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economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas).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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SCGB2A1 (secretoglobin, family 2A, member 1)

Identity

Other namesLPHC
LPNC
MGB2
UGB3
HGNC (Hugo) SCGB2A1
LocusID (NCBI) 4246
Location 11q12.3
Location_base_pair Starts at 61976140 and ends at 61981411 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)SCGB2A1   7051
Cards
Entrez_Gene (NCBI)SCGB2A1  4246  secretoglobin, family 2A, member 1
GeneCards (Weizmann)SCGB2A1
Ensembl hg19 (Hinxton)ENSG00000124939 [Gene_View]  chr11:61976140-61981411 [Contig_View]  SCGB2A1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000124939 [Gene_View]  chr11:61976140-61981411 [Contig_View]  SCGB2A1 [Vega]
ICGC DataPortalENSG00000124939
cBioPortalSCGB2A1
AceView (NCBI)SCGB2A1
Genatlas (Paris)SCGB2A1
WikiGenes4246
SOURCE (Princeton)SCGB2A1
Genomic and cartography
GoldenPath hg19 (UCSC)SCGB2A1  -     chr11:61976140-61981411 +  11q12.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SCGB2A1  -     11q12.3   [Description]    (hg38-Dec_2013)
EnsemblSCGB2A1 - 11q12.3 [CytoView hg19]  SCGB2A1 - 11q12.3 [CytoView hg38]
Mapping of homologs : NCBISCGB2A1 [Mapview hg19]  SCGB2A1 [Mapview hg38]
OMIM604398   
Gene and transcription
Genbank (Entrez)AF071219 AJ224173 BC062218
RefSeq transcript (Entrez)NM_002407
RefSeq genomic (Entrez)NC_000011 NC_018922 NT_167190 NW_004929380
Consensus coding sequences : CCDS (NCBI)SCGB2A1
Cluster EST : UnigeneHs.97644 [ NCBI ]
CGAP (NCI)Hs.97644
Alternative Splicing : Fast-db (Paris)GSHG0004916
Alternative Splicing GalleryENSG00000124939
Gene ExpressionSCGB2A1 [ NCBI-GEO ]     SCGB2A1 [ SEEK ]   SCGB2A1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75556 (Uniprot)
NextProtO75556  [Medical]
With graphics : InterProO75556
Splice isoforms : SwissVarO75556 (Swissvar)
Domaine pattern : Prosite (Expaxy)SCGB (PS51311)   
Domains : Interpro (EBI)Secretoglobin   
Related proteins : CluSTrO75556
Domain families : Pfam (Sanger)Uteroglobin (PF01099)   
Domain families : Pfam (NCBI)pfam01099   
DMDM Disease mutations4246
Blocks (Seattle)O75556
Human Protein AtlasENSG00000124939
Peptide AtlasO75556
HPRD05096
IPIIPI00026126   
Protein Interaction databases
DIP (DOE-UCLA)O75556
IntAct (EBI)O75556
FunCoupENSG00000124939
BioGRIDSCGB2A1
IntegromeDBSCGB2A1
STRING (EMBL)SCGB2A1
Ontologies - Pathways
QuickGOO75556
Ontology : AmiGOextracellular space  androgen receptor signaling pathway  protein heterodimerization activity  
Ontology : EGO-EBIextracellular space  androgen receptor signaling pathway  protein heterodimerization activity  
Protein Interaction DatabaseSCGB2A1
DoCM (Curated mutations)SCGB2A1
Wikipedia pathwaysSCGB2A1
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSCGB2A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SCGB2A1
dbVarSCGB2A1
ClinVarSCGB2A1
1000_GenomesSCGB2A1 
Exome Variant ServerSCGB2A1
SNP (GeneSNP Utah)SCGB2A1
SNP : HGBaseSCGB2A1
Genetic variants : HAPMAPSCGB2A1
Genomic Variants (DGV)SCGB2A1 [DGVbeta]
Mutations
ICGC Data PortalENSG00000124939 
Somatic Mutations in Cancer : COSMICSCGB2A1 
CONAN: Copy Number AnalysisSCGB2A1 
LOVD (Leiden Open Variation Database)Whole genome datasets
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)11:61976140-61981411
Mutations and Diseases : HGMDSCGB2A1
OMIM604398   
MedgenSCGB2A1
NextProtO75556 [Medical]
GENETestsSCGB2A1
Disease Genetic AssociationSCGB2A1
Huge Navigator SCGB2A1 [HugePedia]  SCGB2A1 [HugeCancerGEM]
snp3D : Map Gene to Disease4246
DGIdb (Drug Gene Interaction db)SCGB2A1
General knowledge
Homologs : HomoloGeneSCGB2A1
Homology/Alignments : Family Browser (UCSC)SCGB2A1
Phylogenetic Trees/Animal Genes : TreeFamSCGB2A1
Chemical/Protein Interactions : CTD4246
Chemical/Pharm GKB GenePA34992
Clinical trialSCGB2A1
Cancer Resource (Charite)ENSG00000124939
Other databases
Probes
Litterature
PubMed26 Pubmed reference(s) in Entrez
CoreMineSCGB2A1
GoPubMedSCGB2A1
iHOPSCGB2A1
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 17:13:58 CET 2015

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.