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loxl3b lysyl oxidase-like 3b [ Danio rerio (zebrafish) ]

Gene ID: 336266, updated on 4-Jan-2025

Summary

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Official Symbol
loxl3bprovided by ZNC
Official Full Name
lysyl oxidase-like 3bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-8210
See related
Ensembl:ENSDARG00000039563 AllianceGenome:ZFIN:ZDB-GENE-030131-8210
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
loxl3; fj60c12; im:7157119; wu:fj60c12; zgc:162959
Summary
Predicted to enable fibronectin binding activity and protein-lysine 6-oxidase activity. Acts upstream of or within embryonic viscerocranium morphogenesis. Predicted to be located in cytoplasm and nucleus. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Is expressed in several structures, including axis; cartilage element; mesoderm; pharyngeal arch; and yolk syncytial layer. Human ortholog(s) of this gene implicated in myopia. Orthologous to human LOXL3 (lysyl oxidase like 3). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
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Genomic context

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See loxl3b in Genome Data Viewer
Location:
chromosome: 13
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (15234507..15404571)
105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (15103402..15274321)

Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene mitochondrial antiviral signaling protein Neighboring gene microRNA 103 Neighboring gene pantothenate kinase 2 Neighboring gene uncharacterized LOC137487379 Neighboring gene uncharacterized LOC137487378

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. Lysyl oxidase-like 3b is critical for cartilage maturation during zebrafish craniofacial development. van Boxtel AL, et al. Matrix Biol, 2011 Apr. PMID 21244857, Free PMC Article
  2. Essential role of lysyl oxidases in notochord development. Gansner JM, et al. Dev Biol, 2007 Jul 15. PMID 17543297, Free PMC Article
  3. The novel human HtrA2 ortholog in zebrafish: New molecular insight and challenges into the imbalance of homeostasis. Nam MK, et al. Gene, 2022 Apr 20. PMID 35121025
  4. LMO1 Synergizes with MYCN to Promote Neuroblastoma Initiation and Metastasis. Zhu S, et al. Cancer Cell, 2017 Sep 11. PMID 28867147, Free PMC Article
  5. Zebrafish cyp17a1 knockout reveals that androgen-mediated signaling is important for male brain sex differentiation. Shu T, et al. Gen Comp Endocrinol, 2020 Sep 1. PMID 32283058

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables copper ion binding IEA
Inferred from Electronic Annotation
more info
  
enables fibronectin binding ISS
Inferred from Sequence or Structural Similarity
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
  
enables protein-lysine 6-oxidase activity ISS
Inferred from Sequence or Structural Similarity
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 embryonic viscerocranium morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in fibronectin fibril organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in lung development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of T-helper 17 cell lineage commitment ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in peptidyl-lysine oxidation IEA
Inferred from Electronic Annotation
more info
  
involved_in peptidyl-lysine oxidation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of integrin-mediated signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in roof of mouth development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in somite development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spinal cord development ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
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
  
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
lysyl oxidase homolog 3B
Names
lysyl oxidase-like protein 3B
NP_001139156.1
XP_005156601.1
XP_009305423.1
XP_009305424.1
XP_009305425.1
XP_021336213.1
XP_068081036.1
XP_068081037.1

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_001145684.2 → NP_001139156.1  lysyl oxidase homolog 3B precursor

    Status: VALIDATED

    Source sequence(s)
    BX323842, BX649269
    UniProtKB/Swiss-Prot
    A4QP70, A6MH33, B8A4W9, B8A5R6, B8A5R8, E7EY82, Q5CZM0
    Related
    ENSDARP00000109545.2, ENSDART00000129314.4
    Conserved Domains (2) summary
    smart00202
    Location:50 → 149
    SR; Scavenger receptor Cys-rich
    pfam01186
    Location:584 → 782
    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_007124.7 Reference GRCz11 Primary Assembly

    Range
    15234507..15404571
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005156544.5 → XP_005156601.1  lysyl oxidase homolog 3B isoform X1

    UniProtKB/TrEMBL
    A0A8M6Z3R1
    Conserved Domains (3) summary
    smart00202
    Location:50 → 149
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:58 → 150
    SRCR; Scavenger receptor cysteine-rich domain
    pfam01186
    Location:626 → 820
    Lysyl_oxidase; Lysyl oxidase

  2. XM_009307148.4 → XP_009305423.1  lysyl oxidase homolog 3B isoform X3

    UniProtKB/TrEMBL
    A0A8M3B7U8
    Conserved Domains (3) summary
    smart00202
    Location:50 → 149
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:58 → 150
    SRCR; Scavenger receptor cysteine-rich domain
    pfam01186
    Location:574 → 768
    Lysyl_oxidase; Lysyl oxidase

  3. XM_068224935.1 → XP_068081036.1  lysyl oxidase homolog 3B isoform X5

  4. XM_009307149.4 → XP_009305424.1  lysyl oxidase homolog 3B isoform X4

    UniProtKB/TrEMBL
    A0A8M3B524
    Conserved Domains (3) summary
    smart00202
    Location:50 → 149
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:58 → 150
    SRCR; Scavenger receptor cysteine-rich domain
    pfam01186
    Location:569 → 763
    Lysyl_oxidase; Lysyl oxidase

  5. XM_068224936.1 → XP_068081037.1  lysyl oxidase homolog 3B isoform X7

  6. XM_021480538.2 → XP_021336213.1  lysyl oxidase homolog 3B isoform X2

    UniProtKB/TrEMBL
    A0A8M9Q9L1
    Conserved Domains (2) summary
    smart00202
    Location:50 → 149
    SR; Scavenger receptor Cys-rich
    pfam01186
    Location:609 → 807
    Lysyl_oxidase; Lysyl oxidase

  7. XM_009307150.4 → XP_009305425.1  lysyl oxidase homolog 3B isoform X6

    UniProtKB/TrEMBL
    A0A8M3AYX6
    Conserved Domains (3) summary
    smart00202
    Location:50 → 149
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:58 → 150
    SRCR; Scavenger receptor cysteine-rich domain
    pfam01186
    Location:532 → 726
    Lysyl_oxidase; Lysyl oxidase

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001089342.1: Suppressed sequence

    Description
    NM_001089342.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript and protein.
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
B8A4W9.1 GenPept UniProtKB/Swiss-Prot:B8A4W9

Gene LinkOut

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