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SNX1 (sorting nexin 1)

Identity

Other namesHsT17379
VPS5
HGNC (Hugo) SNX1
LocusID (NCBI) 6642
Atlas_Id 49891
Location 15q22.31
Location_base_pair Starts at 64388083 and ends at 64436433 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2015)
FAM96A 15q22.31 / SNX1 15q22.31SNX1 15q22.31 / FAM96A 15q22.31SNX1 15q22.31 / SCG5 15q13.3

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)SNX1   11172
Cards
Entrez_Gene (NCBI)SNX1  6642  sorting nexin 1
GeneCards (Weizmann)SNX1
Ensembl hg19 (Hinxton) [Gene_View]  chr15:64388083-64436433 [Contig_View]  SNX1 [Vega]
Ensembl hg38 (Hinxton) [Gene_View]  chr15:64388083-64436433 [Contig_View]  SNX1 [Vega]
TCGA cBioPortalSNX1
AceView (NCBI)SNX1
Genatlas (Paris)SNX1
WikiGenes6642
SOURCE (Princeton)SNX1
Genomic and cartography
GoldenPath hg19 (UCSC)SNX1  -     chr15:64388083-64436433 +  15q22.31   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SNX1  -     15q22.31   [Description]    (hg38-Dec_2013)
EnsemblSNX1 - 15q22.31 [CytoView hg19]  SNX1 - 15q22.31 [CytoView hg38]
Mapping of homologs : NCBISNX1 [Mapview hg19]  SNX1 [Mapview hg38]
OMIM601272   
Gene and transcription
Genbank (Entrez)AB209013 AF065483 AF065484 AF131792 AK128179
RefSeq transcript (Entrez)NM_001242933 NM_003099 NM_148955 NM_152826
RefSeq genomic (Entrez)NC_000015 NC_018926 NG_029708 NT_010194 NW_004929398
Consensus coding sequences : CCDS (NCBI)SNX1
Cluster EST : UnigeneHs.188634 [ NCBI ]
CGAP (NCI)Hs.188634
Alternative Splicing : Fast-db (Paris)GSHG0009928
Gene ExpressionSNX1 [ NCBI-GEO ]     SNX1 [ SEEK ]   SNX1 [ MEM ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)6642
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13596 (Uniprot)
NextProtQ13596  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13596
Splice isoforms : SwissVarQ13596 (Swissvar)
PhosPhoSitePlusQ13596
Domaine pattern : Prosite (Expaxy)PX (PS50195)   
Domains : Interpro (EBI)Phox    SNX1    Sorting_nexin_N    Vps5_C   
Domain families : Pfam (Sanger)PX (PF00787)    Sorting_nexin (PF03700)    Vps5 (PF09325)   
Domain families : Pfam (NCBI)pfam00787    pfam03700    pfam09325   
Domain families : Smart (EMBL)PX (SM00312)  
DMDM Disease mutations6642
Blocks (Seattle)SNX1
PDB (SRS)2I4K    4FZS   
PDB (PDBSum)2I4K    4FZS   
PDB (IMB)2I4K    4FZS   
PDB (RSDB)2I4K    4FZS   
Structural Biology KnowledgeBase2I4K    4FZS   
SCOP (Structural Classification of Proteins)2I4K    4FZS   
CATH (Classification of proteins structures)2I4K    4FZS   
Peptide AtlasQ13596
HPRD03171
IPIIPI00220527   IPI00183274   IPI00556082   IPI00183530   
Protein Interaction databases
DIP (DOE-UCLA)Q13596
IntAct (EBI)Q13596
BioGRIDSNX1
IntegromeDBSNX1
STRING (EMBL)SNX1
ZODIACSNX1
Ontologies - Pathways
QuickGOQ13596
Ontology : AmiGOepidermal growth factor receptor binding  insulin receptor binding  protein binding  cytoplasm  Golgi apparatus  cytosol  intracellular protein transport  endosome membrane  membrane  vesicle organization  extrinsic component of membrane  lamellipodium  retromer complex  retromer, tubulation complex  receptor internalization  early endosome membrane  early endosome to Golgi transport  phosphatidylinositol binding  retrograde transport, endosome to Golgi  retrograde transport, endosome to Golgi  identical protein binding  protein homodimerization activity  intracellular membrane-bounded organelle  protein complex  positive regulation of protein catabolic process  protein heterodimerization activity  protein heterodimerization activity  lamellipodium morphogenesis  transferrin receptor binding  leptin receptor binding  
Ontology : EGO-EBIepidermal growth factor receptor binding  insulin receptor binding  protein binding  cytoplasm  Golgi apparatus  cytosol  intracellular protein transport  endosome membrane  membrane  vesicle organization  extrinsic component of membrane  lamellipodium  retromer complex  retromer, tubulation complex  receptor internalization  early endosome membrane  early endosome to Golgi transport  phosphatidylinositol binding  retrograde transport, endosome to Golgi  retrograde transport, endosome to Golgi  identical protein binding  protein homodimerization activity  intracellular membrane-bounded organelle  protein complex  positive regulation of protein catabolic process  protein heterodimerization activity  protein heterodimerization activity  lamellipodium morphogenesis  transferrin receptor binding  leptin receptor binding  
Protein Interaction DatabaseSNX1
Atlas of Cancer Signalling NetworkSNX1
Wikipedia pathwaysSNX1
Orthology - Evolution
OrthoDB6642
Phylogenetic Trees/Animal Genes : TreeFamSNX1
Homologs : HomoloGeneSNX1
Homology/Alignments : Family Browser (UCSC)SNX1
Gene fusions - Rearrangements
Fusion: TCGAFAM96A 15q22.31 SNX1 15q22.31 BRCA
Fusion: TCGASNX1 15q22.31 FAM96A 15q22.31 BRCA
Fusion: TCGASNX1 15q22.31 SCG5 15q13.3 SKCM
Polymorphisms : SNP, variants
NCBI Variation ViewerSNX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SNX1
dbVarSNX1
ClinVarSNX1
1000_GenomesSNX1 
Exome Variant ServerSNX1
SNP (GeneSNP Utah)SNX1
SNP : HGBaseSNX1
Genetic variants : HAPMAPSNX1
Genomic Variants (DGV)SNX1 [DGVbeta]
Mutations
ICGC Data PortalSNX1 
TCGA Data PortalSNX1 
Tumor PortalSNX1
TCGA Copy Number PortalSNX1
Somatic Mutations in Cancer : COSMICSNX1 
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
BioMutasearch SNX1
DgiDB (Drug Gene Interaction Database)SNX1
DoCM (Curated mutations)SNX1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SNX1 (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)15:64388083-64436433
CONAN: Copy Number AnalysisSNX1 
Mutations and Diseases : HGMDSNX1
OMIM601272   
MedgenSNX1
NextProtQ13596 [Medical]
TSGene6642
GENETestsSNX1
Huge Navigator SNX1 [HugePedia]  SNX1 [HugeCancerGEM]
snp3D : Map Gene to Disease6642
BioCentury BCIQSNX1
General knowledge
Chemical/Protein Interactions : CTD6642
Chemical/Pharm GKB GenePA36011
Clinical trialSNX1
Other databases
Probes
Litterature
PubMed55 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSNX1
GoPubMedSNX1
iHOPSNX1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Jan 16 19:32:20 CET 2016

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