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    WHRN whirlin [ Homo sapiens (human) ]

    Gene ID: 25861, updated on 6-Jun-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See WHRN in Genome Data Viewer
    Location:
    9q32
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (114402080..114505473, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (126594499..126697864, complement)
    105.20220307 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

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1526, DKFZp434N014

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein 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 cerebellar Purkinje cell layer formation IEA
    Inferred from Electronic Annotation
    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 protein localization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner ear receptor cell differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    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 positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retina homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in retina homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sensory perception of light stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory perception of sound IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    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 ciliary basal body IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in growth cone IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in periciliary membrane compartment ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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
     
    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 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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in stereocilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in stereocilium tip IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in stereocilium tip ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in 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)

    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_2023_10

    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

    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
      ENSP00000514397.1, ENST00000699486.1
      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
    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