ush1c Usher syndrome 1C [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: ush1cprovided by ZNC
Official Full Name: Usher syndrome 1Cprovided by ZNC
Primary source: ZFIN:ZDB-GENE-060312-41
See related: Ensembl:ENSDARG00000051876 AllianceGenome:ZFIN:ZDB-GENE-060312-41
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: zgc:136806
Summary: Acts upstream of or within neuron development; startle response; and synapse organization. Predicted to be located in cell projection. Predicted to be part of stereocilia ankle link complex. Predicted to be active in several cellular components, including cilium; photoreceptor inner segment; and stereocilium tip. Is expressed in brain; hair cell; pleuroperitoneal region; sensory system; and trunk musculature. Used to study Usher syndrome. 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]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 25

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	25	NC_007136.7 (22643936..22704233)
105	previous assembly	GRCz10 (GCF_000002035.5)	25	NC_007136.6 (22546361..22606685)

Chromosome 25 - NC_007136.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

glutathionylation promotes the interaction between Ush1c and Ush1ga.
Title: Grxcr1 Promotes Hair Bundle Development by Destabilizing the Physical Interaction between Harmonin and Sans Usher Syndrome Proteins.
This study shows that visual defects associated with loss of ush1c function in zebrafish can be detected from the onset of vision.
Title: Harmonin (Ush1c) is required in zebrafish Müller glial cells for photoreceptor synaptic development and function.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within auditory receptor cell morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear receptor cell stereocilium organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retinal cone cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within startle response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synapse organization	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cell projection	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: harmonin

Names: Usher syndrome 1C (autosomal recessive, severe); harmonin pseudogene

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_001039929.1 → NP_001035018.1 harmonin

See identical proteins and their annotated locations for NP_001035018.1

Status: PROVISIONAL

Source sequence(s)

BC114278

UniProtKB/TrEMBL

A0A8M1N8H8, E7FD99, Q29RC0

Related

ENSDARP00000104974.2, ENSDART00000121791.4

Conserved Domains (3) summary

cd00992
Location:212 → 292

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

cl23720
Location:317 → 379

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007136.7 Reference GRCz11 Primary Assembly

Range

22643936..22704233

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009298038.4 → XP_009296313.1 harmonin isoform X2

See identical proteins and their annotated locations for XP_009296313.1

UniProtKB/TrEMBL

A0A8M3AZQ5

Conserved Domains (3) summary

cd00992
Location:212 → 292

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

cl23720
Location:317 → 379

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_068217396.1 → XP_068073497.1 harmonin isoform X1