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Aliases for LUM Gene

Aliases for LUM Gene

  • Lumican 2 3
  • LDC 3 4 6
  • Keratan Sulfate Proteoglycan Lumican 3 4
  • Lumican Proteoglycan 2 3
  • KSPG Lumican 3 4
  • SLRR2D 3 4

External Ids for LUM Gene

Previous Symbols for LUM Gene

  • LDC

Summaries for LUM Gene

Entrez Gene Summary for LUM Gene

  • 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]

GeneCards Summary for LUM Gene

LUM (Lumican) is a Protein Coding gene. Diseases associated with LUM include posterior amorphous corneal dystrophy and cornea plana. Among its related pathways are Proteoglycans in cancer and Disease. GO annotations related to this gene include extracellular matrix structural constituent and collagen binding. An important paralog of this gene is ECM2.

Gene Wiki entry for LUM Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LUM Gene

Genomics for LUM Gene

Genomic Location for LUM Gene

Start:
91,102,629 bp from pter
End:
91,111,831 bp from pter
Size:
9,203 bases
Orientation:
Minus strand

Genomic View for LUM Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LUM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LUM Gene

Regulatory Elements for LUM Gene

Proteins for LUM Gene

  • Protein details for LUM Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51884-LUM_HUMAN
    Recommended name:
    Lumican
    Protein Accession:
    P51884
    Secondary Accessions:
    • B2R6R5
    • Q96QM7

    Protein attributes for LUM Gene

    Size:
    338 amino acids
    Molecular mass:
    38429 Da
    Quaternary structure:
    • Binds to laminin.

neXtProt entry for LUM Gene

Proteomics data for LUM Gene at MOPED

Post-translational modifications for LUM Gene

  • Sulfated on tyrosine residue(s).
  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn88, Asn127, Asn160, and Asn252

Other Protein References for LUM Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for LUM Gene

Domains for LUM Gene

Gene Families for LUM Gene

HGNC:
  • SLRR :Proteoglycans / Extracellular Matrix : Small leucine-rich repeats

UniProtKB/Swiss-Prot:

LUM_HUMAN
Domain:
  • Contains 1 LRRNT domain.:
    • P51884
Family:
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.:
    • P51884
Similarity:
  • Contains 11 LRR (leucine-rich) repeats.:
    • P51884
genes like me logo Genes that share domains with LUM: view

Function for LUM Gene

Molecular function for LUM Gene

GENATLAS Biochemistry: lumican,keratan sulfate proteoglycan one of the three major constituents of the corneal stroma,playing a role in the regulation of collagen assembly into fibrils in various connective tissues,small-leucine-rich proteoglycans family

Gene Ontology (GO) - Molecular Function for LUM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent NAS 10892350
GO:0005515 protein binding IPI 25304424
GO:0005518 collagen binding IDA 10892350
genes like me logo Genes that share ontologies with LUM: view
genes like me logo Genes that share phenotypes with LUM: view

Animal Models for LUM Gene

MGI Knock Outs for LUM:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for LUM Gene

Localization for LUM Gene

Subcellular locations from UniProtKB/Swiss-Prot for LUM Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LUM Gene COMPARTMENTS Subcellular localization image for LUM gene
Compartment Confidence
extracellular 5
golgi apparatus 4
lysosome 4
vacuole 4
cytoskeleton 1
endoplasmic reticulum 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for LUM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix TAS 7665616
GO:0005583 fibrillar collagen trimer IDA 10734230
GO:0005615 extracellular space IDA 20551380
GO:0005796 Golgi lumen TAS --
genes like me logo Genes that share ontologies with LUM: view

Pathways for LUM Gene

genes like me logo Genes that share pathways with LUM: view

Pathways by source for LUM Gene

Gene Ontology (GO) - Biological Process for LUM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process TAS --
GO:0007601 visual perception IEA --
GO:0014070 response to organic cyclic compound IEA --
GO:0018146 keratan sulfate biosynthetic process TAS --
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with LUM: view

Transcripts for LUM Gene

mRNA/cDNA for LUM Gene

Unigene Clusters for LUM Gene

Lumican:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LUM Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b · 3c
SP1:
SP2: - -
SP3: -

Relevant External Links for LUM Gene

GeneLoc Exon Structure for
LUM
ECgene alternative splicing isoforms for
LUM

Expression for LUM Gene

mRNA expression in normal human tissues for LUM Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LUM Gene

This gene is overexpressed in Lung (4.4), Heart - Atrial Appendage (4.1), and Adipose - Visceral (Omentum) (4.0).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for LUM Gene

SOURCE GeneReport for Unigene cluster for LUM Gene Hs.406475

mRNA Expression by UniProt/SwissProt for LUM Gene

P51884-LUM_HUMAN
Tissue specificity: Cornea and other tissues
genes like me logo Genes that share expressions with LUM: view

Orthologs for LUM Gene

This gene was present in the common ancestor of chordates.

