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Whrn whirlin [ Mus musculus (house mouse) ]

Gene ID: 73750, updated on 4-Jul-2015
Official Symbol
Whrnprovided by MGI
Official Full Name
whirlinprovided by MGI
Primary source
MGI:MGI:2682003
See related
Ensembl:ENSMUSG00000039137; Vega:OTTMUSG00000000249
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
wi; 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]
Orthologs
See Whrn in Epigenomics, MapViewer
Location:
4 33.97 cM; 4 C1
Exon count:
15
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) 4 NC_000070.6 (63414909..63496078, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 4 NC_000070.5 (63075944..63156985, complement)

Chromosome 4 - NC_000070.6Genomic Context describing neighboring genes Neighboring gene orosomucoid 2 Neighboring gene AT-hook transcription factor Neighboring gene AT-hook transcription factor, opposite strand Neighboring gene RIKEN cDNA 6330416G13 gene Neighboring gene ATPase, H+ transporting, lysosomal V1 subunit G1 Neighboring gene predicted gene, 38592

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA1526, MGC183668, bM340H1.8

Gene Ontology Provided by MGI

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding ISO
Inferred from Sequence Orthology
more info
 
protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
establishment of protein localization IMP
Inferred from Mutant Phenotype
more info
PubMed 
inner ear receptor stereocilium organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
retina homeostasis ISO
Inferred from Sequence Orthology
more info
 
sensory perception of light stimulus ISO
Inferred from Sequence Orthology
more info
 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
USH2 complex IDA
Inferred from Direct Assay
more info
PubMed 
actin filament IDA
Inferred from Direct Assay
more info
PubMed 
axon ISO
Inferred from Sequence Orthology
more info
 
cell projection IEA
Inferred from Electronic Annotation
more info
 
ciliary basal body IDA
Inferred from Direct Assay
more info
PubMed 
cilium IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
dendrite ISO
Inferred from Sequence Orthology
more info
 
dendritic shaft ISO
Inferred from Sequence Orthology
more info
 
membrane ISO
Inferred from Sequence Orthology
more info
 
neuronal cell body ISO
Inferred from Sequence Orthology
more info
 
colocalizes_with neuronal cell body ISO
Inferred from Sequence Orthology
more info
 
periciliary membrane compartment IDA
Inferred from Direct Assay
more info
PubMed 
photoreceptor connecting cilium IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with photoreceptor connecting cilium ISO
Inferred from Sequence Orthology
more info
 
photoreceptor inner segment IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with photoreceptor inner segment ISO
Inferred from Sequence Orthology
more info
 
stereocilia ankle link IDA
Inferred from Direct Assay
more info
PubMed 
stereocilia ankle link complex IDA
Inferred from Direct Assay
more info
PubMed 
stereocilium IDA
Inferred from Direct Assay
more info
PubMed 
stereocilium ISO
Inferred from Sequence Orthology
more info
 
stereocilium bundle IDA
Inferred from Direct Assay
more info
PubMed 
stereocilium bundle tip IDA
Inferred from Direct Assay
more info
PubMed 
synapse ISO
Inferred from Sequence Orthology
more info
 

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, OTTMUSP00000019122, ENSMUST00000084510, OTTMUST00000042551
    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, OTTMUSP00000019121, ENSMUST00000107393, OTTMUST00000042550
    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, OTTMUSP00000000317, ENSMUST00000102867, OTTMUST00000000709
    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, OTTMUSP00000000316, ENSMUST00000063650, OTTMUST00000000708
    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 105

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

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000070.6 Reference GRCm38.p3 C57BL/6J

    Range
    63414909..63496078
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006538309.2XP_006538372.1  

    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. XM_011250121.1XP_011248423.1  

    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
  3. XM_011250122.1XP_011248424.1  

    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_390346.2 RNA Sequence

  2. XR_881074.1 RNA Sequence

Alternate Mm_Celera

Genomic

  1. AC_000026.1 Alternate Mm_Celera

    Range
    62074390..62155782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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.