Ush1c USH1 protein network component harmonin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ush1cprovided by RGD
Official Full Name: USH1 protein network component harmoninprovided by RGD
Primary source: RGD:1303329
See related: EnsemblRapid:ENSRNOG00000021149 AllianceGenome:RGD:1303329
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable spectrin binding activity. Predicted to be involved in several processes, including G2/M transition of mitotic cell cycle; neuron development; and photoreceptor cell maintenance. Predicted to act upstream of or within inner ear development; neuromuscular process controlling balance; and parallel actin filament bundle assembly. Located in photoreceptor inner segment; photoreceptor outer segment; and stereocilium. Human ortholog(s) of this gene implicated in Usher syndrome; Usher syndrome type 1; Usher syndrome type 1C; and autosomal recessive nonsyndromic deafness 18A. Orthologous to human USH1C (USH1 protein network component harmonin). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Restricted expression toward (RPKM 240.1) See more
Orthologs: human mouse all
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Genomic context

Location:: 1q22

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (105831719..105880082, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (96695303..96743671, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (102207096..102256779, complement)

Chromosome 1 - NC_086019.1 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
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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables spectrin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in G2/M transition of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within actin filament bundle assembly	ISO Inferred from Sequence Orthology more info
involved_in auditory receptor cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in brush border assembly	ISO Inferred from Sequence Orthology more info
involved_in equilibrioception	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear auditory receptor cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in inner ear receptor cell stereocilium organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within inner ear receptor cell stereocilium organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuromuscular process controlling balance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within parallel actin filament bundle assembly	ISO Inferred from Sequence Orthology more info
involved_in photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
involved_in protein localization to microvillus	ISO Inferred from Sequence Orthology more info
involved_in protein-containing complex assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of microvillus length	ISO Inferred from Sequence Orthology more info
involved_in retinal cone cell development	IBA Inferred from Biological aspect of Ancestor more info
involved_in sensory perception of light stimulus	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in apical part of cell	ISO Inferred from Sequence Orthology more info
located_in brush border	ISO Inferred from Sequence Orthology more info
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in microvillus	ISO Inferred from Sequence Orthology more info
is_active_in photoreceptor inner segment	IBA Inferred from Biological aspect of Ancestor more info
located_in photoreceptor inner segment	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor inner segment	ISO Inferred from Sequence Orthology more info
located_in photoreceptor outer segment	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor outer segment	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of stereocilia ankle link complex	IBA Inferred from Biological aspect of Ancestor more info
located_in stereocilium	IDA Inferred from Direct Assay more info	PubMed
is_active_in stereocilium	ISO Inferred from Sequence Orthology more info
located_in stereocilium	ISO Inferred from Sequence Orthology more info
is_active_in stereocilium tip	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	ISO Inferred from Sequence Orthology more info
located_in upper tip-link density	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: harmonin

Names: Usher syndrome 1C homolog; harmonin a1

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_212521.2 → NP_997686.2 harmonin

See identical proteins and their annotated locations for NP_997686.2

Status: PROVISIONAL

Source sequence(s)

BC098641

UniProtKB/TrEMBL

A6JBB6, F7FHE4, Q4KMB9, Q6PPF3

Related

ENSRNOP00000061783.1, ENSRNOT00000067392.4

Conserved Domains (4) summary

cd00992
Location:85 → 165

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd07353
Location:2 → 80

harmonin_N; N-terminal protein-binding module of harmonin

TIGR02794
Location:302 → 383

tolA_full; TolA protein

pfam03879
Location:316 → 358

Cgr1; Cgr1 family

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_086019.1 Reference GRCr8

Range

105831719..105880082 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006229222.5 → XP_006229284.1 harmonin isoform X1

UniProtKB/TrEMBL

A0A8I5ZR66

Related

ENSRNOP00000080627.1, ENSRNOT00000100210.2

Conserved Domains (3) summary

cd00992
Location:85 → 165

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd07353
Location:2 → 80

harmonin_N; N-terminal protein-binding module of harmonin

pfam03879
Location:316 → 358

Cgr1; Cgr1 family