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WHRN whirlin [ Homo sapiens (human) ]

Gene ID: 25861, updated on 10-Dec-2024

Summary

Official Symbol
WHRNprovided by HGNC
Official Full Name
whirlinprovided by HGNC
Primary source
HGNC:HGNC:16361
See related
Ensembl:ENSG00000095397 MIM:607928; AllianceGenome:HGNC:16361
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
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Genomic context

See WHRN in Genome Data Viewer
Location:
9q32
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (114402080..114505473, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (126594499..126697864, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (117164360..117267753, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117096322-117096822 Neighboring gene orosomucoid 2 Neighboring gene AT-hook transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117129412-117130360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117131354-117132058 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117143871-117144852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117144987-117145802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117149889-117150624 Neighboring gene uncharacterized LOC124902253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117167737-117168238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117183585-117184085 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117197109-117197608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28867 Neighboring gene uncharacterized LOC124902254 Neighboring gene small EDRK-rich factor 2 pseudogene Neighboring gene Sharpr-MPRA regulatory region 12257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117266242-117267132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117267133-117268023 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:117276161-117276362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28868 Neighboring gene uncharacterized LOC105376229 Neighboring gene small nucleolar RNA U13 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:117345492-117345996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117348508-117349327 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117349328-117350146 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

Associated conditions

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

General gene information

Clone Names

  • KIAA1526, DKFZp434N014

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding  
enables protein binding PubMed 
Process Evidence Code Pubs
involved_in auditory receptor cell stereocilium organization  
involved_in cerebellar Purkinje cell layer formation  
involved_in detection of mechanical stimulus involved in sensory perception of sound  
involved_in establishment of localization in cell  
acts_upstream_of_or_within establishment of protein localization  
involved_in inner ear receptor cell differentiation PubMed 
involved_in inner ear receptor cell stereocilium organization  
involved_in paranodal junction maintenance  
involved_in positive regulation of gene expression  
involved_in retina homeostasis PubMed 
involved_in retina homeostasis  
involved_in sensory perception of light stimulus PubMed 
involved_in sensory perception of sound  
involved_in sensory perception of sound PubMed 
Component Evidence Code Pubs
part_of USH2 complex  
located_in actin filament  
located_in ciliary basal body  
is_active_in cilium  
located_in cytoplasm PubMed 
located_in growth cone  
colocalizes_with neuronal cell body  
located_in periciliary membrane compartment  
colocalizes_with photoreceptor connecting cilium  
colocalizes_with photoreceptor inner segment  
is_active_in plasma membrane  
located_in stereocilia ankle link  
part_of stereocilia ankle link complex  
part_of stereocilia ankle link complex  
located_in stereocilium  
is_active_in stereocilium tip  
located_in stereocilium tip  
located_in synapse  

General protein information

Preferred Names
whirlin
Names
CASK-interacting protein CIP98
autosomal recessive deafness type 31 protein

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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), LRG_1094

mRNA and Protein(s)

  1. NM_001083885.3NP_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/TrEMBL
    A0A669KBJ1
    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/TrEMBL
    B9EGE6
    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
    pfam05109
    Location:516803
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  3. NM_001346890.1NP_001333819.1  whirlin isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AL138895, KF459656, KF459658
    UniProtKB/TrEMBL
    A0A669KBJ1
    Related
    ENST00000674048.1
  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
    A0A0C4DFT9, A5PKU1, A5PKZ9, Q5TAU9, Q5TAV0, Q5TAV1, Q5TAV2, Q96MZ9, Q9H9F4, Q9P202, Q9UFZ3
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    114402080..114505473 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423168.1XP_047279124.1  whirlin isoform X10

  2. XM_047423165.1XP_047279121.1  whirlin isoform X7

  3. XM_047423164.1XP_047279120.1  whirlin isoform X6

  4. XM_047423166.1XP_047279122.1  whirlin isoform X8

    Related
    ENSP00000501297.5, ENST00000674036.9
  5. XM_047423163.1XP_047279119.1  whirlin isoform X4

