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LUM lumican [ Homo sapiens (human) ]

Gene ID: 4060, updated on 25-Oct-2020

Summary

Official Symbol
LUMprovided by HGNC
Official Full Name
lumicanprovided by HGNC
Primary source
HGNC:HGNC:6724
See related
Ensembl:ENSG00000139329 MIM:600616
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
LDC; SLRR2D
Summary
This gene encodes a member of the small leucine-rich proteoglycan (SLRP) family that includes decorin, biglycan, fibromodulin, keratocan, epiphycan, and osteoglycin. In these bifunctional molecules, the protein moiety binds collagen fibrils and the highly charged hydrophilic glycosaminoglycans regulate interfibrillar spacings. Lumican is the major keratan sulfate proteoglycan of the cornea but is also distributed in interstitial collagenous matrices throughout the body. Lumican may regulate collagen fibril organization and circumferential growth, corneal transparency, and epithelial cell migration and tissue repair. [provided by RefSeq, Jul 2008]
Expression
Broad expression in gall bladder (RPKM 981.2), urinary bladder (RPKM 643.2) and 14 other tissues See more
Orthologs

Genomic context

See LUM in Genome Data Viewer
Location:
12q21.33
Exon count:
3
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (91102629..91111494, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (91497232..91505542, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene epiphycan Neighboring gene keratocan Neighboring gene VISTA enhancer hs2540 Neighboring gene decorin Neighboring gene uncharacterized LOC105369898 Neighboring gene uncharacterized LOC107984544

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?

Phenotypes

Associated conditions

Description Tests
Gene-alcohol interactions identify several novel blood pressure loci including a promising locus near SLC16A9.
GeneReviews: Not available
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
collagen binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen binding IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix structural constituent NAS
Non-traceable Author Statement
more info
PubMed 
extracellular matrix structural constituent conferring compression resistance ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular matrix structural constituent conferring compression resistance RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cartilage development IEA
Inferred from Electronic Annotation
more info
 
collagen fibril organization NAS
Non-traceable Author Statement
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
keratan sulfate biosynthetic process TAS
Traceable Author Statement
more info
 
keratan sulfate catabolic process TAS
Traceable Author Statement
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transforming growth factor beta1 production IEA
Inferred from Electronic Annotation
more info
 
response to growth factor IEA
Inferred from Electronic Annotation
more info
 
response to organic cyclic compound IEA
Inferred from Electronic Annotation
more info
 
visual perception IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
lumican
Names
KSPG lumican
epididymis secretory sperm binding protein
keratan sulfate proteoglycan lumican
lumican proteoglycan

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.

mRNA and Protein(s)

  1. NM_002345.4NP_002336.1  lumican precursor

    See identical proteins and their annotated locations for NP_002336.1

    Status: REVIEWED

    Source sequence(s)
    AA036658, AC078873, BC007038
    Consensus CDS
    CCDS9038.1
    UniProtKB/Swiss-Prot
    P51884
    Related
    ENSP00000266718.4, ENST00000266718.5
    Conserved Domains (2) summary
    sd00033
    Location:6891
    LRR_RI; leucine-rich repeat [structural motif]
    cl26018
    Location:42242
    NEL; C-terminal novel E3 ligase, LRR-interacting

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    91102629..91111494 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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