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    lhx9 LIM homeobox 9 [ Danio rerio (zebrafish) ]

    Gene ID: 550405, updated on 9-Dec-2024

    Summary

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    Official Symbol
    lhx9provided by ZNC
    Official Full Name
    LIM homeobox 9provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050417-210
    See related
    Ensembl:ENSDARG00000056979 AllianceGenome:ZFIN:ZDB-GENE-050417-210
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:112196; si:dkey-121a9.2
    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 neuron fate specification and thalamus development. Predicted to be active in nucleus. Is expressed in several structures, including brain; forebrain neural keel; hypocretin-secreting neurons; pericardial region; and retina. Orthologous to human LHX9 (LIM homeobox 9). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See lhx9 in Genome Data Viewer
    Location:
    chromosome: 22
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (23242814..23255946, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (23228034..23241119, complement)

    Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase receptor type C Neighboring gene uncharacterized LOC137489016 Neighboring gene NIMA-related kinase 7 Neighboring gene si:dkey-121a9.3 Neighboring gene DENN/MADD domain containing 1B Neighboring gene crumbs cell polarity complex component 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Visualization of two distinct classes of neurons by gad2 and zic1 promoter/enhancer elements in the dorsal hindbrain of developing zebrafish reveals neuronal connectivity related to the auditory and lateral line systems. Sassa T, et al. Dev Dyn, 2007 Mar. PMID 17279576
    2. LIM Homeobox 9 knockdown by morpholino does not affect zebrafish retinal development. Guo R, et al. Biol Open, 2021 Mar 8. PMID 33579692, Free PMC Article
    3. Neural circuitry for stimulus selection in the zebrafish visual system. Fernandes AM, et al. Neuron, 2021 Mar 3. PMID 33357384
    4. Localization of BDNF expression in the developing brain of zebrafish. De Felice E, et al. J Anat, 2014 May. PMID 24588510, Free PMC Article
    5. Multicolor fluorescent in situ hybridization to define abutting and overlapping gene expression in the embryonic zebrafish brain. Lauter G, et al. Neural Dev, 2011 Apr 5. PMID 21466670, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    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
    		  
    Process Evidence Code Pubs
    involved_in dorsal spinal cord interneuron anterior axon guidance ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    acts_upstream_of_or_within neuron fate specification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within 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
    		  
    acts_upstream_of_or_within thalamus development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    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 homeodomain type transcription factor 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_001017710.2 → NP_001017710.2  LIM/homeobox protein Lhx9 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) includes an alternate 3' terminal exon compared to variant 2. The encoded isoform (1) has a shorter and distinct C-terminus compared to isoform 2.
      Source sequence(s)
      BX004971, EH447961, EH473801
      UniProtKB/TrEMBL
      A0A2U3TWB7, A0A8M1N568
      Related
      ENSDARP00000143543.2, ENSDART00000175556.2
      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_001037243.2 → NP_001032320.2  LIM/homeobox protein Lhx9 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longer transcript and encodes the longer isoform (2).
      Source sequence(s)
      BC163023, BX004971, EH447961
      UniProtKB/Swiss-Prot
      Q1LWV4, Q3LHM3
      Related
      ENSDARP00000054806.5, ENSDART00000054807.6
      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

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007133.7 Reference GRCz11 Primary Assembly

      Range
      23242814..23255946 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017353139.3 → XP_017208628.1  LIM/homeobox protein Lhx9 isoform X1

      UniProtKB/Swiss-Prot
      Q1LWV4, Q3LHM3
      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

    2. XM_021469324.2 → XP_021324999.1  LIM/homeobox protein Lhx9 isoform X2

      UniProtKB/TrEMBL
      A0A8M9PJJ4
      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 → 322
      Homeobox; Homeobox domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q1LWV4.1 GenPept UniProtKB/Swiss-Prot:Q1LWV4

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