Ush2a usherin [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ush2aprovided by MGI
Official Full Name: usherinprovided by MGI
Primary source: MGI:MGI:1341292
See related: Ensembl:ENSMUSG00000026609 AllianceGenome:MGI:1341292
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Gm676; Gm983; Ushrn; Mush2a; A930011D15Rik; A930037M10Rik
Summary: Enables collagen binding activity; identical protein binding activity; and myosin binding activity. Acts upstream of or within establishment of protein localization; neuron differentiation; and photoreceptor cell maintenance. Located in several cellular components, including periciliary membrane compartment; photoreceptor connecting cilium; and stereocilium membrane. Part of USH2 complex and stereocilia ankle link complex. Is expressed in sensory organ and testis. Used to study Usher syndrome type 2A. 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 testis adult (RPKM 1.3) and ovary adult (RPKM 0.0) See more
Orthologs: human all
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Genomic context

Location:: 1 H6; 1 92.29 cM

Exon count:: 73

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (187995035..188697694)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (188262838..188965497)

Chromosome 1 - NC_000067.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expression of the human usherin c.2299delG mutation leads to early-onset auditory loss and stereocilia disorganization.
Title: Expression of the human usherin c.2299delG mutation leads to early-onset auditory loss and stereocilia disorganization.
Deafness-Associated ADGRV1 Mutation Impairs USH2A Stability through Improper Phosphorylation of WHRN and WDSUB1 Recruitment.
Title: Deafness-Associated ADGRV1 Mutation Impairs USH2A Stability through Improper Phosphorylation of WHRN and WDSUB1 Recruitment.
The usherin mutation c.2299delG leads to its mislocalization and disrupts interactions with whirlin and VLGR1.
Title: The usherin mutation c.2299delG leads to its mislocalization and disrupts interactions with whirlin and VLGR1.
Peripheral Anomalies in USH2A Cause Central Auditory Anomalies in a Mouse Model of Usher Syndrome and CAPD.
Title: Peripheral Anomalies in USH2A Cause Central Auditory Anomalies in a Mouse Model of Usher Syndrome and CAPD.
Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes.
Title: Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes.
USH2A is a Meissner's corpuscle protein necessary for normal vibration sensing in mice and humans.
Title: USH2A is a Meissner's corpuscle protein necessary for normal vibration sensing in mice and humans.
Conservation of usherin is seen at the nucleotide and amino acid level when comparing the mouse and human gene sequences.
Title: Usherin expression is highly conserved in mouse and human tissues.
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.
usherin in photoreceptors is tethered via its C terminus to the plasma membrane and its large extracellular domain projects into the periciliary matrix, where they may interact with the connecting cilium to fulfill important structural or signaling roles
Title: Usherin is required for maintenance of retinal photoreceptors and normal development of cochlear hair cells.
In mouse inner ears usherin is present at the base of the differentiating stereocilia, which make up the mechanosensitive hair bundles receptive to sound
Title: Usherin, the defective protein in Usher syndrome type IIA, is likely to be a component of interstereocilia ankle links in the inner ear sensory cells.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (1) 1 citation
Endonuclease-mediated (7)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1Mit223 (e-PCR), detects polymorphism
- UniSTS:128565

Ush2a (e-PCR), detects polymorphism
- UniSTS:144738

Ush2a (e-PCR), detects polymorphism
- UniSTS:144739

D1Mit274 (e-PCR), detects polymorphism
- UniSTS:128624

AU024699 (e-PCR)
- UniSTS:178549

D1Dcr19 (e-PCR), detects polymorphism
- UniSTS:507572

D1Dcr20 (e-PCR), detects polymorphism
- UniSTS:507573

GDB:1317552 (e-PCR)
- UniSTS:61644

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables collagen binding	IDA Inferred from Direct Assay more info	PubMed
enables collagen binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables myosin binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in animal organ morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within establishment of localization in cell	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within establishment of protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hair cell differentiation	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within inner ear auditory receptor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in inner ear receptor cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in maintenance of animal organ identity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within photoreceptor cell maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to 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	ISO Inferred from Sequence Orthology more info
involved_in tissue development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of USH2 complex	IDA Inferred from Direct Assay more info	PubMed
part_of USH2 complex	IPI Inferred from Physical Interaction more info	PubMed
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basement membrane	ISO Inferred from Sequence Orthology more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
colocalizes_with neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in periciliary membrane compartment	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor connecting cilium	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with photoreceptor connecting cilium	ISO Inferred from Sequence Orthology more info
located_in photoreceptor inner segment	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with photoreceptor inner segment	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in stereocilia ankle link	IDA Inferred from Direct Assay more info	PubMed
located_in stereocilia ankle link	NAS Non-traceable Author Statement more info	PubMed
part_of stereocilia ankle link complex	IDA Inferred from Direct Assay more info	PubMed
located_in stereocilium bundle	IDA Inferred from Direct Assay more info	PubMed
located_in stereocilium membrane	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with terminal bouton	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: usherin

Names: Usher syndrome 2A (autosomal recessive, mild) 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_021408.3 → NP_067383.3 usherin precursor

See identical proteins and their annotated locations for NP_067383.3

Status: VALIDATED

Source sequence(s)

AC122122, AC129312, AC165230, AK020845, DQ073638

Consensus CDS

CCDS15607.1

UniProtKB/Swiss-Prot

E9QLJ9, Q2QI47, Q9JLP3

Related

ENSMUSP00000050454.8, ENSMUST00000060479.14

Conserved Domains (10) summary

smart00060
Location:1362 → 1445

FN3; Fibronectin type 3 domain

smart00180
Location:792 → 832

EGF_Lam; Laminin-type epidermal growth factor-like domai

smart00560
Location:145 → 280

LamGL; LamG-like jellyroll fold domain

cd00055
Location:896 → 945

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:3956 → 4053

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:1707 → 1857

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:1055 → 1128

fn3; Fibronectin type III domain

pfam00053
Location:844 → 894

Laminin_EGF; Laminin EGF domain

pfam02210
Location:1539 → 1669

Laminin_G_2; Laminin G domain

cl02806
Location:313 → 513

Laminin_N; Laminin N-terminal (Domain VI)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

187995035..188697694

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017319869.1 → XP_017175358.1 usherin isoform X1

Conserved Domains (2) summary

cd00063
Location:2021 → 2118

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:2414 → 2485

fn3; Fibronectin type III domain