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    USH2A usherin [ Homo sapiens (human) ]

    Gene ID: 7399, updated on 6-Nov-2023

    Summary

    Official Symbol
    USH2Aprovided by HGNC
    Official Full Name
    usherinprovided by HGNC
    Primary source
    HGNC:HGNC:12601
    See related
    Ensembl:ENSG00000042781 MIM:608400; AllianceGenome:HGNC:12601
    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
    NEW
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    Genomic context

    See USH2A in Genome Data Viewer
    Location:
    1q41
    Exon count:
    72
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (215622891..216423448, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (214863291..215663779, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (215796233..216596790, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904598 Neighboring gene MPRA-validated peak693 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr1:215677085-215677330 Neighboring gene uncharacterized LOC124904599 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:215740861-215741721 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:215756646-215757845 Neighboring gene MPRA-validated peak696 silencer Neighboring gene small nucleolar RNA SNORD116 Neighboring gene potassium channel tetramerization domain containing 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4139 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:216230868-216232067 Neighboring gene NANOG hESC enhancer GRCh37_chr1:216268639-216269183 Neighboring gene USH2A antisense RNA 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:216356256-216356909 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:216419825-216420431 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4209 Neighboring gene USH2A antisense RNA 1 Neighboring gene mitochondrial ribosomal protein S18B pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:216566486-216566587 Neighboring gene uncharacterized LOC107985596 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:216659268-216659830 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:216771579-216772306 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:216773848-216774416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1817 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2536 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4286 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4347 Neighboring gene estrogen related receptor gamma Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4384 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:216913568-216914135 Neighboring gene uncharacterized LOC124904512

    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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables collagen binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables myosin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in establishment of localization in cell IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within establishment of protein localization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in hair cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner ear auditory receptor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inner ear receptor cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner ear receptor cell differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in maintenance of animal organ identity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of light stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of USH2 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in basement membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in ciliary basal body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in 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
     
    located_in stereocilia ankle link ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of stereocilia ankle link complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in stereocilium bundle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in 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)

    NEW Try the new Transcript table

    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_009497.2 RefSeqGene

      Range
      5001..805558
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_007123.6NP_009054.6  usherin isoform A precursor

      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)
      AC138024, AF055580, AL358858, AL445650
      Consensus CDS
      CCDS1516.1
      Related
      ENSP00000355909.3, ENST00000366942.3
      Conserved Domains (8) 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 ...
      pfam00041
      Location:10581132
      fn3; Fibronectin type III domain
      pfam00053
      Location:641691
      Laminin_EGF; Laminin EGF domain
      cl02806
      Location:291516
      Laminin_N; Laminin N-terminal (Domain VI)
    2. NM_206933.4NP_996816.3  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)
      AC092799, AL445650, AY481573
      Consensus CDS
      CCDS31025.1
      UniProtKB/Swiss-Prot
      O75445, Q5VVM9, Q6S362, Q9NS27
      UniProtKB/TrEMBL
      A0A0K1P7S2
      Related
      ENSP00000305941.3, ENST00000307340.8
      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:11501227
      fn3; Fibronectin type III domain
      pfam00053
      Location:641691
      Laminin_EGF; Laminin EGF domain
      cl02806
      Location:291516
      Laminin_N; Laminin N-terminal (Domain VI)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      215622891..216423448 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      214863291..215663779 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)