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USH1C USH1 protein network component harmonin [ Homo sapiens (human) ]

Gene ID: 10083, updated on 12-Jan-2019

Summary

Official Symbol
USH1Cprovided by HGNC
Official Full Name
USH1 protein network component harmoninprovided by HGNC
Primary source
HGNC:HGNC:12597
See related
Ensembl:ENSG00000006611 MIM:605242
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PDZ73; AIE-75; DFNB18; PDZ-45; PDZ-73; PDZD7C; DFNB18A; NY-CO-37; NY-CO-38; ush1cpst; PDZ-73/NY-CO-38
Summary
This gene encodes a scaffold protein that functions in the assembly of Usher protein complexes. The protein contains PDZ domains, a coiled-coil region with a bipartite nuclear localization signal and a PEST degradation sequence. Defects in this gene are the cause of Usher syndrome type 1C and non-syndromic sensorineural deafness autosomal recessive type 18. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
Expression
Biased expression in small intestine (RPKM 13.7), duodenum (RPKM 13.0) and 6 other tissues See more
Orthologs

Genomic context

See USH1C in Genome Data Viewer
Location:
11p15.1
Exon count:
29
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (17493895..17544416, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (17515442..17565963, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs1977 Neighboring gene ATP binding cassette subfamily C member 8 Neighboring gene succinate dehydrogenase complex subunit C pseudogene 4 Neighboring gene otogelin Neighboring gene uncharacterized LOC102723330

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin filament binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
spectrin binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
G2/M transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
actin filament bundle assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
brush border assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
brush border assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
brush border assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular protein-containing complex assembly IDA
Inferred from Direct Assay
more info
PubMed 
equilibrioception IMP
Inferred from Mutant Phenotype
more info
PubMed 
inner ear auditory receptor cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inner ear auditory receptor cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
inner ear morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inner ear morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
inner ear receptor cell stereocilium organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inner ear receptor cell stereocilium organization ISS
Inferred from Sequence or Structural Similarity
more info
 
parallel actin filament bundle assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
photoreceptor cell maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to microvillus IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to microvillus ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of microvillus length ISS
Inferred from Sequence or Structural Similarity
more info
 
retinal cone cell development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sensory perception of light stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sensory perception of light stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
apical part of cell IDA
Inferred from Direct Assay
more info
PubMed 
brush border IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
microvillus IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with photoreceptor connecting cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with photoreceptor inner segment IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
photoreceptor inner segment ISS
Inferred from Sequence or Structural Similarity
more info
 
photoreceptor outer segment ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
stereocilia ankle link IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stereocilia ankle link complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stereocilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stereocilium ISS
Inferred from Sequence or Structural Similarity
more info
 
stereocilium TAS
Traceable Author Statement
more info
PubMed 
stereocilium tip IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
harmonin
Names
Usher syndrome 1C (autosomal recessive, severe)
antigen NY-CO-38/NY-CO-37
autoimmune enteropathy-related antigen AIE-75
renal carcinoma antigen NY-REN-3
usher syndrome type-1C protein

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_011883.2 RefSeqGene

    Range
    5001..55522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001297764.1NP_001284693.1  harmonin isoform c

    See identical proteins and their annotated locations for NP_001284693.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the coding region, compared to variant b3, one of which results in a translational frameshift. The resulting protein (isoform c) has a distinct C-terminus and is shorter than isoform b3.
    Source sequence(s)
    AB018687, AF039699, AK225614, BC016057
    Consensus CDS
    CCDS73265.1
    UniProtKB/Swiss-Prot
    Q9Y6N9
    UniProtKB/TrEMBL
    A0A0S2Z4V1
    Related
    ENSP00000436934.1, ENST00000527020.5
    Conserved Domains (4) 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
    TIGR02794
    Location:283364
    tolA_full; TolA protein
    pfam03879
    Location:297339
    Cgr1; Cgr1 family
  2. NM_005709.3NP_005700.2  harmonin isoform a

    See identical proteins and their annotated locations for NP_005700.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) has multiple differences in the coding region, compared to variant b3, one of which results in a translational frameshift. The resulting protein (isoform a) has a distinct C-terminus and is shorter than isoform b3.
    Source sequence(s)
    AC124799, KF455327
    Consensus CDS
    CCDS31438.1
    UniProtKB/Swiss-Prot
    Q9Y6N9
    UniProtKB/TrEMBL
    A0A0S2Z4U9
    Related
    ENSP00000317018.4, ENST00000318024.8
    Conserved Domains (4) 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
    TIGR02794
    Location:302383
    tolA_full; TolA protein
    pfam03879
    Location:316358
    Cgr1; Cgr1 family
  3. NM_153676.4NP_710142.1  harmonin isoform b3

    See identical proteins and their annotated locations for NP_710142.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b3) encodes the longest isoform (b3).
    Source sequence(s)
    AC124799, KF455327
    Consensus CDS
    CCDS7825.1
    UniProtKB/Swiss-Prot
    Q9Y6N9
    Related
    ENSP00000005226.7, ENST00000005226.11
    Conserved Domains (4) 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
    TIGR02794
    Location:302383
    tolA_full; TolA protein
    pfam03879
    Location:316358
    Cgr1; Cgr1 family

RNA

  1. NR_123738.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences compared to variant b3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB018687, AC124799, AF039699, AK225614
    Related
    ENST00000526313.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    17493895..17544416 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519832.3XP_011518134.1  harmonin isoform X3

    Conserved Domains (4) 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
    TIGR02794
    Location:302383
    tolA_full; TolA protein
    pfam03879
    Location:309358
    Cgr1; Cgr1 family
  2. XM_017017075.1XP_016872564.1  harmonin isoform X6

  3. XM_017017073.1XP_016872562.1  harmonin isoform X2

  4. XM_017017074.1XP_016872563.1  harmonin isoform X4

  5. XM_017017072.1XP_016872561.1  harmonin isoform X1

  6. XM_011519834.2XP_011518136.1  harmonin isoform X5

    Conserved Domains (4) 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
    TIGR02794
    Location:302383
    tolA_full; TolA protein
    pfam03879
    Location:316358
    Cgr1; Cgr1 family

RNA

  1. XR_001747717.2 RNA Sequence

  2. XR_930842.1 RNA Sequence

  3. XR_930841.1 RNA Sequence

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