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economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas).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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SAMHD1 (SAM domain and HD domain 1)

Identity

Other namesCHBL2
DCIP
HDDC1
MOP-5
SBBI88
HGNC (Hugo) SAMHD1
LocusID (NCBI) 25939
Location 20q11.23
Location_base_pair Starts at 35520227 and ends at 35580246 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

External links

Nomenclature
HGNC (Hugo)SAMHD1   15925
Cards
Entrez_Gene (NCBI)SAMHD1  25939  SAM domain and HD domain 1
GeneCards (Weizmann)SAMHD1
Ensembl hg19 (Hinxton) [Gene_View]  chr20:35520227-35580246 [Contig_View]  SAMHD1 [Vega]
Ensembl hg38 (Hinxton) [Gene_View]  chr20:35520227-35580246 [Contig_View]  SAMHD1 [Vega]
cBioPortalSAMHD1
AceView (NCBI)SAMHD1
Genatlas (Paris)SAMHD1
WikiGenes25939
SOURCE (Princeton)SAMHD1
Genomic and cartography
GoldenPath hg19 (UCSC)SAMHD1  -     chr20:35520227-35580246 -  20q11.23   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SAMHD1  -     20q11.23   [Description]    (hg38-Dec_2013)
EnsemblSAMHD1 - 20q11.23 [CytoView hg19]  SAMHD1 - 20q11.23 [CytoView hg38]
Mapping of homologs : NCBISAMHD1 [Mapview hg19]  SAMHD1 [Mapview hg38]
OMIM606754   612952   614415   
Gene and transcription
Genbank (Entrez)AB013847 AB208944 AF228421 AK027811 AK304187
RefSeq transcript (Entrez)NM_015474
RefSeq genomic (Entrez)NC_000020 NC_018931 NG_017059 NT_011362 NW_004929418
Consensus coding sequences : CCDS (NCBI)SAMHD1
Cluster EST : UnigeneHs.580681 [ NCBI ]
CGAP (NCI)Hs.580681
Alternative Splicing : Fast-db (Paris)GSHG0019164
Gene ExpressionSAMHD1 [ NCBI-GEO ]     SAMHD1 [ SEEK ]   SAMHD1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y3Z3 (Uniprot)
NextProtQ9Y3Z3  [Medical]
With graphics : InterProQ9Y3Z3
Splice isoforms : SwissVarQ9Y3Z3 (Swissvar)
Catalytic activity : Enzyme3.1.5.- [ Enzyme-Expasy ]   3.1.5.-3.1.5.- [ IntEnz-EBI ]   3.1.5.- [ BRENDA ]   3.1.5.- [ KEGG ]   
Domaine pattern : Prosite (Expaxy)SAM_DOMAIN (PS50105)   
Domains : Interpro (EBI)HD/PDEase_dom    HD_domain    SAM    SAM/pointed    SAM_2   
Related proteins : CluSTrQ9Y3Z3
Domain families : Pfam (Sanger)HD (PF01966)    SAM_2 (PF07647)   
Domain families : Pfam (NCBI)pfam01966    pfam07647   
Domain families : Smart (EMBL)HDc (SM00471)  SAM (SM00454)  
DMDM Disease mutations25939
Blocks (Seattle)Q9Y3Z3
PDB (SRS)2E8O    3U1N    4BZB    4BZC    4CC9    4MZ7    4QFX    4QFY    4QFZ    4QG0    4QG1    4QG2    4QG4    4TNP    4TNQ    4TNR    4TNX    4TNY    4TNZ    4TO0    4TO1    4TO2    4TO3    4TO4    4TO5    4TO6   
PDB (PDBSum)2E8O    3U1N    4BZB    4BZC    4CC9    4MZ7    4QFX    4QFY    4QFZ    4QG0    4QG1    4QG2    4QG4    4TNP    4TNQ    4TNR    4TNX    4TNY    4TNZ    4TO0    4TO1    4TO2    4TO3    4TO4    4TO5    4TO6   
PDB (IMB)2E8O    3U1N    4BZB    4BZC    4CC9    4MZ7    4QFX    4QFY    4QFZ    4QG0    4QG1    4QG2    4QG4    4TNP    4TNQ    4TNR    4TNX    4TNY    4TNZ    4TO0    4TO1    4TO2    4TO3    4TO4    4TO5    4TO6   
PDB (RSDB)2E8O    3U1N    4BZB    4BZC    4CC9    4MZ7    4QFX    4QFY    4QFZ    4QG0    4QG1    4QG2    4QG4    4TNP    4TNQ    4TNR    4TNX    4TNY    4TNZ    4TO0    4TO1    4TO2    4TO3    4TO4    4TO5    4TO6   
Peptide AtlasQ9Y3Z3
HPRD08418
IPIIPI00294739   IPI00943982   IPI00553034   
Protein Interaction databases
DIP (DOE-UCLA)Q9Y3Z3
IntAct (EBI)Q9Y3Z3
BioGRIDSAMHD1
IntegromeDBSAMHD1
STRING (EMBL)SAMHD1
Ontologies - Pathways
QuickGOQ9Y3Z3
Ontology : AmiGOnucleic acid binding  RNA binding  protein binding  intracellular  nucleus  nucleoplasm  nucleoplasm  plasma membrane  dGTP catabolic process  immune response  zinc ion binding  dGTPase activity  cytokine-mediated signaling pathway  dGTP binding  regulation of innate immune response  dATP catabolic process  protein homotetramerization  defense response to virus  type I interferon signaling pathway  
Ontology : EGO-EBInucleic acid binding  RNA binding  protein binding  intracellular  nucleus  nucleoplasm  nucleoplasm  plasma membrane  dGTP catabolic process  immune response  zinc ion binding  dGTPase activity  cytokine-mediated signaling pathway  dGTP binding  regulation of innate immune response  dATP catabolic process  protein homotetramerization  defense response to virus  type I interferon signaling pathway  
Protein Interaction DatabaseSAMHD1
DoCM (Curated mutations)SAMHD1
Wikipedia pathwaysSAMHD1
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSAMHD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SAMHD1
dbVarSAMHD1
ClinVarSAMHD1
1000_GenomesSAMHD1 
Exome Variant ServerSAMHD1
SNP (GeneSNP Utah)SAMHD1
SNP : HGBaseSAMHD1
Genetic variants : HAPMAPSAMHD1
Genomic Variants (DGV)SAMHD1 [DGVbeta]
Mutations
Somatic Mutations in Cancer : COSMICSAMHD1 
CONAN: Copy Number AnalysisSAMHD1 
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
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
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)20:35520227-35580246
Mutations and Diseases : HGMDSAMHD1
OMIM606754    612952    614415   
MedgenSAMHD1
NextProtQ9Y3Z3 [Medical]
GENETestsSAMHD1
Disease Genetic AssociationSAMHD1
Huge Navigator SAMHD1 [HugePedia]  SAMHD1 [HugeCancerGEM]
snp3D : Map Gene to Disease25939
DGIdb (Drug Gene Interaction db)SAMHD1
General knowledge
Homologs : HomoloGeneSAMHD1
Homology/Alignments : Family Browser (UCSC)SAMHD1
Phylogenetic Trees/Animal Genes : TreeFamSAMHD1
Chemical/Protein Interactions : CTD25939
Chemical/Pharm GKB GenePA34938
Clinical trialSAMHD1
Other databases
Probes
Litterature
PubMed124 Pubmed reference(s) in Entrez
CoreMineSAMHD1
GoPubMedSAMHD1
iHOPSAMHD1
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 17:13:06 CET 2015

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.