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

    Gene ID: 72088, updated on 8-Jul-2021

    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
    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
    ha; harmonin; 2010016F01Rik
    Expression
    Biased expression in large intestine adult (RPKM 31.9), colon adult (RPKM 22.1) and 4 other tissues See more
    Orthologs
    NEW
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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
    109 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)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 7 NC_000073.5 (53450721..53493860, 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 (CFTR/MRP), member 8 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

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables actin filament binding IEA
    Inferred from Electronic Annotation
    more info
     
    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 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 cellular protein-containing complex assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in equilibrioception ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in inner ear auditory receptor cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    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 morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    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
    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 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 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
    PubMed 
    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
    PubMed 
    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
     
    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
     
    colocalizes_with photoreceptor connecting cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
    PubMed 
    located_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
    PubMed 
    located_in synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synapse ISO
    Inferred from Sequence Orthology
    more info
     
    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)

    NEW Try the new Transcript table

    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/Swiss-Prot
      Q9ES64
      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
      Related
      ENSMUSP00000119676.2, ENSMUST00000143155.8
      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
    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/Swiss-Prot
      Q9ES64
      UniProtKB/TrEMBL
      A0A0R4J0Z8
      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
      Q9ES64
      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: Mus musculus Annotation Release 109 details...Open this link in a new tab

    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
      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)
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