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LUM (lumican)

Identity

Alias_namesLDC
Alias_symbol (synonym)SLRR2D
Other alias
HGNC (Hugo) LUM
LocusID (NCBI) 4060
Atlas_Id 254
Location 12q21.33  [Link to chromosome band 12q21]
Location_base_pair Starts at 91497232 and ends at 91505542 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
PABPC1L (20q13.12) / LUM (12q21.33)SCCPDH (1q44) / LUM (12q21.33)UPF2 (10p14) / LUM (12q21.33)
ZPBP (7p12.2) / LUM (12q21.33)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)LUM   6724
Cards
Entrez_Gene (NCBI)LUM  4060  lumican
AliasesLDC; SLRR2D
GeneCards (Weizmann)LUM
Ensembl hg19 (Hinxton)ENSG00000139329 [Gene_View]  chr12:91497232-91505542 [Contig_View]  LUM [Vega]
Ensembl hg38 (Hinxton)ENSG00000139329 [Gene_View]  chr12:91497232-91505542 [Contig_View]  LUM [Vega]
ICGC DataPortalENSG00000139329
TCGA cBioPortalLUM
AceView (NCBI)LUM
Genatlas (Paris)LUM
WikiGenes4060
SOURCE (Princeton)LUM
Genetics Home Reference (NIH)LUM
Genomic and cartography
GoldenPath hg19 (UCSC)LUM  -     chr12:91497232-91505542 -  12q21.33   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)LUM  -     12q21.33   [Description]    (hg38-Dec_2013)
EnsemblLUM - 12q21.33 [CytoView hg19]  LUM - 12q21.33 [CytoView hg38]
Mapping of homologs : NCBILUM [Mapview hg19]  LUM [Mapview hg38]
OMIM600616   
Gene and transcription
Genbank (Entrez)AA036658 AK223177 AK312682 BC007038 BC035997
RefSeq transcript (Entrez)NM_002345
RefSeq genomic (Entrez)NC_000012 NC_018923 NT_029419 NW_004929384
Consensus coding sequences : CCDS (NCBI)LUM
Cluster EST : UnigeneHs.406475 [ NCBI ]
CGAP (NCI)Hs.406475
Alternative Splicing GalleryENSG00000139329
Gene ExpressionLUM [ NCBI-GEO ]   LUM [ EBI - ARRAY_EXPRESS ]   LUM [ SEEK ]   LUM [ MEM ]
Gene Expression Viewer (FireBrowse)LUM [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4060
GTEX Portal (Tissue expression)LUM
Protein : pattern, domain, 3D structure
UniProt/SwissProtP51884   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP51884  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP51884
Splice isoforms : SwissVarP51884
PhosPhoSitePlusP51884
Domaine pattern : Prosite (Expaxy)LRR (PS51450)   
Domains : Interpro (EBI)L_dom-like    Leu-rich_rpt    Leu-rich_rpt_typical-subtyp    LRRNT    Lumican   
Domain families : Pfam (Sanger)LRR_8 (PF13855)    LRRNT (PF01462)   
Domain families : Pfam (NCBI)pfam13855    pfam01462   
Domain families : Smart (EMBL)LRR_TYP (SM00369)  LRRNT (SM00013)  
Conserved Domain (NCBI)LUM
DMDM Disease mutations4060
Blocks (Seattle)LUM
SuperfamilyP51884
Human Protein AtlasENSG00000139329
Peptide AtlasP51884
HPRD02793
IPIIPI00020986   
Protein Interaction databases
DIP (DOE-UCLA)P51884
IntAct (EBI)P51884
FunCoupENSG00000139329
BioGRIDLUM
STRING (EMBL)LUM
ZODIACLUM
Ontologies - Pathways
QuickGOP51884
Ontology : AmiGOextracellular matrix structural constituent  protein binding  collagen binding  extracellular region  extracellular region  proteinaceous extracellular matrix  fibrillar collagen trimer  extracellular space  Golgi lumen  axonogenesis  visual perception  response to organic cyclic compound  keratan sulfate biosynthetic process  extracellular matrix organization  collagen fibril organization  extracellular matrix  extracellular matrix  positive regulation of transforming growth factor beta1 production  keratan sulfate catabolic process  lysosomal lumen  positive regulation of transcription from RNA polymerase II promoter  cartilage development  extracellular exosome  response to growth factor  
Ontology : EGO-EBIextracellular matrix structural constituent  protein binding  collagen binding  extracellular region  extracellular region  proteinaceous extracellular matrix  fibrillar collagen trimer  extracellular space  Golgi lumen  axonogenesis  visual perception  response to organic cyclic compound  keratan sulfate biosynthetic process  extracellular matrix organization  collagen fibril organization  extracellular matrix  extracellular matrix  positive regulation of transforming growth factor beta1 production  keratan sulfate catabolic process  lysosomal lumen  positive regulation of transcription from RNA polymerase II promoter  cartilage development  extracellular exosome  response to growth factor  
Pathways : BIOCARTASmall Leucine-rich Proteoglycan (SLRP) molecules [Genes]   
Pathways : KEGGProteoglycans in cancer   
NDEx NetworkLUM
Atlas of Cancer Signalling NetworkLUM
Wikipedia pathwaysLUM
Orthology - Evolution
OrthoDB4060
GeneTree (enSembl)ENSG00000139329
Phylogenetic Trees/Animal Genes : TreeFamLUM
HOVERGENP51884
HOGENOMP51884
Homologs : HomoloGeneLUM
Homology/Alignments : Family Browser (UCSC)LUM
Gene fusions - Rearrangements
Fusion Cancer (Beijing)UPF2 [10p14]  -  LUM [12q21.33]  [FUSC002599]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLUM [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LUM
dbVarLUM
ClinVarLUM
1000_GenomesLUM 
Exome Variant ServerLUM
ExAC (Exome Aggregation Consortium)LUM (select the gene name)
Genetic variants : HAPMAP4060
Genomic Variants (DGV)LUM [DGVbeta]
DECIPHER (Syndromes)12:91497232-91505542  ENSG00000139329
CONAN: Copy Number AnalysisLUM 
Mutations
ICGC Data PortalLUM 
TCGA Data PortalLUM 
Broad Tumor PortalLUM
OASIS PortalLUM [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLUM  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLUM
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LUM
DgiDB (Drug Gene Interaction Database)LUM
DoCM (Curated mutations)LUM (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LUM (select a term)
intoGenLUM
Cancer3DLUM(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600616   
Orphanet
MedgenLUM
Genetic Testing Registry LUM
NextProtP51884 [Medical]
TSGene4060
GENETestsLUM
Huge Navigator LUM [HugePedia]
snp3D : Map Gene to Disease4060
BioCentury BCIQLUM
ClinGenLUM
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD4060
Chemical/Pharm GKB GenePA30486
Clinical trialLUM
Miscellaneous
canSAR (ICR)LUM (select the gene name)
Probes
Litterature
PubMed86 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLUM
EVEXLUM
GoPubMedLUM
iHOPLUM
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Mar 14 13:13:57 CET 2017

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