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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 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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