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Whrn whirlin [ Mus musculus (house mouse) ]

Gene ID: 73750, updated on 28-Oct-2021

Summary

Official Symbol
Whrnprovided by MGI
Official Full Name
whirlinprovided by MGI
Primary source
MGI:MGI:2682003
See related
Ensembl:ENSMUSG00000039137
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
wi; Ush2d; Dfnb31; AW122018; AW742671; 1110035G07Rik; C430046P22Rik
Summary
This gene encodes a protein required for elongation and actin polymerization in the hair cell stereocilia. The encoded protein is localized to the cytoplasm and co-localizes with the growing end of actin filaments. Mutations in this gene have been linked to deafness. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2013]
Expression
Broad expression in adrenal adult (RPKM 29.0), thymus adult (RPKM 26.8) and 22 other tissues See more
Orthologs
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Genomic context

See Whrn in Genome Data Viewer
Location:
4 B3; 4 33.97 cM
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (63333145..63414320, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (63414908..63496083, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 4 NC_000070.5 (63075944..63156985, complement)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene AT-hook transcription factor Neighboring gene AT-hook transcription factor, opposite strand Neighboring gene predicted gene, 52742 Neighboring gene ATPase, H+ transporting, lysosomal V1 subunit G1 Neighboring gene predicted gene, 38592 Neighboring gene transmembrane protein 268 Neighboring gene predicted gene, 24448

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

Clone Names

  • KIAA1526, MGC183668, bM340H1.8

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein domain specific binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in auditory receptor cell stereocilium organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within auditory receptor cell stereocilium organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cerebellar Purkinje cell layer formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in detection of mechanical stimulus involved in sensory perception of sound IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within establishment of protein localization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in inner ear receptor cell stereocilium organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in paranodal junction maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
involved_in retina homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in retina homeostasis ISO
Inferred from Sequence Orthology
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
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
part_of USH2 complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in actin filament IDA
Inferred from Direct Assay
more info
PubMed 
located_in apical dendrite ISO
Inferred from Sequence Orthology
more info
 
located_in axon collateral ISO
Inferred from Sequence Orthology
more info
 
located_in cell junction IEA
Inferred from Electronic Annotation
more info
 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
 
located_in ciliary basal body IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cilium IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in dendritic shaft ISO
Inferred from Sequence Orthology
more info
 
located_in membrane ISO
Inferred from Sequence Orthology
more info
 
colocalizes_with neuronal cell body ISO
Inferred from Sequence Orthology
more info
 
located_in neuronal cell body ISO
Inferred from Sequence Orthology
more info
 
located_in periciliary membrane compartment IDA
Inferred from Direct Assay
more info
PubMed 
located_in perinuclear region of cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in photoreceptor connecting cilium IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with photoreceptor connecting cilium ISO
Inferred from Sequence Orthology
more info
 
colocalizes_with photoreceptor inner segment IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in photoreceptor inner segment IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with photoreceptor inner 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 postsynapse ISO
Inferred from Sequence Orthology
more info
 
located_in presynapse ISO
Inferred from Sequence Orthology
more info
 
located_in stereocilia ankle link IDA
Inferred from Direct Assay
more info
PubMed 
located_in stereocilia ankle link ISO
Inferred from Sequence Orthology
more info
 
part_of stereocilia ankle link complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of stereocilia ankle link complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in stereocilium IDA
Inferred from Direct Assay
more info
PubMed 
located_in stereocilium ISO
Inferred from Sequence Orthology
more info
 
located_in stereocilium bundle IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in stereocilium tip IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in stereocilium tip IDA
Inferred from Direct Assay
more info
PubMed 
located_in stereocilium tip ISO
Inferred from Sequence Orthology
more info
 
located_in synapse IEA
Inferred from Electronic Annotation
more info
 

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_001008791.2NP_001008791.1  whirlin isoform 2

    See identical proteins and their annotated locations for NP_001008791.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
    Source sequence(s)
    AK157955, AY739115
    Consensus CDS
    CCDS18255.1
    UniProtKB/Swiss-Prot
    Q80VW5
    Related
    ENSMUSP00000081557.2, ENSMUST00000084510.8
    Conserved Domains (3) summary
    cd00992
    Location:278358
    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) ...
    cd07356
    Location:38113
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:420500
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  2. NM_001008792.2NP_001008792.1  whirlin isoform 3

    See identical proteins and their annotated locations for NP_001008792.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site and lacks an in-frame exon in the coding region, compared to variant 2. The encoded isoform (3) is shorter than isoform 2.
    Source sequence(s)
    AK157955, AY739116
    Consensus CDS
    CCDS38778.1
    UniProtKB/Swiss-Prot
    Q80VW5
    Related
    ENSMUSP00000103016.2, ENSMUST00000107393.8
    Conserved Domains (3) summary
    cd00992
    Location:278358
    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) ...
    cd07356
    Location:38113
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:424504
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  3. NM_001008793.2NP_001008793.1  whirlin isoform 4

    See identical proteins and their annotated locations for NP_001008793.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon and uses an alternate in-frame splice site in the coding region, compared to variant 2. The encoded isoform (4) is shorter than isoform 2.
    Source sequence(s)
    AK157955, AY739117
    Consensus CDS
    CCDS18256.1
    UniProtKB/Swiss-Prot
    Q80VW5
    Related
    ENSMUSP00000099931.2, ENSMUST00000102867.8
    Conserved Domains (3) summary
    cd00992
    Location:278358
    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) ...
    cd07356
    Location:38113
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:420500
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  4. NM_001276371.1NP_001263300.1  whirlin isoform 10

    See identical proteins and their annotated locations for NP_001263300.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) uses an alternate 3' terminal exon, compared to variant 2. It encodes isoform 10 which is shorter and has a distinct C-terminus, compared to isoform 2.
    Source sequence(s)
    AK157955, HQ148553
    UniProtKB/Swiss-Prot
    Q80VW5
    Conserved Domains (2) summary
    cd00992
    Location:139216
    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) ...
    cd07356
    Location:38113
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
  5. NM_028640.2NP_082916.1  whirlin isoform 1

    See identical proteins and their annotated locations for NP_082916.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon in the 3' coding region, compared to variant 2. The encoded isoform (1) is shorter than isoform 2.
    Source sequence(s)
    AK157955, AY739114
    Consensus CDS
    CCDS18257.1
    UniProtKB/Swiss-Prot
    Q80VW5
    Related
    ENSMUSP00000069664.4, ENSMUST00000063650.10
    Conserved Domains (3) summary
    cd00992
    Location:278358
    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) ...
    cd07356
    Location:38113
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:420500
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains

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_000070.7 Reference GRCm39 C57BL/6J

    Range
    63333145..63414320 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006538309.4XP_006538372.1  whirlin isoform X1

    Conserved Domains (3) summary
    cd00992
    Location:278358
    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) ...
    cd07356
    Location:38113
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:420500
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains

RNA

  1. XR_004941996.1 RNA Sequence

  2. XR_001784212.2 RNA Sequence

  3. XR_001784211.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001008794.1: Suppressed sequence

    Description
    NM_001008794.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  2. NM_001008795.1: Suppressed sequence

    Description
    NM_001008795.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  3. NM_001008796.1: Suppressed sequence

    Description
    NM_001008796.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  4. NM_001008797.1: Suppressed sequence

    Description
    NM_001008797.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  5. NM_001008798.1: Suppressed sequence

    Description
    NM_001008798.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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