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USH2A usherin [ Homo sapiens (human) ]

Gene ID: 7399, updated on 23-Dec-2018

Summary

Official Symbol
USH2Aprovided by HGNC
Official Full Name
usherinprovided by HGNC
Primary source
HGNC:HGNC:12601
See related
Ensembl:ENSG00000042781 MIM:608400
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]
Expression
Biased expression in liver (RPKM 1.7), testis (RPKM 0.3) and 1 other tissue See more
Orthologs

Genomic context

See USH2A in Genome Data Viewer
Location:
1q41
Exon count:
72
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 LOC105372919 Neighboring gene potassium channel tetramerization domain containing 3 Neighboring gene uncharacterized LOC102723833 Neighboring gene uncharacterized LOC105372918 Neighboring gene mitochondrial ribosomal protein S18B pseudogene 1 Neighboring gene uncharacterized LOC107985596 Neighboring gene estrogen related receptor gamma

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Dissecting the genetics of chronic mucus hypersecretion in smokers with and without COPD.
NHGRI GWA Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
establishment of protein localization ISS
Inferred from Sequence or Structural Similarity
more info
 
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 animal 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
USH2 complex ISS
Inferred from Sequence or Structural Similarity
more info
 
apical plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
basement membrane IDA
Inferred from Direct Assay
more info
PubMed 
ciliary basal body IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
 
periciliary membrane compartment ISS
Inferred from Sequence or Structural Similarity
more info
 
colocalizes_with photoreceptor connecting cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
colocalizes_with photoreceptor inner segment ISS
Inferred from Sequence or Structural Similarity
more info
 
stereocilia ankle link ISS
Inferred from Sequence or Structural Similarity
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
 
colocalizes_with terminal bouton ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
usherin
Names
Usher syndrome 2A (autosomal recessive, mild)
usher syndrome type IIa protein
usher syndrome type-2A protein

NCBI Reference Sequences (RefSeq)

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 RefSeqGene

    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
    ENSP00000355909.3, ENST00000366942.3
    Conserved Domains (7) summary
    smart00060
    Location:13681451
    FN3; Fibronectin type 3 domain
    smart00180
    Location:847897
    EGF_Lam; Laminin-type epidermal growth factor-like domai
    smart00560
    Location:146283
    LamGL; LamG-like jellyroll fold domain
    cd00055
    Location:900948
    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
    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 ...
    pfam00053
    Location:641691
    Laminin_EGF; Laminin EGF domain
    cl02806
    Location:295516
    Laminin_N; Laminin N-terminal (Domain VI)
  2. NM_206933.3NP_996816.2  usherin isoform B precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is the longer transcript and it encodes the longer isoform (B).
    Source sequence(s)
    AA883599, AADB02001158, AC092799, AF055580, AL445650, AY481573
    Consensus CDS
    CCDS31025.1
    UniProtKB/Swiss-Prot
    O75445
    Related
    ENSP00000305941.3, ENST00000307340.7
    Conserved Domains (9) summary
    smart00060
    Location:13681451
    FN3; Fibronectin type 3 domain
    smart00180
    Location:847897
    EGF_Lam; Laminin-type epidermal growth factor-like domai
    smart00560
    Location:146283
    LamGL; LamG-like jellyroll fold domain
    cd00055
    Location:900948
    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
    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
    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 ...
    pfam00041
    Location:19562044
    fn3; Fibronectin type III domain
    pfam00053
    Location:641691
    Laminin_EGF; Laminin EGF domain
    cl02806
    Location:295516
    Laminin_N; Laminin N-terminal (Domain VI)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

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