3) summary
    cd09377
    Location:128 → 186
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61 → 124
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:270 → 323
    Homeobox; Homeobox domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9WUH2.3 GenPept UniProtKB/Swiss-Prot:Q9WUH2

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous