Whrn whirlin [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Whrnprovided by MGI
Official Full Name: whirlinprovided by MGI
Primary source: MGI:MGI:2682003
See related: Ensembl:ENSMUSG00000039137 AllianceGenome:MGI:2682003
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; 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: human all
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Genomic context

Location:: 4 B3; 4 33.97 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	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)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Deafness-Associated ADGRV1 Mutation Impairs USH2A Stability through Improper Phosphorylation of WHRN and WDSUB1 Recruitment.
Title: Deafness-Associated ADGRV1 Mutation Impairs USH2A Stability through Improper Phosphorylation of WHRN and WDSUB1 Recruitment.
Interaction of protocadherin-15 with the scaffold protein whirlin supports its anchoring of hair-bundle lateral links in cochlear hair cells.
Title: Interaction of protocadherin-15 with the scaffold protein whirlin supports its anchoring of hair-bundle lateral links in cochlear hair cells.
Gpsm2 defines an approximately 200 nm nanodomain at the tips of stereocilia and this localization requires the presence of Galphai3, myosin 15 and whirlin.
Title: Defective Gpsm2/Gα(i3) signalling disrupts stereocilia development and growth cone actin dynamics in Chudley-McCullough syndrome.
C-terminal hairpin extensions of the whirlin PDZ domains mediate the transient supramodular assembly, which improves the binding capacity of the first domain towards its partners, such as Sans.
Title: Structural Characterization of Whirlin Reveals an Unexpected and Dynamic Supramodule Conformation of Its PDZ Tandem.
the major long (WHRN-L) and short (WHRN-S) isoforms of WHRN have distinct localizations within stereocilia and also across hair cell types.
Title: Alternative Splice Forms Influence Functions of Whirlin in Mechanosensory Hair Cell Stereocilia.
vestibular dysfunction in Dfnb31 mutant mice
Title: A study of whirlin isoforms in the mouse vestibular system suggests potential vestibular dysfunction in DFNB31-deficient patients.
disruption of distinct whirlin isoforms by Dfnb31 mutations leads to a variety of phenotype configurations
Title: Distinct expression and function of whirlin isoforms in the inner ear and retina: an insight into pathogenesis of USH2D and DFNB31.
findings indicate that Whirlin and TRPV1 are associated in a subset of nociceptors and that TRPV1 protein stability is increased through the interaction with the cytoskeletal scaffold protein.
Title: Whirlin increases TRPV1 channel expression and cellular stability.
This study showed here that Whirlin/Deafness autosomal recessive 31 (DFNB31), a PDZ-scaffold protein involved in vestibular and auditory hair cell transduction, is also expressed by proprioceptive sensory neurons (pSNs) in dorsal root ganglia in mice.
Title: The PDZ-domain protein Whirlin facilitates mechanosensory signaling in mammalian proprioceptors.
Whrn acts as a cytoskeletal linker to ensure proper paranodal compaction and stabilization of the axonal cytoskeleton in myelinated axons.
Title: Whirlin, a cytoskeletal scaffolding protein, stabilizes the paranodal region and axonal cytoskeleton in myelinated axons.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Variation

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Alleles

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

Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (1)
Spontaneous (1) 1 citation
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW742671 (e-PCR)
- UniSTS:207627

AW530332 (e-PCR)
- UniSTS:244520

AW122018 (e-PCR)
- UniSTS:179017

NoName (e-PCR)
- UniSTS:234937

Whrn (e-PCR), detects polymorphism
- UniSTS:496611

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
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 localization in cell	IMP Inferred from Mutant Phenotype 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 differentiation	NAS Non-traceable Author Statement 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	IEA Inferred from Electronic Annotation 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
part_of USH2 complex	IDA Inferred from Direct Assay more info	PubMed
part_of USH2 complex	IPI Inferred from Physical Interaction 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 ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
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 growth cone	IEA Inferred from Electronic Annotation more info
located_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
colocalizes_with neuronal cell body	ISS Inferred from Sequence or Structural Similarity 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
located_in photoreceptor connecting cilium	ISO Inferred from Sequence Orthology 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
colocalizes_with photoreceptor inner segment	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
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
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
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

General protein information

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Preferred Names: whirlin

Names: whirler

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)

NM_001008791.2 → NP_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

A2AGD2, I6MML6, I6MML7, Q3TZC8, Q5MLF1, Q5MLF2, Q5MLF3, Q5MLF4, Q5MLF5, Q5MLF6, Q5MLF7, Q5MLF8, Q5MLF9, Q80TC2, Q80VW4, Q80VW5

UniProtKB/TrEMBL

B2RWY4

Related

ENSMUSP00000081557.2, ENSMUST00000084510.8

Conserved Domains (3) summary

cd00992
Location:278 → 358

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:38 → 113

HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains

cd07357
Location:420 → 500

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
NM_001008792.2 → NP_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/TrEMBL

B2RWY4

Related

ENSMUSP00000103016.2, ENSMUST00000107393.8

Conserved Domains (3) summary

cd00992
Location:278 → 358

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:38 → 113

HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains

cd07357
Location:424 → 504

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
NM_001008793.2 → NP_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/TrEMBL

B2RWY4

Related

ENSMUSP00000099931.2, ENSMUST00000102867.8

Conserved Domains (3) summary

cd00992
Location:278 → 358

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:38 → 113

HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains

cd07357
Location:420 → 500

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
NM_001276371.1 → NP_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:139 → 216

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:38 → 113

HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
NM_028640.2 → NP_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/TrEMBL

B2RWY4

Related

ENSMUSP00000069664.4, ENSMUST00000063650.10

Conserved Domains (3) summary

cd00992
Location:278 → 358

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:38 → 113

HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains

cd07357
Location:420 → 500

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: 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

NC_000070.7 Reference GRCm39 C57BL/6J

Range

63333145..63414320 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006538309.4 → XP_006538372.1 whirlin isoform X1

UniProtKB/TrEMBL

B2RWY4

Conserved Domains (3) summary

cd00992
Location:278 → 358

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:38 → 113

HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains

cd07357
Location:420 → 500

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains

RNA

XR_004941996.1 RNA Sequence
XR_001784212.2 RNA Sequence
XR_001784211.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.
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.
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.
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.
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.