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

Gene ID: 84695, updated on 1-Jun-2020

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
109.20200522 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 TOR1B pseudogene 1 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 Functions

What's a GeneRIF?

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
NP_001276093.1
NP_001276094.1
NP_115992.1
XP_011531436.1
XP_016860601.1
XP_024308944.1
XP_024308945.1
XP_024308946.1

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
    4994..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
    Related
    ENST00000470907.6
    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 Updated 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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