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USH2A (usherin)

Identity

Alias_namesUSH2
Usher syndrome 2A (autosomal recessive, mild)
Alias_symbol (synonym)RP39
Other aliasUS2
dJ1111A8.1
HGNC (Hugo) USH2A
LocusID (NCBI) 7399
Atlas_Id 75518
Location 1q41  [Link to chromosome band 1q41]
Location_base_pair Starts at 216173948 and ends at 216423396 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
CD46 (1q32.2) / USH2A (1q41)EPRS (1q41) / USH2A (1q41)USH2A (1q41) / EPC2 (2q23.1)
USH2A (1q41) / GARS (7p14.3)USH2A (1q41) / ROBO2 (3p12.3)

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)USH2A   12601
Cards
Entrez_Gene (NCBI)USH2A  7399  usherin
AliasesRP39; US2; USH2; dJ1111A8.1
GeneCards (Weizmann)USH2A
Ensembl hg19 (Hinxton)ENSG00000042781 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000042781 [Gene_View]  chr1:216173948-216423396 [Contig_View]  USH2A [Vega]
ICGC DataPortalENSG00000042781
TCGA cBioPortalUSH2A
AceView (NCBI)USH2A
Genatlas (Paris)USH2A
WikiGenes7399
SOURCE (Princeton)USH2A
Genetics Home Reference (NIH)USH2A
Genomic and cartography
GoldenPath hg38 (UCSC)USH2A  -     chr1:216173948-216423396 -  1q41   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)USH2A  -     1q41   [Description]    (hg19-Feb_2009)
EnsemblUSH2A - 1q41 [CytoView hg19]  USH2A - 1q41 [CytoView hg38]
Mapping of homologs : NCBIUSH2A [Mapview hg19]  USH2A [Mapview hg38]
OMIM276901   608400   613809   
Gene and transcription
Genbank (Entrez)AA883599 AF055580 AY481573
RefSeq transcript (Entrez)NM_007123 NM_206933
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)USH2A
Cluster EST : UnigeneHs.655974 [ NCBI ]
CGAP (NCI)Hs.655974
Alternative Splicing GalleryENSG00000042781
Gene ExpressionUSH2A [ NCBI-GEO ]   USH2A [ EBI - ARRAY_EXPRESS ]   USH2A [ SEEK ]   USH2A [ MEM ]
Gene Expression Viewer (FireBrowse)USH2A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)7399
GTEX Portal (Tissue expression)USH2A
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75445   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO75445  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75445
Splice isoforms : SwissVarO75445
PhosPhoSitePlusO75445
Domaine pattern : Prosite (Expaxy)EGF_1 (PS00022)    EGF_LAM_1 (PS01248)    EGF_LAM_2 (PS50027)    FN3 (PS50853)    LAM_G_DOMAIN (PS50025)    LAMININ_NTER (PS51117)   
Domains : Interpro (EBI)ConA-like_dom    FN3_dom    Ig-like_fold    LamG-like    Laminin_EGF    Laminin_G    Laminin_N    USH2A   
Domain families : Pfam (Sanger)fn3 (PF00041)    Laminin_EGF (PF00053)    Laminin_G_2 (PF02210)    Laminin_N (PF00055)   
Domain families : Pfam (NCBI)pfam00041    pfam00053    pfam02210    pfam00055   
Domain families : Smart (EMBL)EGF_Lam (SM00180)  FN3 (SM00060)  LamG (SM00282)  LamGL (SM00560)  LamNT (SM00136)  
Conserved Domain (NCBI)USH2A
DMDM Disease mutations7399
Blocks (Seattle)USH2A
SuperfamilyO75445
Human Protein AtlasENSG00000042781
Peptide AtlasO75445
HPRD02042
IPIIPI00410150   IPI00289540   IPI00741527   
Protein Interaction databases
DIP (DOE-UCLA)O75445
IntAct (EBI)O75445
FunCoupENSG00000042781
BioGRIDUSH2A
STRING (EMBL)USH2A
ZODIACUSH2A
Ontologies - Pathways
QuickGOO75445
Ontology : AmiGOphotoreceptor inner segment  stereocilia ankle link complex  protein binding  collagen binding  basement membrane  cytoplasm  visual perception  sensory perception of sound  integral component of membrane  apical plasma membrane  myosin binding  photoreceptor connecting cilium  stereocilium bundle  hair cell differentiation  ciliary basal body  protein homodimerization activity  establishment of protein localization  photoreceptor cell maintenance  maintenance of animal organ identity  response to stimulus  sensory perception of light stimulus  inner ear receptor cell differentiation  stereocilium membrane  periciliary membrane compartment  USH2 complex  
Ontology : EGO-EBIphotoreceptor inner segment  stereocilia ankle link complex  protein binding  collagen binding  basement membrane  cytoplasm  visual perception  sensory perception of sound  integral component of membrane  apical plasma membrane  myosin binding  photoreceptor connecting cilium  stereocilium bundle  hair cell differentiation  ciliary basal body  protein homodimerization activity  establishment of protein localization  photoreceptor cell maintenance  maintenance of animal organ identity  response to stimulus  sensory perception of light stimulus  inner ear receptor cell differentiation  stereocilium membrane  periciliary membrane compartment  USH2 complex  
NDEx NetworkUSH2A
Atlas of Cancer Signalling NetworkUSH2A
Wikipedia pathwaysUSH2A
Orthology - Evolution
OrthoDB7399
GeneTree (enSembl)ENSG00000042781
Phylogenetic Trees/Animal Genes : TreeFamUSH2A
HOVERGENO75445
HOGENOMO75445
Homologs : HomoloGeneUSH2A
Homology/Alignments : Family Browser (UCSC)USH2A
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerUSH2A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)USH2A
dbVarUSH2A
ClinVarUSH2A
1000_GenomesUSH2A 
Exome Variant ServerUSH2A
ExAC (Exome Aggregation Consortium)USH2A (select the gene name)
Genetic variants : HAPMAP7399
Genomic Variants (DGV)USH2A [DGVbeta]
DECIPHERUSH2A [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisUSH2A 
Mutations
ICGC Data PortalUSH2A 
TCGA Data PortalUSH2A 
Broad Tumor PortalUSH2A
OASIS PortalUSH2A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICUSH2A  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDUSH2A
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)Retinal and hearing impairment genetic mutation database
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch USH2A
DgiDB (Drug Gene Interaction Database)USH2A
DoCM (Curated mutations)USH2A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)USH2A (select a term)
intoGenUSH2A
Cancer3DUSH2A(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM276901    608400    613809   
Orphanet659    19168   
MedgenUSH2A
Genetic Testing Registry USH2A
NextProtO75445 [Medical]
TSGene7399
GENETestsUSH2A
Target ValidationUSH2A
Huge Navigator USH2A [HugePedia]
snp3D : Map Gene to Disease7399
BioCentury BCIQUSH2A
ClinGenUSH2A
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD7399
Chemical/Pharm GKB GenePA37228
Clinical trialUSH2A
Miscellaneous
canSAR (ICR)USH2A (select the gene name)
Probes
Litterature
PubMed96 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineUSH2A
EVEXUSH2A
GoPubMedUSH2A
iHOPUSH2A
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 18 13:43:21 CEST 2017

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