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    lmo3 LIM domain only 3 [ Danio rerio (zebrafish) ]

    Gene ID: 553774, updated on 2-Nov-2024

    Summary

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    Official Symbol
    lmo3provided by ZNC
    Official Full Name
    LIM domain only 3provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050522-201
    See related
    Ensembl:ENSDARG00000008720 AllianceGenome:ZFIN:ZDB-GENE-050522-201
    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
    LMO-3; lmo3b; zgc:110149
    Summary
    Predicted to enable DNA-binding transcription factor binding activity and transcription coactivator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Is expressed in basal plate midbrain region; nervous system; neural plate; notochord; and presumptive diencephalon. Orthologous to human LMO3 (LIM domain only 3). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See lmo3 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 4 NC_007115.7 (12612726..12679290)
    105 previous assembly GRCz10 (GCF_000002035.5) 4 NC_007115.6 (12613621..12680441)

    Chromosome 4 - NC_007115.7Genomic Context describing neighboring genes Neighboring gene Rho guanine nucleotide exchange factor (GEF) 39 Neighboring gene uncharacterized LOC103910417 Neighboring gene microsomal glutathione S-transferase 1.1 Neighboring gene microsomal glutathione S-transferase 1.2

    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. Comparative genomic analysis of teleost fish bmal genes. Wang H. Genetica, 2009 May. PMID 18850331
    2. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Wagner DE, et al. Science, 2018 Jun 1. PMID 29700229, Free PMC Article
    3. 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
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    5. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Clone Names

    • MGC110149

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive 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 domain only protein 3

    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_001020739.2 → NP_001018575.1  LIM domain only protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001018575.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AL954848
      UniProtKB/Swiss-Prot
      Q503U0
      Related
      ENSDARP00000015268.6, ENSDART00000003583.8
      Conserved Domains (2) summary
      cd09388
      Location:13 → 67
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cl02475
      Location:77 → 131
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

    2. NM_001328595.1 → NP_001315524.1  LIM domain only protein 3 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL954848, EH435155
      UniProtKB/TrEMBL
      A0A8M1P455, B0R1F5
      Related
      ENSDARP00000098627.2, ENSDART00000112860.3
      Conserved Domains (2) summary
      cd09388
      Location:35 → 89
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cd09389
      Location:99 → 153
      LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

    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_007115.7 Reference GRCz11 Primary Assembly

      Range
      12612726..12679290
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005164631.5 → XP_005164688.1  LIM domain only protein 3 isoform X1

      See identical proteins and their annotated locations for XP_005164688.1

      UniProtKB/TrEMBL
      A0A8M2BBY5
      Conserved Domains (2) summary
      cd09388
      Location:25 → 79
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cd09389
      Location:89 → 143
      LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

    2. XM_005164633.5 → XP_005164690.1  LIM domain only protein 3 isoform X3

      See identical proteins and their annotated locations for XP_005164690.1

      UniProtKB/Swiss-Prot
      Q503U0
      Related
      ENSDARP00000152478.1, ENSDART00000181201.1
      Conserved Domains (2) summary
      cd09388
      Location:13 → 67
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cl02475
      Location:77 → 131
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

    3. XM_021475015.2 → XP_021330690.1  LIM domain only protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8M9QB71
      Conserved Domains (2) summary
      cd09388
      Location:24 → 78
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cd09389
      Location:88 → 142
      LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

    4. XM_005164630.5 → XP_005164687.1  LIM domain only protein 3 isoform X1

      See identical proteins and their annotated locations for XP_005164687.1

      UniProtKB/TrEMBL
      A0A8M2BBY5
      Conserved Domains (2) summary
      cd09388
      Location:25 → 79
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cd09389
      Location:89 → 143
      LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

    5. XM_005164629.4 → XP_005164686.1  LIM domain only protein 3 isoform X1

      See identical proteins and their annotated locations for XP_005164686.1

      UniProtKB/TrEMBL
      A0A8M2BBY5
      Conserved Domains (2) summary
      cd09388
      Location:25 → 79
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cd09389
      Location:89 → 143
      LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394553.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      247165..310386
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q503U0.1 GenPept UniProtKB/Swiss-Prot:Q503U0

    Gene LinkOut

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