Atlas of Genetics and Cytogenetics in Oncology and Haematology


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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret jlhuret@AtlasGeneticsOncology.org
Donations are also welcome
If each casual visitor gives 3 Euros or Dollars, the Atlas is saved in a week !
If each professional gives 100 Euros or Dollars once a year (now), the Atlas is saved in 2 weeks !
Don't let the Atlas imminent demise
Note: we send fiscal receipts for donations equal or above 50 Euros or Dollars

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LEMD3 (LEM domain containing 3)

Identity

Other namesMAN1
HGNC (Hugo) LEMD3
LocusID (NCBI) 23592
Location 12q14.3
Location_base_pair Starts at 65563351 and ends at 65642141 bp from pter ( according to hg19-Feb_2009)
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)LEMD3   28887
Cards
Entrez_Gene (NCBI)LEMD3  23592  LEM domain containing 3
GeneCards (Weizmann)LEMD3
Ensembl hg19 (Hinxton)ENSG00000174106 [Gene_View]  chr12:65563351-65642141 [Contig_View]  LEMD3 [Vega]
Ensembl hg38 (Hinxton)ENSG00000174106 [Gene_View]  chr12:65563351-65642141 [Contig_View]  LEMD3 [Vega]
ICGC DataPortalENSG00000174106
cBioPortalLEMD3
AceView (NCBI)LEMD3
Genatlas (Paris)LEMD3
WikiGenes23592
SOURCE (Princeton)LEMD3
Genomic and cartography
GoldenPath hg19 (UCSC)LEMD3  -     chr12:65563351-65642141 +  12q14.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)LEMD3  -     12q14.3   [Description]    (hg38-Dec_2013)
EnsemblLEMD3 - 12q14.3 [CytoView hg19]  LEMD3 - 12q14.3 [CytoView hg38]
Mapping of homologs : NCBILEMD3 [Mapview hg19]  LEMD3 [Mapview hg38]
OMIM155950   166700   607844   
Gene and transcription
Genbank (Entrez)AF112299 AK024954 AK295406 AK304317 AK312473
RefSeq transcript (Entrez)NM_001167614 NM_014319
RefSeq genomic (Entrez)NC_000012 NC_018923 NG_016210 NT_029419 NW_004929384
Consensus coding sequences : CCDS (NCBI)LEMD3
Cluster EST : UnigeneHs.744150 [ NCBI ]
CGAP (NCI)Hs.744150
Alternative Splicing : Fast-db (Paris)GSHG0006803
Alternative Splicing GalleryENSG00000174106
Gene ExpressionLEMD3 [ NCBI-GEO ]     LEMD3 [ SEEK ]   LEMD3 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y2U8 (Uniprot)
NextProtQ9Y2U8  [Medical]
With graphics : InterProQ9Y2U8
Splice isoforms : SwissVarQ9Y2U8 (Swissvar)
Domaine pattern : Prosite (Expaxy)LEM (PS50954)   
Domains : Interpro (EBI)Inner-Nucl-membr_MAN1    LEM/LEM-like_dom    LEM_dom    Nucleotide-bd_a/b_plait   
Related proteins : CluSTrQ9Y2U8
Domain families : Pfam (Sanger)LEM (PF03020)    MSC (PF09402)   
Domain families : Pfam (NCBI)pfam03020    pfam09402   
Domain families : Smart (EMBL)LEM (SM00540)  
DMDM Disease mutations23592
Blocks (Seattle)Q9Y2U8
PDB (SRS)2CH0   
PDB (PDBSum)2CH0   
PDB (IMB)2CH0   
PDB (RSDB)2CH0   
Human Protein AtlasENSG00000174106
Peptide AtlasQ9Y2U8
HPRD09704
IPIIPI00032491   IPI00954965   
Protein Interaction databases
DIP (DOE-UCLA)Q9Y2U8
IntAct (EBI)Q9Y2U8
FunCoupENSG00000174106
BioGRIDLEMD3
IntegromeDBLEMD3
STRING (EMBL)LEMD3
Ontologies - Pathways
QuickGOQ9Y2U8
Ontology : AmiGOnucleotide binding  blood vessel endothelial cell migration involved in intussusceptive angiogenesis  DNA binding  protein binding  nuclear inner membrane  integral component of nuclear inner membrane  nucleus organization  membrane  integral component of membrane  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of BMP signaling pathway  negative regulation of activin receptor signaling pathway  skeletal muscle cell differentiation  regulation of cell cycle  regulation of extracellular matrix organization  
Ontology : EGO-EBInucleotide binding  blood vessel endothelial cell migration involved in intussusceptive angiogenesis  DNA binding  protein binding  nuclear inner membrane  integral component of nuclear inner membrane  nucleus organization  membrane  integral component of membrane  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of BMP signaling pathway  negative regulation of activin receptor signaling pathway  skeletal muscle cell differentiation  regulation of cell cycle  regulation of extracellular matrix organization  
Protein Interaction DatabaseLEMD3
DoCM (Curated mutations)LEMD3
Wikipedia pathwaysLEMD3
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerLEMD3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LEMD3
dbVarLEMD3
ClinVarLEMD3
1000_GenomesLEMD3 
Exome Variant ServerLEMD3
SNP (GeneSNP Utah)LEMD3
SNP : HGBaseLEMD3
Genetic variants : HAPMAPLEMD3
Genomic Variants (DGV)LEMD3 [DGVbeta]
Mutations
ICGC Data PortalENSG00000174106 
Somatic Mutations in Cancer : COSMICLEMD3 
CONAN: Copy Number AnalysisLEMD3 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)12:65563351-65642141
Mutations and Diseases : HGMDLEMD3
OMIM155950    166700    607844   
MedgenLEMD3
NextProtQ9Y2U8 [Medical]
GENETestsLEMD3
Disease Genetic AssociationLEMD3
Huge Navigator LEMD3 [HugePedia]  LEMD3 [HugeCancerGEM]
snp3D : Map Gene to Disease23592
DGIdb (Drug Gene Interaction db)LEMD3
General knowledge
Homologs : HomoloGeneLEMD3
Homology/Alignments : Family Browser (UCSC)LEMD3
Phylogenetic Trees/Animal Genes : TreeFamLEMD3
Chemical/Protein Interactions : CTD23592
Chemical/Pharm GKB GenePA134907442
Clinical trialLEMD3
Cancer Resource (Charite)ENSG00000174106
Other databases
Probes
Litterature
PubMed31 Pubmed reference(s) in Entrez
CoreMineLEMD3
GoPubMedLEMD3
iHOPLEMD3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated02-2015Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Mar 28 15:50:02 CET 2015

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.