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

    Gene ID: 16876, updated on 11-Apr-2024

    Summary

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    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
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    Genomic context

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    See Lhx9 in Genome Data Viewer
    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    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

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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

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    Preferred Names
    LIM/homeobox protein Lhx9

    NCBI Reference Sequences (RefSeq)

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    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

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