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    loxl5b lysyl oxidase-like 5b [ Danio rerio (zebrafish) ]

    Gene ID: 100124531, updated on 18-Sep-2024

    Summary

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    Official Symbol
    loxl5bprovided by ZNC
    Official Full Name
    lysyl oxidase-like 5bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-070818-3
    See related
    Ensembl:ENSDARG00000076904 AllianceGenome:ZFIN:ZDB-GENE-070818-3
    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
    Summary
    Predicted to enable protein-lysine 6-oxidase activity. Acts upstream of or within notochord morphogenesis. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Is expressed in notochord and prechordal plate. [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See loxl5b in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (55993727..56041890)
    105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (55869746..55918045)

    Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene ATCAY kinesin light chain interacting caytaxin b Neighboring gene uncharacterized LOC137488294 Neighboring gene uncharacterized LOC108180184 Neighboring gene nicotinamide riboside kinase 2 Neighboring gene uncharacterized LOC137488302 Neighboring gene si:ch211-178n15.1 Neighboring gene JunD proto-oncogene, AP-1 transcription factor subunit

    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. Dithiocarbamates are teratogenic to developing zebrafish through inhibition of lysyl oxidase activity. van Boxtel AL, et al. Toxicol Appl Pharmacol, 2010 Apr 15. PMID 20045017
    2. Essential role for fibrillin-2 in zebrafish notochord and vascular morphogenesis. Gansner JM, et al. Dev Dyn, 2008 Oct. PMID 18816837, Free PMC Article
    3. Essential role of lysyl oxidases in notochord development. Gansner JM, et al. Dev Biol, 2007 Jul 15. PMID 17543297, Free PMC Article
    4. Modulation of the secretory pathway rescues zebrafish polycystic kidney disease pathology. Le Corre S, et al. J Am Soc Nephrol, 2014 Aug. PMID 24627348, Free PMC Article
    5. The small molecule Mek1/2 inhibitor U0126 disrupts the chordamesoderm to notochord transition in zebrafish. Hawkins TA, et al. BMC Dev Biol, 2008 Apr 17. PMID 18419805, Free PMC Article

    See all (6) 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 copper ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein-lysine 6-oxidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein-lysine 6-oxidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within notochord development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within notochord morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in peptidyl-lysine oxidation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in platelet-derived growth factor receptor-beta signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    lysyl oxidase-like 5b
    NP_001096044.1
    XP_017212858.1
    XP_017212861.1

    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_001102574.1 → NP_001096044.1  lysyl oxidase-like 5b precursor

      See identical proteins and their annotated locations for NP_001096044.1

      Status: PROVISIONAL

      Source sequence(s)
      EF030486
      UniProtKB/TrEMBL
      A6MH35
      Related
      ENSDARP00000152572.1, ENSDART00000188702.1
      Conserved Domains (1) summary
      pfam01186
      Location:241 → 435
      Lysyl_oxidase; Lysyl oxidase

    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_007113.7 Reference GRCz11 Primary Assembly

      Range
      55993727..56041890
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017357372.3 → XP_017212861.1  lysyl oxidase-like 5b isoform X2

      UniProtKB/TrEMBL
      A0A8M6Z7N5
      Conserved Domains (1) summary
      pfam01186
      Location:196 → 390
      Lysyl_oxidase; Lysyl oxidase

    2. XM_017357369.3 → XP_017212858.1  lysyl oxidase-like 5b isoform X1

      UniProtKB/TrEMBL
      A0A8M6Z846, F1QGY9
      Related
      ENSDARP00000123413.1, ENSDART00000146160.2
    Nucleotide Protein Strain
    Heading Accession and Version

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