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economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas).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
Donations are also welcome

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LDB3 (LIM domain binding 3)

Identity

Other namesCMD1C
CMPD3
CYPHER
LDB3Z1
LDB3Z4
LVNC3
MFM4
ORACLE
PDLIM6
ZASP
HGNC (Hugo) LDB3
LocusID (NCBI) 11155
Location 10q23.2
Location_base_pair Starts at 88428426 and ends at 88495824 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)LDB3   15710
Cards
Entrez_Gene (NCBI)LDB3  11155  LIM domain binding 3
GeneCards (Weizmann)LDB3
Ensembl hg19 (Hinxton)ENSG00000122367 [Gene_View]  chr10:88428426-88495824 [Contig_View]  LDB3 [Vega]
Ensembl hg38 (Hinxton)ENSG00000122367 [Gene_View]  chr10:88428426-88495824 [Contig_View]  LDB3 [Vega]
ICGC DataPortalENSG00000122367
cBioPortalLDB3
AceView (NCBI)LDB3
Genatlas (Paris)LDB3
WikiGenes11155
SOURCE (Princeton)LDB3
Genomic and cartography
GoldenPath hg19 (UCSC)LDB3  -     chr10:88428426-88495824 +  10q23.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)LDB3  -     10q23.2   [Description]    (hg38-Dec_2013)
EnsemblLDB3 - 10q23.2 [CytoView hg19]  LDB3 - 10q23.2 [CytoView hg38]
Mapping of homologs : NCBILDB3 [Mapview hg19]  LDB3 [Mapview hg38]
OMIM601493   605906   609452   
Gene and transcription
Genbank (Entrez)AA180065 AB014513 AF086263 AF276807 AF276808
RefSeq transcript (Entrez)NM_001080114 NM_001080115 NM_001080116 NM_001171610 NM_001171611 NM_007078
RefSeq genomic (Entrez)AC_000142 NC_000010 NC_018921 NG_008876 NT_030059 NW_001837992 NW_004929376
Consensus coding sequences : CCDS (NCBI)LDB3
Cluster EST : UnigeneHs.657271 [ NCBI ]
CGAP (NCI)Hs.657271
Alternative Splicing : Fast-db (Paris)GSHG0033146
Alternative Splicing GalleryENSG00000122367
Gene ExpressionLDB3 [ NCBI-GEO ]     LDB3 [ SEEK ]   LDB3 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75112 (Uniprot)
NextProtO75112  [Medical]
With graphics : InterProO75112
Splice isoforms : SwissVarO75112 (Swissvar)
Domaine pattern : Prosite (Expaxy)LIM_DOMAIN_1 (PS00478)    LIM_DOMAIN_2 (PS50023)    PDZ (PS50106)   
Domains : Interpro (EBI)PDZ    ZASP    Znf_LIM   
Related proteins : CluSTrO75112
Domain families : Pfam (Sanger)LIM (PF00412)    PDZ (PF00595)   
Domain families : Pfam (NCBI)pfam00412    pfam00595   
Domain families : Smart (EMBL)LIM (SM00132)  PDZ (SM00228)  ZM (SM00735)  
DMDM Disease mutations11155
Blocks (Seattle)O75112
PDB (SRS)1RGW   
PDB (PDBSum)1RGW   
PDB (IMB)1RGW   
PDB (RSDB)1RGW   
Human Protein AtlasENSG00000122367
Peptide AtlasO75112
HPRD16172
IPIIPI00514458   IPI00294959   IPI00294958   IPI00552865   IPI00654766   IPI00165263   IPI00909356   IPI01009910   IPI00909817   IPI00978614   IPI00978988   
Protein Interaction databases
DIP (DOE-UCLA)O75112
IntAct (EBI)O75112
FunCoupENSG00000122367
BioGRIDLDB3
IntegromeDBLDB3
STRING (EMBL)LDB3
Ontologies - Pathways
QuickGOO75112
Ontology : AmiGOprotein kinase C binding  protein binding  cytoskeleton  cytoskeletal protein binding  zinc ion binding  Z disc  pseudopodium  sarcomere organization  perinuclear region of cytoplasm  muscle alpha-actinin binding  
Ontology : EGO-EBIprotein kinase C binding  protein binding  cytoskeleton  cytoskeletal protein binding  zinc ion binding  Z disc  pseudopodium  sarcomere organization  perinuclear region of cytoplasm  muscle alpha-actinin binding  
Protein Interaction DatabaseLDB3
DoCM (Curated mutations)LDB3
Wikipedia pathwaysLDB3
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerLDB3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LDB3
dbVarLDB3
ClinVarLDB3
1000_GenomesLDB3 
Exome Variant ServerLDB3
SNP (GeneSNP Utah)LDB3
SNP : HGBaseLDB3
Genetic variants : HAPMAPLDB3
Genomic Variants (DGV)LDB3 [DGVbeta]
Mutations
ICGC Data PortalENSG00000122367 
Somatic Mutations in Cancer : COSMICLDB3 
CONAN: Copy Number AnalysisLDB3 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)Leiden Muscular Dystrophy pages
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Zhejiang University Center for Genetic and Genomic Medicine (ZJU-CGGM)
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)10:88428426-88495824
Mutations and Diseases : HGMDLDB3
OMIM601493    605906    609452   
MedgenLDB3
NextProtO75112 [Medical]
GENETestsLDB3
Disease Genetic AssociationLDB3
Huge Navigator LDB3 [HugePedia]  LDB3 [HugeCancerGEM]
snp3D : Map Gene to Disease11155
DGIdb (Drug Gene Interaction db)LDB3
General knowledge
Homologs : HomoloGeneLDB3
Homology/Alignments : Family Browser (UCSC)LDB3
Phylogenetic Trees/Animal Genes : TreeFamLDB3
Chemical/Protein Interactions : CTD11155
Chemical/Pharm GKB GenePA30318
Clinical trialLDB3
Cancer Resource (Charite)ENSG00000122367
Other databases
Probes
Litterature
PubMed31 Pubmed reference(s) in Entrez
CoreMineLDB3
GoPubMedLDB3
iHOPLDB3
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
Updated12-2014Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Feb 14 16:33:53 CET 2015

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.