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    LOXL3 lysyl oxidase like 3 [ Homo sapiens (human) ]

    Gene ID: 84695, updated on 17-Jun-2019

    Summary

    Official Symbol
    LOXL3provided by HGNC
    Official Full Name
    lysyl oxidase like 3provided by HGNC
    Primary source
    HGNC:HGNC:13869
    See related
    Ensembl:ENSG00000115318 MIM:607163
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LOXL
    Summary
    This gene encodes a lysyl oxidase, which likely functions as an amine oxidase and plays a role in the formation of crosslinks in collagens and elastin. Deletion of the related gene in mouse causes neonatal mortality with cleft palate, spine deformity, and defects in collagen organization. A mutation in this gene was found in a family with Stickler syndrome. [provided by RefSeq, Sep 2016]
    Expression
    Ubiquitous expression in placenta (RPKM 7.6), bone marrow (RPKM 5.2) and 24 other tissues See more
    Orthologs

    Genomic context

    See LOXL3 in Genome Data Viewer
    Location:
    2p13.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (74532258..74555719, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (74759946..74781088, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene DEAQ-box RNA dependent ATPase 1 Neighboring gene AUP1 lipid droplet regulating VLDL assembly factor Neighboring gene HtrA serine peptidase 2 Neighboring gene docking protein 1 Neighboring gene meiosis 1 associated protein Neighboring gene torsin family 1 member B pseudogene Neighboring gene TVP23B pseudogene 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
      Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • Crosslinking of collagen fibrils, organism-specific biosystem (from REACTOME)
      Crosslinking of collagen fibrils, organism-specific biosystemAfter removal of the N- and C-procollagen propeptides, fibrillar collagen molecules aggregate into microfibrillar arrays, stabilized by covalent intermolecular cross-links. These depend on the oxidat...
    • Elastic fibre formation, organism-specific biosystem (from REACTOME)
      Elastic fibre formation, organism-specific biosystemElastic fibres (EF) are a major structural constituent of dynamic connective tissues such as large arteries and lung parenchyma, where they provide essential properties of elastic recoil and resilien...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    copper ion binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    fibronectin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein-lysine 6-oxidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein-lysine 6-oxidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein-lysine 6-oxidase activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    scavenger receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    epithelial to mesenchymal transition IDA
    Inferred from Direct Assay
    more info
    PubMed 
    fibronectin fibril organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    inflammatory response IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    lung development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of T-helper 17 cell lineage commitment ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    peptidyl-lysine oxidation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    peptidyl-lysine oxidation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of integrin-mediated signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    roof of mouth development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    somite development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    spinal cord development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular space ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    lysyl oxidase homolog 3
    Names
    lysyl oxidase-like protein 3

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_033047.1 RefSeqGene

      Range
      4941..26678
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001289164.3NP_001276093.1  lysyl oxidase homolog 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001276093.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. Its encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AC005033, AC005041
      Consensus CDS
      CCDS74527.1
      UniProtKB/Swiss-Prot
      P58215
      Related
      ENSP00000377512.2, ENST00000393937.6
      Conserved Domains (2) summary
      smart00202
      Location:162262
      SR; Scavenger receptor Cys-rich
      pfam01186
      Location:385583
      Lysyl_oxidase; Lysyl oxidase
    2. NM_001289165.2NP_001276094.1  lysyl oxidase homolog 3 isoform 3

      See identical proteins and their annotated locations for NP_001276094.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as sv1) represents the use of an alternate promoter, differs in the 5' UTR, and lacks a portion of the 5' coding region, compared to variant 1. This results in an isoform (3) which has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      DQ378059
      UniProtKB/Swiss-Prot
      P58215
      Conserved Domains (3) summary
      smart00202
      Location:56164
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:61164
      SRCR; Scavenger receptor cysteine-rich domain
      pfam01186
      Location:169363
      Lysyl_oxidase; Lysyl oxidase
    3. NM_032603.5NP_115992.1  lysyl oxidase homolog 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_115992.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC005033, AF284815, DQ378059
      Consensus CDS
      CCDS1953.1
      UniProtKB/Swiss-Prot
      P58215
      Related
      ENSP00000264094.3, ENST00000264094.8
      Conserved Domains (2) summary
      smart00202
      Location:307407
      SR; Scavenger receptor Cys-rich
      pfam01186
      Location:530728
      Lysyl_oxidase; Lysyl oxidase

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      74532258..74555719 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024453176.1XP_024308944.1  lysyl oxidase homolog 3 isoform X1

      Conserved Domains (2) summary
      smart00202
      Location:307407
      SR; Scavenger receptor Cys-rich
      pfam01186
      Location:530728
      Lysyl_oxidase; Lysyl oxidase
    2. XM_024453177.1XP_024308945.1  lysyl oxidase homolog 3 isoform X1

      Conserved Domains (2) summary
      smart00202
      Location:307407
      SR; Scavenger receptor Cys-rich
      pfam01186
      Location:530728
      Lysyl_oxidase; Lysyl oxidase
    3. XM_017005112.1XP_016860601.1  lysyl oxidase homolog 3 isoform X2

      UniProtKB/Swiss-Prot
      P58215
      Conserved Domains (3) summary
      smart00202
      Location:56164
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:61164
      SRCR; Scavenger receptor cysteine-rich domain
      pfam01186
      Location:169363
      Lysyl_oxidase; Lysyl oxidase
    4. XM_024453178.1XP_024308946.1  lysyl oxidase homolog 3 isoform X1

      Conserved Domains (2) summary
      smart00202
      Location:307407
      SR; Scavenger receptor Cys-rich
      pfam01186
      Location:530728
      Lysyl_oxidase; Lysyl oxidase
    5. XM_011533134.2XP_011531436.1  lysyl oxidase homolog 3 isoform X1

      See identical proteins and their annotated locations for XP_011531436.1

      UniProtKB/Swiss-Prot
      P58215
      Related
      ENSP00000386696.1, ENST00000409549.5
      Conserved Domains (2) summary
      smart00202
      Location:307407
      SR; Scavenger receptor Cys-rich
      pfam01186
      Location:530728
      Lysyl_oxidase; Lysyl oxidase
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