    UniProtKB/TrEMBL
    B9EGE6
    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
    pfam05109
    Location:516803
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  6. XM_047423161.1XP_047279117.1  whirlin isoform X3

    UniProtKB/Swiss-Prot
    A0A0C4DFT9, A5PKU1, A5PKZ9, Q5TAU9, Q5TAV0, Q5TAV1, Q5TAV2, Q96MZ9, Q9H9F4, Q9P202, Q9UFZ3
  7. XM_011518485.2XP_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
  8. XM_047423169.1XP_047279125.1  whirlin isoform X11

  9. XM_011518487.3XP_011516789.1  whirlin isoform X5

  10. XM_047423167.1XP_047279123.1  whirlin isoform X9

  11. XM_011518486.3XP_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
  12. XM_047423171.1XP_047279127.1  whirlin isoform X13

  13. XM_047423170.1XP_047279126.1  whirlin isoform X12

  14. XM_011518492.3XP_011516794.1  whirlin isoform X15

    See identical proteins and their annotated locations for XP_011516794.1

    UniProtKB/TrEMBL
    A0A8V8TQ31
    Related
    ENSP00000514397.2, ENST00000699486.2
    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
  15. XM_047423173.1XP_047279129.1  whirlin isoform X14

  16. XM_047423174.1XP_047279130.1  whirlin isoform X17

  17. XM_011518491.4XP_011516793.1  whirlin isoform X15

    See identical proteins and their annotated locations for XP_011516793.1

    UniProtKB/TrEMBL
    A0A8V8TQ31
    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
  18. XM_011518494.4XP_011516796.1  whirlin isoform X16

    UniProtKB/TrEMBL
    A0A8V8TQ31
    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_929757.3 RNA Sequence

  2. XR_929750.4 RNA Sequence

  3. XR_929749.3 RNA Sequence

  4. XR_929752.3 RNA Sequence

  5. XR_929756.3 RNA Sequence

  6. XR_929754.3 RNA Sequence

  7. XR_929753.4 RNA Sequence

  8. XR_929755.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    126594499..126697864 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362646.1XP_054218621.1  whirlin isoform X11

  2. XM_054362645.1XP_054218620.1  whirlin isoform X10

  3. XM_054362642.1XP_054218617.1  whirlin isoform X7

  4. XM_054362641.1XP_054218616.1  whirlin isoform X6

  5. XM_054362640.1XP_054218615.1  whirlin isoform X5

  6. XM_054362644.1XP_054218619.1  whirlin isoform X9

  7. XM_054362643.1XP_054218618.1  whirlin isoform X8

  8. XM_054362639.1XP_054218614.1  whirlin isoform X2

  9. XM_054362638.1XP_054218613.1  whirlin isoform X1

  10. XM_054362648.1XP_054218623.1  whirlin isoform X13

  11. XM_054362647.1XP_054218622.1  whirlin isoform X12

  12. XM_054362651.1XP_054218626.1  whirlin isoform X15

    UniProtKB/TrEMBL
    A0A8V8TQ31
  13. XM_054362653.1XP_054218628.1  whirlin isoform X17

  14. XM_054362649.1XP_054218624.1  whirlin isoform X14

  15. XM_054362650.1XP_054218625.1  whirlin isoform X15

    UniProtKB/TrEMBL
    A0A8V8TQ31
  16. XM_054362652.1XP_054218627.1  whirlin isoform X16

    UniProtKB/TrEMBL
    A0A8V8TQ31

RNA

  1. XR_008487979.1 RNA Sequence

  2. XR_008487974.1 RNA Sequence

  3. XR_008487973.1 RNA Sequence

  4. XR_008487975.1 RNA Sequence

  5. XR_008487978.1 RNA Sequence

  6. XR_008487976.1 RNA Sequence

  7. XR_008487977.1 RNA Sequence

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