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USH2A Usher syndrome 2A (autosomal recessive, mild) [ Homo sapiens (human) ]

Gene ID: 7399, updated on 6-Jul-2014
Official Symbol
USH2Aprovided by HGNC
Official Full Name
Usher syndrome 2A (autosomal recessive, mild)provided by HGNC
Primary source
HGNC:12601
See related
Ensembl:ENSG00000042781; HPRD:02042; HPRD:09759; MIM:608400; Vega:OTTHUMG00000037079
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
US2; RP39; USH2; dJ1111A8.1
Summary
This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
See USH2A in Epigenomics, MapViewer
Location:
1q41
Exon count :
72
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 1 NC_000001.11 (215622894..216423396, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (215796236..216596738, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929612 Neighboring gene potassium channel tetramerization domain containing 3 Neighboring gene uncharacterized LOC102723833 Neighboring gene mitochondrial ribosomal protein S18B pseudogene 1 Neighboring gene estrogen-related receptor gamma Neighboring gene G patch domain containing 2

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Retinitis pigmentosa 39
MedGen: C3151138 OMIM: 613809 GeneReviews: Retinitis Pigmentosa Overview
Compare labs
Usher syndrome, type 2A
MedGen: C1848634 OMIM: 276901 GeneReviews: Usher Syndrome Type II
Compare labs

NHGRI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
NHGRI GWA Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
collagen binding IDA
Inferred from Direct Assay
more info
PubMed 
myosin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
 
Process Evidence Code Pubs
hair cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
inner ear receptor cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
maintenance of organ identity IMP
Inferred from Mutant Phenotype
more info
PubMed 
photoreceptor cell maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to stimulus IEA
Inferred from Electronic Annotation
more info
 
sensory perception of light stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
apical plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
basement membrane IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
stereocilia ankle link complex ISS
Inferred from Sequence or Structural Similarity
more info
 
stereocilium bundle ISS
Inferred from Sequence or Structural Similarity
more info
 
stereocilium membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
Preferred Names
usherin
Names
usherin
usher syndrome type-2A protein
usher syndrome type IIa protein

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009497.1 

    Range
    5001..805503
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_007123.5NP_009054.5  usherin isoform A

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) uses a different splice site in its 3' coding region when compared to variant 2. The resulting protein (isoform A) has a shorter and distinct C-terminus, compared to isoform B.
    Source sequence(s)
    AF055580, AY481573
    Consensus CDS
    CCDS1516.1
    UniProtKB/Swiss-Prot
    O75445
    Related
    ENSP00000355909, OTTHUMP00000035145, ENST00000366942, OTTHUMT00000090016
    Conserved Domains (4) summary
    smart00560
    Location:146283
    Blast Score: 341
    LamGL; LamG-like jellyroll fold domain
    cd00055
    Location:900948
    Blast Score: 149
    EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
    cd00063
    Location:12421357
    Blast Score: 169
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cl02806
    Location:313516
    Blast Score: 238
    Laminin_N; Laminin N-terminal (Domain VI)
  2. NM_206933.2NP_996816.2  usherin isoform B

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is the longer transcript and it encodes the longer isoform (B).
    Source sequence(s)
    AA883599, AADB02001158, AF055580, AY481573
    Consensus CDS
    CCDS31025.1
    UniProtKB/Swiss-Prot
    O75445
    Related
    ENSP00000305941, OTTHUMP00000063383, ENST00000307340, OTTHUMT00000128138
    Conserved Domains (5) summary
    smart00560
    Location:146283
    Blast Score: 341
    LamGL; LamG-like jellyroll fold domain
    cd00055
    Location:900948
    Blast Score: 171
    EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
    cd00063
    Location:25332619
    Blast Score: 161
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd00110
    Location:17161868
    Blast Score: 264
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    cl02806
    Location:313516
    Blast Score: 243
    Laminin_N; Laminin N-terminal (Domain VI)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000001.11 

    Range
    215622894..216423396
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000133.1 

    Range
    186470498..187272188
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 

    Range
    217068567..217869890
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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