Human Gene LUM (uc001tbm.3)
  Description: Homo sapiens lumican (LUM), mRNA.
RefSeq Summary (NM_002345): 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].
Transcript (Including UTRs)
   Position: hg19 chr12:91,497,232-91,505,542 Size: 8,311 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr12:91,497,942-91,502,756 Size: 4,815 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:91,497,232-91,505,542)mRNA (may differ from genome)Protein (338 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LUM_HUMAN
DESCRIPTION: RecName: Full=Lumican; AltName: Full=Keratan sulfate proteoglycan lumican; Short=KSPG lumican; Flags: Precursor;
SUBUNIT: Binds to laminin (By similarity).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix (By similarity).
TISSUE SPECIFICITY: Cornea and other tissues.
DEVELOPMENTAL STAGE: Present in the extracellular matrix of human articular cartilage at all ages, although its abundance is far greater in the adult. In the adult cartilage lumican exists predominantly in a glycoprotein form lacking keratan sulfate, whereas the juvenile form of the molecule is a proteoglycan.
PTM: Sulfated on tyrosine residue(s).
SIMILARITY: Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.
SIMILARITY: Contains 11 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 LRRNT domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LUM
CDC HuGE Published Literature: LUM
Positive Disease Associations: myopia
Related Studies:
  1. myopia
    Wang, I. J. et al. 2006, The association of single nucleotide polymorphisms in the 5'-regulatory region of the lumican gene with susceptibility to high myopia in Taiwan, Mol Vis 2006 12 852-7. [PubMed 16902402]
    Our results indicate that an SNP (rs3759223), which is located in the promoter region of the lumican gene, may be worth further investigation to determine its association with development of high myopia.

-  MalaCards Disease Associations
  MalaCards Gene Search: LUM
Diseases sorted by gene-association score: cornea plana (17), degenerative myopia (8), corneal dystrophy, posterior amorphous (7), corneal dystrophy, congenital stromal (6), la crosse encephalitis (6), actinic keratosis (6), eye degenerative disease (5), stromal dystrophy (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D001564 Benzo(a)pyrene
  • D013749 Tetrachlorodibenzodioxin
  • D004997 Ethinyl Estradiol
  • C076994 perfluorooctane sulfonic acid
  • D015655 1-Methyl-4-phenylpyridinium
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • C049584 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine
  • D015122 6-Mercaptopurine
  • D015124 8-Bromo Cyclic Adenosine Monophosphate
  • C547126 AZM551248
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 211.96 RPKM in Lung
Total median expression: 2207.08 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -105.01389-0.270 Picture PostScript Text
3' UTR -148.47710-0.209 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp
IPR000372 - LRR-contain_N

Pfam Domains:
PF01462 - Leucine rich repeat N-terminal domain
PF12799 - Leucine Rich repeats (2 copies)
PF13306 - Leucine rich repeats (6 copies)
PF13516 - Leucine Rich repeat
PF13855 - Leucine rich repeat

SCOP Domains:
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1

ModBase Predicted Comparative 3D Structure on P51884
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005201 extracellular matrix structural constituent
GO:0005515 protein binding
GO:0005518 collagen binding

Biological Process:
GO:0007601 visual perception
GO:0014070 response to organic cyclic compound
GO:0018146 keratan sulfate biosynthetic process
GO:0030198 extracellular matrix organization
GO:0030199 collagen fibril organization
GO:0032914 positive regulation of transforming growth factor beta1 production
GO:0042340 keratan sulfate catabolic process
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051216 cartilage development
GO:0070848 response to growth factor
GO:0007409 axonogenesis

