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WHRN whirlin [ Homo sapiens (human) ]

Gene ID: 25861, updated on 12-Oct-2019

Summary

Official Symbol
WHRNprovided by HGNC
Official Full Name
whirlinprovided by HGNC
Primary source
HGNC:HGNC:16361
See related
Ensembl:ENSG00000095397 MIM:607928
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
WI; CIP98; USH2D; DFNB31; PDZD7B
Summary
This gene is thought to function in the organization and stabilization of sterocilia elongation and actin cystoskeletal assembly, based on studies of the related mouse gene. Mutations in this gene have been associated with autosomal recessive non-syndromic deafness and Usher Syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
Expression
Broad expression in adrenal (RPKM 14.4), testis (RPKM 9.7) and 18 other tissues See more
Orthologs

Genomic context

See WHRN in Genome Data Viewer
Location:
9q32
Exon count:
21
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (114402078..114505500, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (117164360..117267789, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene orosomucoid 2 Neighboring gene AT-hook transcription factor Neighboring gene small EDRK-rich factor 2 pseudogene Neighboring gene uncharacterized LOC105376228 Neighboring gene uncharacterized LOC105376229 Neighboring gene ATPase H+ transporting V1 subunit G1

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 Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Propensity score-based nonparametric test revealing genetic variants underlying bipolar disorder.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1526, DKFZp434N014

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
auditory receptor cell stereocilium organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cerebellar Purkinje cell layer formation IEA
Inferred from Electronic Annotation
more info
 
detection of mechanical stimulus involved in sensory perception of sound ISS
Inferred from Sequence or Structural Similarity
more info
 
establishment of protein localization ISS
Inferred from Sequence or Structural Similarity
more info
 
inner ear receptor cell stereocilium organization ISS
Inferred from Sequence or Structural Similarity
more info
 
paranodal junction maintenance IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
retina homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
retina homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
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
USH2 complex ISS
Inferred from Sequence or Structural Similarity
more info
 
actin filament IEA
Inferred from Electronic Annotation
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
ciliary basal body IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
growth cone IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
 
periciliary membrane compartment ISS
Inferred from Sequence or Structural Similarity
more info
 
colocalizes_with photoreceptor connecting cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with photoreceptor connecting cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
colocalizes_with photoreceptor inner segment IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with photoreceptor inner segment ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stereocilia ankle link IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stereocilia ankle link ISS
Inferred from Sequence or Structural Similarity
more info
 
stereocilia ankle link complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stereocilia ankle link complex ISS
Inferred from Sequence or Structural Similarity
more info
 
stereocilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stereocilium ISS
Inferred from Sequence or Structural Similarity
more info
 
stereocilium tip IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stereocilium tip ISS
Inferred from Sequence or Structural Similarity
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
whirlin
Names
CASK-interacting protein CIP98
autosomal recessive deafness type 31 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_016700.1 RefSeqGene

    Range
    4984..108377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001083885.2NP_001077354.2  whirlin isoform 2

    See identical proteins and their annotated locations for NP_001077354.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences in the presence and absence of exons at its 5' end, compared to variant 1. These differences produce a unique 5' UTR and cause translation initiation at a downstream start codon, compared to variant 1. The encoded protein (isoform 2) is shorter than isoform 1.
    Source sequence(s)
    AL110228, BC136416, BC142614, DA502065
    Consensus CDS
    CCDS43870.1
    UniProtKB/Swiss-Prot
    Q9P202
    UniProtKB/TrEMBL
    A0A0C4DFN4, B9EGE6
    Related
    ENSP00000265134.6, ENST00000265134.10
    Conserved Domains (2) summary
    cd00992
    Location:433504
    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) ...
    cd07357
    Location:36116
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  2. NM_001173425.2NP_001166896.1  whirlin isoform 3

    See identical proteins and their annotated locations for NP_001166896.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate, in-frame splice site in the 3' coding region, compared to variant 1. The encoded protein (isoform 3) is shorter than isoform 1.
    Source sequence(s)
    AL138895, BC014524, BC136416, BC142614, BC142684
    UniProtKB/Swiss-Prot
    Q9P202
    UniProtKB/TrEMBL
    B9EGE6
    Conserved Domains (3) summary
    cd00992
    Location:277357
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:419499
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  3. NM_001346890.1NP_001333819.1  whirlin isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AL138895, KF459656, KF459658
    Consensus CDS
    CCDS87678.1
    UniProtKB/TrEMBL
    A0A0A0MRR8
    Related
    ENSP00000363172.3, ENST00000374059.7
  4. NM_015404.4NP_056219.3  whirlin isoform 1

    See identical proteins and their annotated locations for NP_056219.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL138895, BC136416, BC142614, BC142684
    Consensus CDS
    CCDS6806.1
    UniProtKB/Swiss-Prot
    Q9P202
    UniProtKB/TrEMBL
    A0A0C4DFT9, B9EGE6
    Related
    ENSP00000354623.3, ENST00000362057.4
    Conserved Domains (4) summary
    cd00992
    Location:277357
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:419499
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
    cl25496
    Location:516804
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    114402078..114505500 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518485.1XP_011516787.1  whirlin isoform X1

    See identical proteins and their annotated locations for XP_011516787.1

    Conserved Domains (3) summary
    cd00992
    Location:277357
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:419499
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  2. XM_011518487.2XP_011516789.1  whirlin isoform X3

    Conserved Domains (4) summary
    cd00992
    Location:138215
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:377457
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
    cl00117
    Location:279315
    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. ...
  3. XM_011518488.2XP_011516790.1  whirlin isoform X4

    Conserved Domains (3) summary
    cd00992
    Location:277357
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cl11968
    Location:419475
    harmonin_N_like; N-terminal protein-binding module of harmonin and similar domains, also known as HHD (harmonin homology domain)
  4. XM_011518486.2XP_011516788.1  whirlin isoform X2

    Conserved Domains (3) summary
    cd00992
    Location:277357
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:419499
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  5. XM_011518492.2XP_011516794.1  whirlin isoform X6

    See identical proteins and their annotated locations for XP_011516794.1

    Conserved Domains (3) summary
    cd00992
    Location:277357
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:419499
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  6. XM_011518489.3XP_011516791.1  whirlin isoform X5

    Conserved Domains (3) summary
    cd00992
    Location:277357
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:419499
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  7. XM_011518491.3XP_011516793.1  whirlin isoform X6

    See identical proteins and their annotated locations for XP_011516793.1

    Conserved Domains (3) summary
    cd00992
    Location:277357
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:419499
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains
  8. XM_011518494.3XP_011516796.1  whirlin isoform X7

    Conserved Domains (3) summary
    cd00992
    Location:277357
    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:37112
    HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
    cd07357
    Location:419499
    HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains

RNA

  1. XR_929748.2 RNA Sequence

  2. XR_929747.2 RNA Sequence

  3. XR_929757.2 RNA Sequence

  4. XR_929750.3 RNA Sequence

  5. XR_929749.2 RNA Sequence

  6. XR_929752.2 RNA Sequence

  7. XR_929756.2 RNA Sequence

  8. XR_929754.2 RNA Sequence

  9. XR_929753.3 RNA Sequence

  10. XR_929755.3 RNA Sequence

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