Orthologs for LUM Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LUM 36
  • 99.41 (n)
  • 99.41 (a)
LUM 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LUM 36
  • 87.67 (n)
  • 89.35 (a)
LUM 37
  • 88 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LUM 36
  • 89.64 (n)
  • 91.12 (a)
LUM 37
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lum 36
  • 82.45 (n)
  • 86.69 (a)
Lum 16
Lum 37
  • 87 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LUM 37
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LUM 37
  • 74 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lum 36
  • 82.05 (n)
  • 85.21 (a)
chicken
(Gallus gallus)
Aves LUM 36
  • 69.94 (n)
  • 70.24 (a)
LUM 37
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LUM 37
  • 65 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia MGC64527 36
tropical clawed frog
(Silurana tropicalis)
Amphibia lum 36
  • 63.01 (n)
  • 64.39 (a)
Str.15551 36
zebrafish
(Danio rerio)
Actinopterygii lum 36
  • 57.35 (n)
  • 51.75 (a)
lum 37
  • 45 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 28 (a)
OneToMany
Species with no ortholog for LUM:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LUM Gene

ENSEMBL:
Gene Tree for LUM (if available)
TreeFam:
Gene Tree for LUM (if available)

Paralogs for LUM Gene

Paralogs for LUM Gene

Selected SIMAP similar genes for LUM Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with LUM: view

Variants for LUM Gene

Sequence variations from dbSNP and Humsavar for LUM Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type MAF
rs11478 -- 91,103,540(-) ACTGT(A/G)TTTGA utr-variant-3-prime
rs11756 -- 91,103,047(+) GAGTA(G/T)TTATC downstream-variant-500B
rs11855 -- 91,103,747(-) GGTGG(A/T)AGATA utr-variant-3-prime
rs14956 -- 91,103,848(-) TAAAT(A/C)TTAAT utr-variant-3-prime
rs1019269 -- 91,109,455(-) CATAT(A/T)CCCGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LUM Gene

Variant ID Type Subtype PubMed ID
nsv899425 CNV Gain 21882294
nsv899428 CNV Gain 21882294
nsv899429 CNV Loss 21882294
dgv210n27 CNV Loss 19166990

Relevant External Links for LUM Gene

HapMap Linkage Disequilibrium report
LUM
Human Gene Mutation Database (HGMD)
LUM

Disorders for LUM Gene

(1) University of Copenhagen DISEASES for LUM Gene

Relevant External Links for LUM

Genetic Association Database (GAD)
LUM
Human Genome Epidemiology (HuGE) Navigator
LUM
genes like me logo Genes that share disorders with LUM: view

No data available for UniProtKB/Swiss-Prot for LUM Gene

Publications for LUM Gene

  1. Primary structure of human lumican (keratan sulfate proteoglycan) and localization of the gene (LUM) to chromosome 12q21.3-q22. (PMID: 7558030) Chakravarti S. … Hassell J.R. (Genomics 1995) 2 3 4 23
  2. Association of the lumican gene functional 3'-UTR polymorphism with high myopia. (PMID: 19643966) Lin H.J. … Tsai F.J. (Invest. Ophthalmol. Vis. Sci. 2010) 3 23 49
  3. The human lumican gene. Organization, chromosomal location, and expression in articular cartilage. (PMID: 7665616) Grover J. … Roughley P.J. (J. Biol. Chem. 1995) 3 4
  4. Screening for N-glycosylated proteins by liquid chromatography mass spectrometry. (PMID: 14760718) Bunkenborg J. … Wisniewski J.R. (Proteomics 2004) 3 4
  5. The association of single nucleotide polymorphisms in the 5'-regulatory region of the lumican gene with susceptibility to high myopia in Taiwan. (PMID: 16902402) Wang I.J. … Lin L.L. (Mol. Vis. 2006) 3 49

Products for LUM Gene

Sources for LUM Gene

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