Cellular Component:
GO:0005576 extracellular region
GO:0005583 fibrillar collagen trimer
GO:0005615 extracellular space
GO:0005796 Golgi lumen
GO:0031012 extracellular matrix
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  KJ891557 - Synthetic construct Homo sapiens clone ccsbBroadEn_00951 LUM gene, encodes complete protein.
KJ897149 - Synthetic construct Homo sapiens clone ccsbBroadEn_06543 LUM gene, encodes complete protein.
LF208874 - JP 2014500723-A/16377: Polycomb-Associated Non-Coding RNAs.
U18728 - Human lumican mRNA, complete cds.
U21128 - Human lumican mRNA, complete cds.
BC035997 - Homo sapiens lumican, mRNA (cDNA clone MGC:32797 IMAGE:4688606), complete cds.
GQ891472 - Homo sapiens clone HEL-S-193 epididymis secretory sperm binding protein mRNA, complete cds.
BC007038 - Homo sapiens lumican, mRNA (cDNA clone MGC:12410 IMAGE:3950745), complete cds.
AK223177 - Homo sapiens mRNA for lumican variant, clone: LNG15808.
JD026250 - Sequence 7274 from Patent EP1572962.
JD028910 - Sequence 9934 from Patent EP1572962.
LF323606 - JP 2014500723-A/131109: Polycomb-Associated Non-Coding RNAs.
LF323605 - JP 2014500723-A/131108: Polycomb-Associated Non-Coding RNAs.
JD096889 - Sequence 77913 from Patent EP1572962.
JD350896 - Sequence 331920 from Patent EP1572962.
JD147355 - Sequence 128379 from Patent EP1572962.
AK312682 - Homo sapiens cDNA, FLJ93075, Homo sapiens lumican (LUM), mRNA.
BT006707 - Homo sapiens lumican mRNA, complete cds.
DQ892554 - Synthetic construct clone IMAGE:100005184; FLH187425.01X; RZPDo839H0272D lumican (LUM) gene, encodes complete protein.
DQ895765 - Synthetic construct Homo sapiens clone IMAGE:100010225; FLH187421.01L; RZPDo839H0262D lumican (LUM) gene, encodes complete protein.
AB590375 - Synthetic construct DNA, clone: pFN21AE1404, Homo sapiens LUM gene for lumican, without stop codon, in Flexi system.
CU675507 - Synthetic construct Homo sapiens gateway clone IMAGE:100020693 5' read LUM mRNA.
CU690252 - Synthetic construct Homo sapiens gateway clone IMAGE:100022218 5' read LUM mRNA.
LF323604 - JP 2014500723-A/131107: Polycomb-Associated Non-Coding RNAs.
LF323603 - JP 2014500723-A/131106: Polycomb-Associated Non-Coding RNAs.
LF323602 - JP 2014500723-A/131105: Polycomb-Associated Non-Coding RNAs.
LF323601 - JP 2014500723-A/131104: Polycomb-Associated Non-Coding RNAs.
LF323600 - JP 2014500723-A/131103: Polycomb-Associated Non-Coding RNAs.
JD048725 - Sequence 29749 from Patent EP1572962.
JD237275 - Sequence 218299 from Patent EP1572962.
JD526427 - Sequence 507451 from Patent EP1572962.
MA559183 - JP 2018138019-A/131109: Polycomb-Associated Non-Coding RNAs.
MA559182 - JP 2018138019-A/131108: Polycomb-Associated Non-Coding RNAs.
MA559181 - JP 2018138019-A/131107: Polycomb-Associated Non-Coding RNAs.
MA559180 - JP 2018138019-A/131106: Polycomb-Associated Non-Coding RNAs.
MA559179 - JP 2018138019-A/131105: Polycomb-Associated Non-Coding RNAs.
MA559178 - JP 2018138019-A/131104: Polycomb-Associated Non-Coding RNAs.
MA559177 - JP 2018138019-A/131103: Polycomb-Associated Non-Coding RNAs.
MA444451 - JP 2018138019-A/16377: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_slrpPathway - Small Leucine-rich Proteoglycan (SLRP) molecules

Reactome (by CSHL, EBI, and GO)

Protein P51884 (Reactome details) participates in the following event(s):

R-HSA-4085133 LUM (lumican) binds integrin alpha2beta1
R-HSA-2046175 Further sulfation on galactose residues produces KSPG
R-HSA-2046222 CHST2,5,6 transfer SO4(2-) to GlcNAc residues on keratan-PG to form KSPG
R-HSA-2046285 The keratan chain can be capped by N-acetylneuraminic acid
R-HSA-2046298 B4GALTs transfer Gal to a branch of keratan
R-HSA-2046265 B4GALTs transfer Gal to the keratan chain
R-HSA-2025724 B3GNT1,2,3,4,7 add GlcNAc to form Keratan-PG
R-HSA-2025723 B4GALTs transfer Gal to the N-glycan precursor
R-HSA-2327886 SLRPs bind TGF Beta
R-NUL-2466133 SLRPs bind TGF beta
R-HSA-216083 Integrin cell surface interactions
R-HSA-2022854 Keratan sulfate biosynthesis
R-HSA-3656243 Defective ST3GAL3 causes MCT12 and EIEE15
R-HSA-2022857 Keratan sulfate degradation
R-HSA-3656225 Defective CHST6 causes MCDC1
R-HSA-3656244 Defective B4GALT1 causes B4GALT1-CDG (CDG-2d)
R-HSA-3000178 ECM proteoglycans
R-HSA-1474244 Extracellular matrix organization
R-HSA-1638074 Keratan sulfate/keratin metabolism
R-HSA-3560782 Diseases associated with glycosaminoglycan metabolism
R-HSA-1630316 Glycosaminoglycan metabolism
R-HSA-3781865 Diseases of glycosylation
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1643685 Disease
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6R5, LDC, LUM_HUMAN, NM_002345, NP_002336, P51884, Q96QM7, SLRR2D
UCSC ID: uc001tbm.3
RefSeq Accession: NM_002345
Protein: P51884 (aka LUM_HUMAN)
CCDS: CCDS9038.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002345.3
exon count: 3CDS single in 3' UTR: no RNA size: 2116
ORF size: 1017CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1999.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.