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economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas).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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TXNDC5 (thioredoxin domain containing 5 (endoplasmic reticulum))

Identity

Other namesENDOPDI
ERP46
HCC-2
PDIA15
STRF8
UNQ364
HGNC (Hugo) TXNDC5
LocusID (NCBI) 81567
Location 6p24.3
Location_base_pair Starts at 7881483 and ends at 7910310 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)TXNDC5   21073
Cards
Entrez_Gene (NCBI)TXNDC5  81567  thioredoxin domain containing 5 (endoplasmic reticulum)
GeneCards (Weizmann)TXNDC5
Ensembl hg19 (Hinxton)ENSG00000239264 [Gene_View]  chr6:7881483-7910310 [Contig_View]  TXNDC5 [Vega]
Ensembl hg38 (Hinxton)ENSG00000239264 [Gene_View]  chr6:7881483-7910310 [Contig_View]  TXNDC5 [Vega]
ICGC DataPortalENSG00000239264
cBioPortalTXNDC5
AceView (NCBI)TXNDC5
Genatlas (Paris)TXNDC5
WikiGenes81567
SOURCE (Princeton)TXNDC5
Genomic and cartography
GoldenPath hg19 (UCSC)TXNDC5  -     chr6:7881483-7910310 -  6p24.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)TXNDC5  -     6p24.3   [Description]    (hg38-Dec_2013)
EnsemblTXNDC5 - 6p24.3 [CytoView hg19]  TXNDC5 - 6p24.3 [CytoView hg38]
Mapping of homologs : NCBITXNDC5 [Mapview hg19]  TXNDC5 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AJ440721 AK025006 AK075291 AK098089 AK315598
RefSeq transcript (Entrez)NM_001145549 NM_022085 NM_030810
RefSeq genomic (Entrez)NC_000006 NC_018917 NT_007592 NW_004929326
Consensus coding sequences : CCDS (NCBI)TXNDC5
Cluster EST : UnigeneHs.150837 [ NCBI ]
CGAP (NCI)Hs.150837
Alternative Splicing : Fast-db (Paris)GSHG0034019
Alternative Splicing GalleryENSG00000239264
Gene ExpressionTXNDC5 [ NCBI-GEO ]     TXNDC5 [ SEEK ]   TXNDC5 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8NBS9 (Uniprot)
NextProtQ8NBS9  [Medical]
With graphics : InterProQ8NBS9
Splice isoforms : SwissVarQ8NBS9 (Swissvar)
Domaine pattern : Prosite (Expaxy)ER_TARGET (PS00014)    THIOREDOXIN_1 (PS00194)    THIOREDOXIN_2 (PS51352)   
Domains : Interpro (EBI)Disulphide_isomerase    Thioredoxin-like_fold    Thioredoxin_CS    Thioredoxin_domain   
Related proteins : CluSTrQ8NBS9
Domain families : Pfam (Sanger)Thioredoxin (PF00085)   
Domain families : Pfam (NCBI)pfam00085   
DMDM Disease mutations81567
Blocks (Seattle)Q8NBS9
PDB (SRS)2DIZ    3UJ1    3UVT    3WGD    3WGE    3WGX   
PDB (PDBSum)2DIZ    3UJ1    3UVT    3WGD    3WGE    3WGX   
PDB (IMB)2DIZ    3UJ1    3UVT    3WGD    3WGE    3WGX   
PDB (RSDB)2DIZ    3UJ1    3UVT    3WGD    3WGE    3WGX   
Human Protein AtlasENSG00000239264
Peptide AtlasQ8NBS9
HPRD18249
Protein Interaction databases
DIP (DOE-UCLA)Q8NBS9
IntAct (EBI)Q8NBS9
FunCoupENSG00000239264
BioGRIDTXNDC5
IntegromeDBTXNDC5
STRING (EMBL)TXNDC5
Ontologies - Pathways
QuickGOQ8NBS9
Ontology : AmiGOprotein disulfide isomerase activity  protein binding  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum lumen  protein folding  post-Golgi vesicle-mediated transport  response to endoplasmic reticulum stress  negative regulation of apoptotic process  lysosomal lumen  apoptotic cell clearance  cell redox homeostasis  membrane organization  extracellular exosome  
Ontology : EGO-EBIprotein disulfide isomerase activity  protein binding  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum lumen  protein folding  post-Golgi vesicle-mediated transport  response to endoplasmic reticulum stress  negative regulation of apoptotic process  lysosomal lumen  apoptotic cell clearance  cell redox homeostasis  membrane organization  extracellular exosome  
Pathways : KEGGProtein processing in endoplasmic reticulum   
Protein Interaction DatabaseTXNDC5
DoCM (Curated mutations)TXNDC5
Wikipedia pathwaysTXNDC5
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerTXNDC5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TXNDC5
dbVarTXNDC5
ClinVarTXNDC5
1000_GenomesTXNDC5 
Exome Variant ServerTXNDC5
SNP (GeneSNP Utah)TXNDC5
SNP : HGBaseTXNDC5
Genetic variants : HAPMAPTXNDC5
Genomic Variants (DGV)TXNDC5 [DGVbeta]
Mutations
ICGC Data PortalENSG00000239264 
Somatic Mutations in Cancer : COSMICTXNDC5 
CONAN: Copy Number AnalysisTXNDC5 
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)6:7881483-7910310
Mutations and Diseases : HGMDTXNDC5
OMIM
MedgenTXNDC5
NextProtQ8NBS9 [Medical]
GENETestsTXNDC5
Disease Genetic AssociationTXNDC5
Huge Navigator TXNDC5 [HugePedia]  TXNDC5 [HugeCancerGEM]
snp3D : Map Gene to Disease81567
DGIdb (Drug Gene Interaction db)TXNDC5
General knowledge
Homologs : HomoloGeneTXNDC5
Homology/Alignments : Family Browser (UCSC)TXNDC5
Phylogenetic Trees/Animal Genes : TreeFamTXNDC5
Chemical/Protein Interactions : CTD81567
Chemical/Pharm GKB GenePA134992492
Clinical trialTXNDC5
Cancer Resource (Charite)ENSG00000239264
Other databases
Probes
Litterature
PubMed47 Pubmed reference(s) in Entrez
CoreMineTXNDC5
GoPubMedTXNDC5
iHOPTXNDC5
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 17:45:28 CET 2015

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.