Whrn whirlin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Whrnprovided by RGD
Official Full Name: whirlinprovided by RGD
Primary source: RGD:631330
See related: Ensembl:ENSRNOG00000001700 AllianceGenome:RGD:631330
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Cip98; Dfnb31
Summary: Enables protein domain specific binding activity. Predicted to be involved in several processes, including detection of mechanical stimulus involved in sensory perception of sound; nervous system development; and paranodal junction maintenance. Predicted to act upstream of or within establishment of protein localization and positive regulation of gene expression. Located in several cellular components, including dendrite; stereocilia ankle link; and stereocilium tip. Colocalizes with neuronal cell body; photoreceptor connecting cilium; and photoreceptor inner segment. Human ortholog(s) of this gene implicated in Usher syndrome type 2D; autosomal recessive nonsyndromic deafness 31; and sensorineural hearing loss. Orthologous to human WHRN (whirlin). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 50.6), Thymus (RPKM 50.4) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q24

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (81843820..81933400, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (76828308..76911945, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (79235541..79317206, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
CIP98, a novel protein (98 kDa) consisting of three PDZ domains and a proline-rich region, is widely expressed in the central nervous system and interacts with CASK (calmodulin-dependent serine kinase)
Title: CIP98, a novel PDZ domain protein, is expressed in the central nervous system and interacts with calmodulin-dependent serine kinase.

Submit: New GeneRIF Correction

General gene information

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Markers

AW530332 (e-PCR)
- UniSTS:244520

RH134143 (e-PCR)
- UniSTS:217425

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in auditory receptor cell stereocilium organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in auditory receptor cell stereocilium organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within auditory receptor cell stereocilium organization	ISO Inferred from Sequence Orthology more info
involved_in cerebellar Purkinje cell layer formation	IEA Inferred from Electronic Annotation more info
involved_in cerebellar Purkinje cell layer formation	ISO Inferred from Sequence Orthology more info
involved_in detection of mechanical stimulus involved in sensory perception of sound	IEA Inferred from Electronic Annotation more info
involved_in detection of mechanical stimulus involved in sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in detection of mechanical stimulus involved in sensory perception of sound	ISS Inferred from Sequence or Structural Similarity more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
involved_in establishment of protein localization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within establishment of protein localization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of protein localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in inner ear receptor cell stereocilium organization	ISO Inferred from Sequence Orthology more info
involved_in inner ear receptor cell stereocilium organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in paranodal junction maintenance	IEA Inferred from Electronic Annotation more info
involved_in paranodal junction maintenance	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in retina homeostasis	IEA Inferred from Electronic Annotation more info
involved_in retina homeostasis	ISO Inferred from Sequence Orthology more info
involved_in retina homeostasis	ISS Inferred from Sequence or Structural Similarity 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	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of USH2 complex	IEA Inferred from Electronic Annotation more info
part_of USH2 complex	ISO Inferred from Sequence Orthology more info
part_of USH2 complex	ISS Inferred from Sequence or Structural Similarity more info
located_in actin filament	IEA Inferred from Electronic Annotation more info
located_in actin filament	ISO Inferred from Sequence Orthology more info
located_in apical dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in axon collateral	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in ciliary basal body	IEA Inferred from Electronic Annotation more info
located_in ciliary basal body	ISO Inferred from Sequence Orthology more info
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in dendritic shaft	IDA Inferred from Direct Assay more info	PubMed
located_in growth cone	IEA Inferred from Electronic Annotation more info
located_in neuron projection	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in periciliary membrane compartment	IEA Inferred from Electronic Annotation more info
located_in periciliary membrane compartment	ISO Inferred from Sequence Orthology more info
located_in periciliary membrane compartment	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor connecting cilium	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor connecting cilium	IEA Inferred from Electronic Annotation more info
located_in photoreceptor connecting cilium	ISO Inferred from Sequence Orthology more info
colocalizes_with photoreceptor inner segment	IBA Inferred from Biological aspect of Ancestor more info
located_in photoreceptor inner segment	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor inner segment	IEA Inferred from Electronic Annotation more info
located_in photoreceptor inner segment	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynapse	IDA Inferred from Direct Assay more info	PubMed
located_in presynapse	IDA Inferred from Direct Assay more info	PubMed
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
located_in stereocilia ankle link	ISS Inferred from Sequence or Structural Similarity more info
part_of stereocilia ankle link complex	IBA Inferred from Biological aspect of Ancestor more info
part_of stereocilia ankle link complex	IEA Inferred from Electronic Annotation more info
part_of stereocilia ankle link complex	ISO Inferred from Sequence Orthology more info
part_of stereocilia ankle link complex	ISS Inferred from Sequence or Structural Similarity more info
located_in stereocilium	IDA Inferred from Direct Assay more info	PubMed
located_in stereocilium	ISO Inferred from Sequence Orthology more info
located_in stereocilium	ISS Inferred from Sequence or Structural Similarity more info
located_in stereocilium bundle	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
located_in stereocilium tip	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: whirlin

Names: CASK-interacting protein CIP98; deafness, autosomal recessive 31

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_001389267.1 → NP_001376196.1 whirlin isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

Q810W9

Related

ENSRNOP00000072172.2, ENSRNOT00000082513.2

Conserved Domains (3) 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

cd07357
Location:418 → 498

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
NM_181088.2 → NP_851602.2 whirlin isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

Q810W9

UniProtKB/TrEMBL

A6J7Y3, G3V675

Related

ENSRNOP00000002309.2, ENSRNOT00000002309.3

Conserved Domains (3) 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

cd07357
Location:418 → 498

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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

81843820..81933400 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039109876.2 → XP_038965804.1 whirlin isoform X4

UniProtKB/Swiss-Prot

Q810W9

Conserved Domains (4) 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

cd07357
Location:376 → 456

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

cl00117
Location:278 → 314

PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...
XM_039109877.2 → XP_038965805.1 whirlin isoform X6

UniProtKB/Swiss-Prot

Q810W9

Conserved Domains (3) 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

cd07357
Location:418 → 498

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
XM_039109875.2 → XP_038965803.1 whirlin isoform X3

UniProtKB/Swiss-Prot

Q810W9

Conserved Domains (3) 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

cd07357
Location:418 → 498

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
XM_063287633.1 → XP_063143703.1 whirlin isoform X5
XM_039109874.2 → XP_038965802.1 whirlin isoform X2

UniProtKB/Swiss-Prot

Q810W9

Conserved Domains (3) 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

cd07357
Location:418 → 498

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
XM_039109873.2 → XP_038965801.1 whirlin isoform X1

UniProtKB/Swiss-Prot

Q810W9

Conserved Domains (3) 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

cd07357
Location:418 → 498

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
XM_039109878.2 → XP_038965806.1 whirlin isoform X7

UniProtKB/Swiss-Prot

Q810W9

Conserved Domains (3) 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

cd07357
Location:418 → 498

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
XM_039109880.2 → XP_038965808.1 whirlin isoform X8

UniProtKB/Swiss-Prot

Q810W9

Conserved Domains (3) 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

cd07357
Location:418 → 498

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
XM_039109879.2 → XP_038965807.1 whirlin isoform X8

UniProtKB/Swiss-Prot

Q810W9

Conserved Domains (3) 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

cd07357
Location:418 → 498

HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
XM_039109881.2 → XP_038965809.1 whirlin isoform X9

UniProtKB/TrEMBL

A6J7Y4

Conserved Domains (3) 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

cd07357
Location:418 → 498

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