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    Lhx9 LIM homeobox 9 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 289048, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Lhx9provided by RGD
    Official Full Name
    LIM homeobox 9provided by RGD
    Primary source
    RGD:727956
    See related
    EnsemblRapid:ENSRNOG00000010357 AllianceGenome:RGD:727956
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    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. Predicted to be involved in dorsal spinal cord interneuron anterior axon guidance; negative regulation of DNA-templated transcription; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within cell population proliferation and gonad development. Predicted to be active in nucleus. Orthologous to human LHX9 (LIM homeobox 9). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 4.9), Testes (RPKM 2.0) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lhx9 in Genome Data Viewer
    Location:
    13q13
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (52941207..52961436, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (50389052..50409947, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (55854543..55879305, complement)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481500 Neighboring gene prothymosin alpha, pseudogene 4 Neighboring gene uncharacterized LOC108352542 Neighboring gene uncharacterized LOC134481501 Neighboring gene similar to human chromosome 1 open reading frame 53 Neighboring gene uncharacterized LOC120096262

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Lhx9 and lhx9alpha: differential biochemical properties and effects on neuronal differentiation. Mollé B, et al. DNA Cell Biol, 2004 Nov. PMID 15585134
    2. Lhx9 expression during gonadal morphogenesis as related to the state of cell differentiation. Mazaud S, et al. Gene Expr Patterns, 2002 Dec. PMID 12617828
    3. The LIM homeobox gene Lhx9 is essential for mouse gonad formation. Birk OS, et al. Nature, 2000 Feb 24. PMID 10706291
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lhx9 and Lhx9alpha isoforms could be implicated in regulating various aspects of neuronal differentiation
      Title: Lhx9 and lhx9alpha: differential biochemical properties and effects on neuronal differentiation.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC156570

    Gene Ontology Provided by RGD

    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 DNA-binding transcription factor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    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 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in dorsal spinal cord interneuron anterior axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within female gonad development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within gonad morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within male gonad development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    LIM/homeobox protein Lhx9
    Names
    LIM homeobox protein 9
    LIM-homeodomain type transcription factor 9

    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_181367.2 → NP_852032.1  LIM/homeobox protein Lhx9

      See identical proteins and their annotated locations for NP_852032.1

      Status: PROVISIONAL

      Source sequence(s)
      AY273890
      UniProtKB/Swiss-Prot
      A1A5M2, Q80W90, Q811Z4
      UniProtKB/TrEMBL
      A0A8I6GJ04
      Related
      ENSRNOP00000092128.1, ENSRNOT00000101843.2
      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

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      52941207..52961436 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006249919.5 → XP_006249981.1  LIM/homeobox protein Lhx9 isoform X4

      See identical proteins and their annotated locations for XP_006249981.1

      UniProtKB/TrEMBL
      A6ICL2
      Related
      ENSRNOP00000014218.6, ENSRNOT00000014218.8
      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

    2. XM_006249918.5 → XP_006249980.1  LIM/homeobox protein Lhx9 isoform X3

      See identical proteins and their annotated locations for XP_006249980.1

      UniProtKB/TrEMBL
      A6ICL2
      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
      smart00389
      Location:267 → 312
      HOX; Homeodomain

    3. XM_006249915.5 → XP_006249977.1  LIM/homeobox protein Lhx9 isoform X2

      UniProtKB/TrEMBL
      A0A8I6GJ04
      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

    4. XM_006249914.5 → XP_006249976.1  LIM/homeobox protein Lhx9 isoform X1

      UniProtKB/TrEMBL
      A0A8I6GJ04
      Related
      ENSRNOP00000105014.1, ENSRNOT00000139280.1
      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 → 324
      Homeobox; Homeobox domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q80W90.1 GenPept UniProtKB/Swiss-Prot:Q80W90

    Gene LinkOut

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

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