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economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas).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

Donate (in Euros)

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COL6A1 (collagen, type VI, alpha 1)

Identity

Other namesOPLL
HGNC (Hugo) COL6A1
LocusID (NCBI) 1291
Location 21q22.3
Location_base_pair Starts at 47401663 and ends at 47424963 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)COL6A1   2211
Cards
Entrez_Gene (NCBI)COL6A1  1291  collagen, type VI, alpha 1
GeneCards (Weizmann)COL6A1
Ensembl hg19 (Hinxton)ENSG00000142156 [Gene_View]  chr21:47401663-47424963 [Contig_View]  COL6A1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000142156 [Gene_View]  chr21:47401663-47424963 [Contig_View]  COL6A1 [Vega]
ICGC DataPortalENSG00000142156
cBioPortalCOL6A1
AceView (NCBI)COL6A1
Genatlas (Paris)COL6A1
WikiGenes1291
SOURCE (Princeton)COL6A1
Genomic and cartography
GoldenPath hg19 (UCSC)COL6A1  -     chr21:47401663-47424963 +  21q22.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)COL6A1  -     21q22.3   [Description]    (hg38-Dec_2013)
EnsemblCOL6A1 - 21q22.3 [CytoView hg19]  COL6A1 - 21q22.3 [CytoView hg38]
Mapping of homologs : NCBICOL6A1 [Mapview hg19]  COL6A1 [Mapview hg38]
OMIM120220   158810   254090   
Gene and transcription
Genbank (Entrez)AK298968 AK299396 AK307989 AU100220 BC005159
RefSeq transcript (Entrez)NM_001848
RefSeq genomic (Entrez)AC_000153 NC_000021 NC_018932 NG_008674 NT_011512 NW_001838716 NW_004929427
Consensus coding sequences : CCDS (NCBI)COL6A1
Cluster EST : UnigeneHs.474053 [ NCBI ]
CGAP (NCI)Hs.474053
Alternative Splicing : Fast-db (Paris)GSHG0019563
Alternative Splicing GalleryENSG00000142156
Gene ExpressionCOL6A1 [ NCBI-GEO ]     COL6A1 [ SEEK ]   COL6A1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP12109 (Uniprot)
NextProtP12109  [Medical]
With graphics : InterProP12109
Splice isoforms : SwissVarP12109 (Swissvar)
Domaine pattern : Prosite (Expaxy)VWFA (PS50234)   
Domains : Interpro (EBI)Collagen    VWF_A   
Related proteins : CluSTrP12109
Domain families : Pfam (Sanger)Collagen (PF01391)    VWA (PF00092)   
Domain families : Pfam (NCBI)pfam01391    pfam00092   
Domain families : Smart (EMBL)VWA (SM00327)  
DMDM Disease mutations1291
Blocks (Seattle)P12109
Human Protein AtlasENSG00000142156
Peptide AtlasP12109
HPRD00370
IPIIPI00291136   IPI01010585   IPI01009421   IPI00977566   
Protein Interaction databases
DIP (DOE-UCLA)P12109
IntAct (EBI)P12109
FunCoupENSG00000142156
BioGRIDCOL6A1
IntegromeDBCOL6A1
STRING (EMBL)COL6A1
Ontologies - Pathways
QuickGOP12109
Ontology : AmiGOosteoblast differentiation  extracellular region  extracellular region  proteinaceous extracellular matrix  collagen type VI trimer  lysosomal membrane  endoplasmic reticulum lumen  cell adhesion  axon guidance  membrane  extracellular matrix disassembly  extracellular matrix organization  collagen catabolic process  extracellular matrix  extracellular matrix  sarcolemma  protein complex  platelet-derived growth factor binding  extracellular vesicular exosome  protein heterotrimerization  cellular response to amino acid stimulus  
Ontology : EGO-EBIosteoblast differentiation  extracellular region  extracellular region  proteinaceous extracellular matrix  collagen type VI trimer  lysosomal membrane  endoplasmic reticulum lumen  cell adhesion  axon guidance  membrane  extracellular matrix disassembly  extracellular matrix organization  collagen catabolic process  extracellular matrix  extracellular matrix  sarcolemma  protein complex  platelet-derived growth factor binding  extracellular vesicular exosome  protein heterotrimerization  cellular response to amino acid stimulus  
Pathways : KEGGPI3K-Akt signaling pathway    Focal adhesion    ECM-receptor interaction    Protein digestion and absorption   
Protein Interaction DatabaseCOL6A1
DoCM (Curated mutations)COL6A1
Wikipedia pathwaysCOL6A1
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerCOL6A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL6A1
dbVarCOL6A1
ClinVarCOL6A1
1000_GenomesCOL6A1 
Exome Variant ServerCOL6A1
SNP (GeneSNP Utah)COL6A1
SNP : HGBaseCOL6A1
Genetic variants : HAPMAPCOL6A1
Genomic Variants (DGV)COL6A1 [DGVbeta]
Mutations
ICGC Data PortalENSG00000142156 
Somatic Mutations in Cancer : COSMICCOL6A1 
CONAN: Copy Number AnalysisCOL6A1 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)21:47401663-47424963
Mutations and Diseases : HGMDCOL6A1
OMIM120220    158810    254090   
MedgenCOL6A1
NextProtP12109 [Medical]
GENETestsCOL6A1
Disease Genetic AssociationCOL6A1
Huge Navigator COL6A1 [HugePedia]  COL6A1 [HugeCancerGEM]
snp3D : Map Gene to Disease1291
DGIdb (Drug Gene Interaction db)COL6A1
General knowledge
Homologs : HomoloGeneCOL6A1
Homology/Alignments : Family Browser (UCSC)COL6A1
Phylogenetic Trees/Animal Genes : TreeFamCOL6A1
Chemical/Protein Interactions : CTD1291
Chemical/Pharm GKB GenePA26727
Clinical trialCOL6A1
Cancer Resource (Charite)ENSG00000142156
Other databases
Probes
Litterature
PubMed70 Pubmed reference(s) in Entrez
CoreMineCOL6A1
GoPubMedCOL6A1
iHOPCOL6A1
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 15:15:56 CET 2015

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jlhuret@AtlasGeneticsOncology.org.