Ush2a usherin [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Ush2aprovided by RGD
Full Name: usherinprovided by RGD
Primary source: RGD:628777
See related: EnsemblRapid:ENSRNOG00000003738 AllianceGenome:RGD:628777
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1560269
Summary: Predicted to enable collagen binding activity; identical protein binding activity; and myosin binding activity. Involved in retina development in camera-type eye. Located in stereocilium and synapse. Colocalizes with several cellular components, including neuronal cell body; photoreceptor connecting cilium; and photoreceptor inner segment. Human ortholog(s) of this gene implicated in Usher syndrome (multiple); nonsyndromic deafness; and retinitis pigmentosa (multiple). Orthologous to human USH2A (usherin). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 3.2), Testes (RPKM 2.1) and 6 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q26

Exon count:: 71

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (102368783..103035230)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (99837445..100503935)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (106750738..107434195)

Chromosome 13 - NC_086031.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expressed in the cells of the outer nuclear layer of the retina and in cochlea, appearing in retina at embryonic day 17.
Title: Identification of the mouse and rat orthologs of the gene mutated in Usher syndrome type IIA and the cellular source of USH2A mRNA in retina, a target tissue of the disease.
Whrn connects to the Usher protein network in the cochlea and retina by direct association with USH2A and VLGR1.
Title: The DFNB31 gene product whirlin connects to the Usher protein network in the cochlea and retina by direct association with USH2A and VLGR1.

Submit: New GeneRIF Correction

General gene information

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Markers

D13Got96 (e-PCR)
- UniSTS:113427

RH137407 (e-PCR)
- UniSTS:219495

D13Got101 (e-PCR)
- UniSTS:114370

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables collagen binding	IEA Inferred from Electronic Annotation more info
enables collagen binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables myosin binding	IEA Inferred from Electronic Annotation more info
enables myosin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in animal organ morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
involved_in establishment of protein localization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within establishment of protein localization	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
involved_in inner ear auditory receptor cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inner ear auditory receptor cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in maintenance of animal organ identity	IEA Inferred from Electronic Annotation more info
involved_in maintenance of animal organ identity	ISO Inferred from Sequence Orthology more info
involved_in photoreceptor cell maintenance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
involved_in photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
involved_in retina development in camera-type eye	IEP Inferred from Expression Pattern more info	PubMed
involved_in sensory perception of light stimulus	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of light stimulus	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in tissue development	IBA Inferred from Biological aspect of Ancestor more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of USH2 complex	IEA Inferred from Electronic Annotation more info
part_of USH2 complex	ISO Inferred from Sequence Orthology more info
part_of USH2 complex	ISS Inferred from Sequence or Structural Similarity more info
located_in apical plasma membrane	IEA Inferred from Electronic Annotation more info
located_in apical plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	IEA Inferred from Electronic Annotation more info
located_in basement membrane	ISO Inferred from Sequence Orthology more info
located_in ciliary basal body	IEA Inferred from Electronic Annotation more info
located_in ciliary basal body	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in periciliary membrane compartment	IEA Inferred from Electronic Annotation more info
located_in periciliary membrane compartment	ISO Inferred from Sequence Orthology more info
located_in periciliary membrane compartment	ISS Inferred from Sequence or Structural Similarity more info
located_in photoreceptor connecting cilium	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor connecting cilium	IEA Inferred from Electronic Annotation more info
located_in photoreceptor connecting cilium	ISO Inferred from Sequence Orthology more info
located_in photoreceptor inner segment	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor inner segment	IEA Inferred from Electronic Annotation more info
located_in photoreceptor inner segment	ISO Inferred from Sequence Orthology more info
located_in stereocilia ankle link	ISO Inferred from Sequence Orthology more info
located_in stereocilia ankle link	ISS Inferred from Sequence or Structural Similarity more info
part_of stereocilia ankle link complex	IEA Inferred from Electronic Annotation more info
part_of stereocilia ankle link complex	ISO Inferred from Sequence Orthology more info
part_of stereocilia ankle link complex	ISS Inferred from Sequence or Structural Similarity more info
located_in stereocilium	IDA Inferred from Direct Assay more info	PubMed
located_in stereocilium bundle	ISO Inferred from Sequence Orthology more info
located_in stereocilium membrane	IEA Inferred from Electronic Annotation more info
located_in stereocilium membrane	ISO Inferred from Sequence Orthology more info
located_in terminal bouton	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: usherin

Names: Usher syndrome 2A (autosomal recessive, mild) homolog; Usher syndrome 2A homolog; usher syndrome type IIa protein homolog; usher syndrome type-2A protein homolog

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_001302219.1 → NP_001289148.1 usherin precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/Swiss-Prot

F1M2F9, Q8K3K1

UniProtKB/TrEMBL

A0A5H1ZRU3

Related

ENSRNOP00000004992.8, ENSRNOT00000004992.9

Conserved Domains (9) summary

smart00060
Location:1361 → 1444

FN3; Fibronectin type 3 domain

smart00560
Location:144 → 279

LamGL; LamG-like jellyroll fold domain

cd00055
Location:895 → 944

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:3954 → 4051

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:1706 → 1856

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:1054 → 1127

fn3; Fibronectin type III domain

pfam00053
Location:791 → 840

Laminin_EGF; Laminin EGF domain

pfam02210
Location:1540 → 1668

Laminin_G_2; Laminin G domain

cl02806
Location:312 → 512

Laminin_N; Laminin N-terminal (Domain VI)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086031.1 Reference GRCr8

Range

102368783..103035230

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001244757.1: Suppressed sequence

Description

NM_001244757.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
NM_172048.1: Suppressed sequence

Description

NM_172048.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.