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    lmo4a LIM domain only 4a [ Danio rerio (zebrafish) ]

    Gene ID: 114412, updated on 9-Dec-2024

    Summary

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    Official Symbol
    lmo4aprovided by ZNC
    Official Full Name
    LIM domain only 4aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-010702-1
    See related
    Ensembl:ENSDARG00000013853 AllianceGenome:ZFIN:ZDB-GENE-010702-1
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    NH13; lmo4; id:ibd2576; id:ibd5151
    Summary
    Predicted to enable metal ion binding activity. Acts upstream of or within embryonic camera-type eye development and forebrain development. Is expressed in several structures, including brain; cardiovascular system; germ ring; mesoderm; and neural keel. Orthologous to human LMO4 (LIM domain only 4). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See lmo4a in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 5 NC_007116.7 (32924669..32946255)
    105 previous assembly GRCz10 (GCF_000002035.5) 5 NC_007116.6 (32324500..32346102)

    Chromosome 5 - NC_007116.7Genomic Context describing neighboring genes Neighboring gene polymerase (DNA directed), epsilon 3 (p17 subunit) Neighboring gene cellular communication network factor 1, like 1 Neighboring gene zgc:55461 Neighboring gene neuropeptide FF receptor 2 Neighboring gene GLI pathogenesis-related 2

    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. lmo4a Contributes to Zebrafish Inner Ear and Vestibular Development via Regulation of the Bmp Pathway. Sun L, et al. Genes (Basel), 2023 Jun 28. PMID 37510276, Free PMC Article
    2. An optimised pipeline for parallel image-based quantification of gene expression and genotyping after in situ hybridisation. Dobrzycki T, et al. Biol Open, 2018 Apr 9. PMID 29535102, Free PMC Article
    3. Dynamic expression and regulation by Fgf8 and Pou2 of the zebrafish LIM-only gene, lmo4. Lane ME, et al. Mech Dev, 2002 Dec. PMID 14516683
    4. Gene expression changes in aging zebrafish (Danio rerio) brains are sexually dimorphic. Arslan-Ergul A, et al. BMC Neurosci, 2014 Feb 18. PMID 24548546, Free PMC Article
    5. A zebrafish LMO4 ortholog limits the size of the forebrain and eyes through negative regulation of six3b and rx3. McCollum CW, et al. Dev Biol, 2007 Sep 15. PMID 17692837, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. lmo4a Contributes to Zebrafish Inner Ear and Vestibular Development via Regulation of the Bmp Pathway.
      Title: lmo4a Contributes to Zebrafish Inner Ear and Vestibular Development via Regulation of the Bmp Pathway.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within embryonic camera-type eye development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within embryonic camera-type eye development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within forebrain development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within forebrain development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    LIM domain transcription factor LMO4a
    Names
    LIM domain only 4

    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_177984.1 → NP_817093.1  LIM domain transcription factor LMO4a

      See identical proteins and their annotated locations for NP_817093.1

      Status: PROVISIONAL

      Source sequence(s)
      BC045835
      UniProtKB/TrEMBL
      A0A2R8Q433, F6PBS1, Q8QG63
      Related
      ENSDARP00000079654.4, ENSDART00000085219.5
      Conserved Domains (2) summary
      cd09386
      Location:24 → 78
      LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)
      cd09387
      Location:88 → 142
      LIM2_LMO4; The second LIM domain of LMO4 (LIM domain only protein 4)

    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_007116.7 Reference GRCz11 Primary Assembly

      Range
      32924669..32946255
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009301446.4 → XP_009299721.1  LIM domain transcription factor LMO4a isoform X2

      UniProtKB/TrEMBL
      A0A2R8RLI6, A0A8M3ASE8
      Related
      ENSDARP00000147813.1, ENSDART00000192397.1
      Conserved Domains (2) summary
      cd09386
      Location:24 → 78
      LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)
      cd09387
      Location:88 → 142
      LIM2_LMO4; The second LIM domain of LMO4 (LIM domain only protein 4)

    2. XM_068221084.1 → XP_068077185.1  LIM domain transcription factor LMO4a isoform X1

      UniProtKB/TrEMBL
      A0A2R8Q433, F6PBS1, Q8QG63

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394587.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      24454..46040
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_2

    Genomic

    1. NW_018395240.1 Reference GRCz11 ALT_DRER_TU_2

      Range
      188048..209882
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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