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Lum lumican [ Mus musculus (house mouse) ]

Gene ID: 17022, updated on 22-Nov-2022

Summary

Official Symbol
Lumprovided by MGI
Official Full Name
lumicanprovided by MGI
Primary source
MGI:MGI:109347
See related
Ensembl:ENSMUSG00000036446 AllianceGenome:MGI:109347
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Ldc; SLRR2D
Summary
Predicted to enable collagen binding activity. Involved in positive regulation of transforming growth factor beta1 production. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in extracellular matrix. Is expressed in several structures, including alimentary system; ear; genitourinary system; heart and pericardium; and nervous system. Used to study Ehlers-Danlos syndrome classic type 1. Human ortholog(s) of this gene implicated in carotid artery disease; coronary artery disease; and pancreatic cancer. Orthologous to human LUM (lumican). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in bladder adult (RPKM 192.5), limb E14.5 (RPKM 161.5) and 13 other tissues See more
Orthologs
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Genomic context

See Lum in Genome Data Viewer
Location:
10 C3; 10 50.32 cM
Exon count:
3
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (97401363..97408565)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (97565501..97572703)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 34114 Neighboring gene microRNA 3966 Neighboring gene decorin Neighboring gene RIKEN cDNA 4930473O22 gene Neighboring gene keratocan

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4)  1 citation
  • Endonuclease-mediated (2) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables collagen binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables collagen binding ISO
Inferred from Sequence Orthology
more info
 
enables extracellular matrix structural constituent conferring compression resistance RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
Component Evidence Code Pubs
located_in collagen-containing extracellular matrix HDA PubMed 
located_in extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular matrix ISO
Inferred from Sequence Orthology
more info
 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of fibrillar collagen trimer ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
lumican
Names
KSPG lumican
keratan sulfate proteoglycan lumican

NCBI Reference Sequences (RefSeq)

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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_008524.2NP_032550.2  lumican precursor

    See identical proteins and their annotated locations for NP_032550.2

    Status: VALIDATED

    Source sequence(s)
    AK075737, CF731113
    Consensus CDS
    CCDS24142.1
    UniProtKB/Swiss-Prot
    P51885, Q9CXK0
    UniProtKB/TrEMBL
    A0A8C6HAK3
    Related
    ENSMUSP00000040877.5, ENSMUST00000038160.6
    Conserved Domains (4) summary
    smart00013
    Location:3771
    LRRNT; Leucine rich repeat N-terminal domain
    cd00116
    Location:66267
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:6891
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:66128
    LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    97401363..97408565
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)