Description: Homo sapiens Usher syndrome 2A (autosomal recessive, mild) (USH2A), transcript variant 2, mRNA. RefSeq Summary (NM_206933): 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]. Transcript (Including UTRs) Position: hg19 chr1:215,796,236-216,596,738 Size: 800,503 Total Exon Count: 72 Strand: - Coding Region Position: hg19 chr1:215,799,123-216,595,678 Size: 796,556 Coding Exon Count: 71
ID:USH2A_HUMAN DESCRIPTION: RecName: Full=Usherin; AltName: Full=Usher syndrome type IIa protein; AltName: Full=Usher syndrome type-2A protein; Flags: Precursor; FUNCTION: Involved in hearing and vision. SUBUNIT: Interacts with collagen IV and fibronectin via its laminin EGF-like domains. Interaction with collagen may be required for stable integration into the basement membrane. Interacts with USH1C and WHRN. Interacts with NINL. Interacts with PDZD7. SUBCELLULAR LOCATION: Cell projection, stereocilium membrane; Single-pass type I membrane protein. Note=Probable component of the interstereocilia ankle links in the inner ear sensory cells. SUBCELLULAR LOCATION: Isoform 2: Secreted. TISSUE SPECIFICITY: Present in the basement membrane of many, but not all tissues. Expressed in retina, cochlea, small and large intestine, pancreas, bladder, prostate, esophagus, trachea, thymus, salivary glands, placenta, ovary, fallopian tube, uterus and testis. Absent in many other tissues such as heart, lung, liver, kidney and brain. In the retina, it is present in the basement membranes in the Bruch's layer choroid capillary basement membranes, where it localizes just beneath the retinal pigment epithelial cells (at protein level). Weakly expressed. Isoform 2 is expressed in fetal eye, cochlea and heart, and at very low level in brain, CNS, intestine, skeleton, tongue, kidney and lung. Isoform 2 is not expressed in stomach and liver. In adult tissues, isoform 2 is expressed in neural retina and testis, and at low level in brain, heart, kidney and liver. Isoform 1 displays a similar pattern of expression but is expressed at very low level in fetal cochlea. DOMAIN: The PDZ-binding motif probably mediates the association with some of the PDZ domains of USH1C and WHRN (By similarity). DISEASE: Defects in USH2A are the cause of Usher syndrome type 2A (USH2A) [MIM:276901]. USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa and sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses. DISEASE: Defects in USH2A are the cause of retinitis pigmentosa type 39 (RP39) [MIM:613809]. RP leads to degeneration of retinal photoreceptor cells. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP39 inheritance is autosomal recessive. SIMILARITY: Contains 35 fibronectin type-III domains. SIMILARITY: Contains 10 laminin EGF-like domains. SIMILARITY: Contains 2 laminin G-like domains. SIMILARITY: Contains 1 laminin N-terminal domain. WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/USH2A";
Apolipoproteins C Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics.
[PubMed 17903299]
Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
Pfam Domains: PF00041 - Fibronectin type III domain PF00053 - Laminin EGF domain PF00054 - Laminin G domain PF00055 - Laminin N-terminal (Domain VI) PF02210 - Laminin G domain PF13385 - Concanavalin A-like lectin/glucanases superfamily
SCOP Domains: 48726 - Immunoglobulin 49265 - Fibronectin type III 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin
ModBase Predicted Comparative 3D Structure on O75445
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
US Server
Sequence and Links to Tools and Databases 
Common Gene Haplotype Alleles 
