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Ush1c USH1 protein network component harmonin [ Mus musculus (house mouse) ]

Gene ID: 72088, updated on 11-Apr-2024

Summary

Official Symbol
Ush1cprovided by MGI
Official Full Name
USH1 protein network component harmoninprovided by MGI
Primary source
MGI:MGI:1919338
See related
Ensembl:ENSMUSG00000030838 AllianceGenome:MGI:1919338
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
harmonin; 2010016F01Rik
Summary
Predicted to enable myosin tail binding activity and spectrin binding activity. Involved in brush border assembly; protein localization to microvillus; and regulation of microvillus length. Acts upstream of or within several processes, including inner ear development; parallel actin filament bundle assembly; and sensory perception of sound. Located in several cellular components, including brush border; photoreceptor inner segment; and upper tip-link density. Is expressed in several structures, including alimentary system; cochlea; genitourinary system; heart; and lung epithelium. Used to study Usher syndrome type 1C and autosomal recessive nonsyndromic deafness 18A. 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, Apr 2022]
Expression
Biased expression in large intestine adult (RPKM 31.9), colon adult (RPKM 22.1) and 4 other tissues See more
Orthologs
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Genomic context

See Ush1c in Genome Data Viewer
Location:
7 B3; 7 29.66 cM
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (45844774..45887984, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (46195350..46238490, complement)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene potassium inwardly rectifying channel, subfamily J, member 11 Neighboring gene predicted gene, 51481 Neighboring gene ATP-binding cassette, sub-family C member 8 Neighboring gene STARR-seq mESC enhancer starr_18861 Neighboring gene otogelin Neighboring gene predicted gene, 45923

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables myosin tail binding ISO
Inferred from Sequence Orthology
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables spectrin binding ISO
Inferred from Sequence Orthology
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
involved_in auditory receptor cell morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in brush border assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in brush border assembly ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in equilibrioception ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within inner ear auditory receptor cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within inner ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within neuromuscular process controlling balance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within parallel actin filament bundle assembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in photoreceptor cell maintenance ISO
Inferred from Sequence Orthology
more info
 
involved_in protein localization to microvillus IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
located_in brush border ISO
Inferred from Sequence Orthology
more info
 
located_in cell projection IEA
Inferred from Electronic Annotation
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 cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in microvillus IDA
Inferred from Direct Assay
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
part_of stereocilia ankle link complex IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in stereocilium EXP
Inferred from Experiment
more info
PubMed 
located_in stereocilium IDA
Inferred from Direct Assay
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
located_in upper tip-link density IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
harmonin
Names
PDZ domain-containing protein
Usher syndrome 1C homolog
usher syndrome type-1C 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)

  1. NM_001163733.1NP_001157205.1  harmonin isoform b4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (b4) has an additional segment in the 3' coding region, resulting in frame-shift, as compared to variant b3. The resulting isoform (b4) is shorter and has a different C-terminus, as compared to isoform b3.
    Source sequence(s)
    AC120135, AF228925, AY246556, BP775197, BY708209
    Consensus CDS
    CCDS52250.1
    UniProtKB/TrEMBL
    E9PYX1, Q6XA19
    Related
    ENSMUSP00000114494.3, ENSMUST00000154292.9
    Conserved Domains (3) summary
    cd00992
    Location:85165
    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:280
    harmonin_N; N-terminal protein-binding module of harmonin
    pfam03879
    Location:309358
    Cgr1; Cgr1 family
  2. NM_001291182.1NP_001278111.1  harmonin isoform b2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (b2) uses an alternate splice junction at the 5' end of an exon compared to variant b3, that causes a frameshift. The resulting isoform (b2) has a shorter and distinct C-terminus compared to isoform b3.
    Source sequence(s)
    AC120135
    Consensus CDS
    CCDS85309.1
    UniProtKB/TrEMBL
    D6RIM8, Q6XA19
    Related
    ENSMUSP00000119676.2, ENSMUST00000143155.8
    Conserved Domains (4) summary
    PHA03247
    Location:555685
    PHA03247; large tegument protein UL36; Provisional
    cd00992
    Location:85165
    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:280
    harmonin_N; N-terminal protein-binding module of harmonin
    pfam13868
    Location:301358
    TPH; Trichohyalin-plectin-homology domain
  3. NM_023649.2NP_076138.2  harmonin isoform a1

    See identical proteins and their annotated locations for NP_076138.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (a1) differs from variant b3 in the middle coding region and in the 3' coding region. The resulting isoform (a1) is much shorter, and it lacks an internal segment and has a different C-terminus, as compared to isoform b3.
    Source sequence(s)
    AF228924, BP775197, BY708209
    Consensus CDS
    CCDS39963.1
    UniProtKB/TrEMBL
    A0A0R4J0Z8, H3BLC4
    Related
    ENSMUSP00000077747.7, ENSMUST00000078680.13
    Conserved Domains (3) summary
    cd00992
    Location:85165
    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:280
    harmonin_N; N-terminal protein-binding module of harmonin
    pfam03879
    Location:316358
    Cgr1; Cgr1 family
  4. NM_153677.2NP_710143.2  harmonin isoform b3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (b3) encodes the longest isoform (b3).
    Source sequence(s)
    AC120135, AF228925, BP775197, BY708209
    Consensus CDS
    CCDS21276.1
    UniProtKB/Swiss-Prot
    Q91XD1, Q9CVG7, Q9ES64, Q9ES65
    UniProtKB/TrEMBL
    E9QMN1
    Related
    ENSMUSP00000009667.6, ENSMUST00000009667.12
    Conserved Domains (3) summary
    cd00992
    Location:85165
    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:280
    harmonin_N; N-terminal protein-binding module of harmonin
    pfam03879
    Location:309358
    Cgr1; Cgr1 family

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

  1. NC_000073.7 Reference GRCm39 C57BL/6J

    Range
    45844774..45887984 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006541212.4XP_006541275.1  harmonin isoform X1

    UniProtKB/TrEMBL
    H3BIZ2, H3BLC4
    Related
    ENSMUSP00000134783.2, ENSMUST00000176371.2
    Conserved Domains (3) summary
    cd00992
    Location:54134
    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) ...
    pfam17380
    Location:267400
    DUF5401; Family of unknown function (DUF5401)
    cl11968
    Location:149
    harmonin_N_like; N-terminal protein-binding module of harmonin and similar domains, also known as HHD (harmonin homology domain)
  2. XM_036153453.1XP_036009346.1  harmonin isoform X2

    Conserved Domains (3) summary
    cd00992
    Location:85165
    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:280
    harmonin_N; N-terminal protein-binding module of harmonin
    pfam17380
    Location:298424
    DUF5401; Family of unknown function (DUF5401)