LOCUS       NM_015404               4070 bp    mRNA    linear   PRI 10-DEC-2024
DEFINITION  Homo sapiens whirlin (WHRN), transcript variant 1, mRNA.
ACCESSION   NM_015404 XM_027012
VERSION     NM_015404.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 4070)
  AUTHORS   AitRaise,I., Amalou,G., Redouane,S., Charoute,H., Snoussi,K.,
            Abdelghaffar,H., Bonnet,C., Petit,C. and Barakat,A.
  TITLE     Novel pathogenic WHRN variant causing hearing loss in a moroccan
            family
  JOURNAL   Mol Biol Rep 50 (12), 10663-10669 (2023)
   PUBMED   37924449
  REMARK    GeneRIF: Novel pathogenic WHRN variant causing hearing loss in a
            moroccan family.
REFERENCE   2  (bases 1 to 4070)
  AUTHORS   Visconti,L., Malagrino,F., Troilo,F., Pagano,L., Toto,A. and
            Gianni,S.
  TITLE     Folding and Misfolding of a PDZ Tandem Repeat
  JOURNAL   J Mol Biol 433 (7), 166862 (2021)
   PUBMED   33539879
  REMARK    GeneRIF: Folding and Misfolding of a PDZ Tandem Repeat.
REFERENCE   3  (bases 1 to 4070)
  AUTHORS   Lin,L., Shi,Y., Wang,M., Wang,C., Lu,Q., Zhu,J. and Zhang,R.
  TITLE     Phase separation-mediated condensation of Whirlin-Myo15-Eps8
            stereocilia tip complex
  JOURNAL   Cell Rep 34 (8), 108770 (2021)
   PUBMED   33626355
  REMARK    GeneRIF: Phase separation-mediated condensation of
            Whirlin-Myo15-Eps8 stereocilia tip complex.
REFERENCE   4  (bases 1 to 4070)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   5  (bases 1 to 4070)
  AUTHORS   van Wijk,E., van der Zwaag,B., Peters,T., Zimmermann,U., Te
            Brinke,H., Kersten,F.F., Marker,T., Aller,E., Hoefsloot,L.H.,
            Cremers,C.W., Cremers,F.P., Wolfrum,U., Knipper,M., Roepman,R. and
            Kremer,H.
  TITLE     The DFNB31 gene product whirlin connects to the Usher protein
            network in the cochlea and retina by direct association with USH2A
            and VLGR1
  JOURNAL   Hum Mol Genet 15 (5), 751-765 (2006)
   PUBMED   16434480
  REMARK    GeneRIF: This paper concludes that this protein plays a role in
            photoreceptor and hair cell synapse organization in the related rat
            gene.
REFERENCE   6  (bases 1 to 4070)
  AUTHORS   Mburu,P., Mustapha,M., Varela,A., Weil,D., El-Amraoui,A.,
            Holme,R.H., Rump,A., Hardisty,R.E., Blanchard,S., Coimbra,R.S.,
            Perfettini,I., Parkinson,N., Mallon,A.M., Glenister,P.,
            Rogers,M.J., Paige,A.J., Moir,L., Clay,J., Rosenthal,A., Liu,X.Z.,
            Blanco,G., Steel,K.P., Petit,C. and Brown,S.D.
  TITLE     Defects in whirlin, a PDZ domain molecule involved in stereocilia
            elongation, cause deafness in the whirler mouse and families with
            DFNB31
  JOURNAL   Nat Genet 34 (4), 421-428 (2003)
   PUBMED   12833159
  REMARK    GeneRIF: Defects in whirlin, a PDZ domain molecule involved in
            stereocilia elongation, cause deafness in the whirler mouse and
            families with DFNB31.
REFERENCE   7  (bases 1 to 4070)
  AUTHORS   Yap,C.C., Liang,F., Yamazaki,Y., Muto,Y., Kishida,H., Hayashida,T.,
            Hashikawa,T. and Yano,R.
  TITLE     CIP98, a novel PDZ domain protein, is expressed in the central
            nervous system and interacts with calmodulin-dependent serine
            kinase
  JOURNAL   J Neurochem 85 (1), 123-134 (2003)
   PUBMED   12641734
  REMARK    GeneRIF: This paper describes a PDZ domain protein and its role in
            synaptic transmission in the related rat gene.
REFERENCE   8  (bases 1 to 4070)
  AUTHORS   Mustapha,M., Chouery,E., Chardenoux,S., Naboulsi,M., Paronnaud,J.,
            Lemainque,A., Megarbane,A., Loiselet,J., Weil,D., Lathrop,M. and
            Petit,C.
  TITLE     DFNB31, a recessive form of sensorineural hearing loss, maps to
            chromosome 9q32-34
  JOURNAL   Eur J Hum Genet 10 (3), 210-212 (2002)
   PUBMED   11973626
REFERENCE   9  (bases 1 to 4070)
  AUTHORS   Shearer,A.E., Hildebrand,M.S., Odell,A.M. and Smith,R.J.H.
  TITLE     Genetic Hearing Loss Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301607
REFERENCE   10 (bases 1 to 4070)
  AUTHORS   Koenekoop,R., Arriaga,M., Trzupek,K.M. and Lentz,J.
  TITLE     Usher Syndrome Type II
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301515
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL138895.16, BC142614.1,
            BC142684.1 and BC136416.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_015404.3.
            
            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].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC142614.1, AB040959.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000362057.4/ ENSP00000354623.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-17                AL138895.16        111965-111981       c
            18-377              BC142614.1         1-360
            378-2024            BC142684.1         336-1982
            2025-2908           BC136416.1         1757-2640
            2909-4070           BC142614.1         2892-4053
FEATURES             Location/Qualifiers
     source          1..4070
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="9"
                     /map="9q32"
     gene            1..4070
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /note="whirlin"
                     /db_xref="GeneID:25861"
                     /db_xref="HGNC:HGNC:16361"
                     /db_xref="MIM:607928"
     exon            1..1290
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     CDS             673..3396
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /note="isoform 1 is encoded by transcript variant 1;
                     CASK-interacting protein CIP98; autosomal recessive
                     deafness type 31 protein"
                     /codon_start=1
                     /product="whirlin isoform 1"
                     /protein_id="NP_056219.3"
                     /db_xref="CCDS:CCDS6806.1"
                     /db_xref="GeneID:25861"
                     /db_xref="HGNC:HGNC:16361"
                     /db_xref="MIM:607928"
                     /translation="MNAPLDGLSVSSSSTGSLGSAAGAGGGGGAGLRLLSANVRQLHQ
                     ALTALLSEAEREQFTHCLNAYHARRNVFDLVRTLRVLLDSPVKRRLLPMLRLVIPRSD
                     QLLFDQYTAEGLYLPATTPYRQPAWGGPDSAGPGEVRLVSLRRAKAHEGLGFSIRGGS
                     EHGVGIYVSLVEPGSLAEKEGLRVGDQILRVNDKSLARVTHAEAVKALKGSKKLVLSV
                     YSAGRIPGGYVTNHIYTWVDPQGRSISPPSGLPQPHGGALRQQEGDRRSTLHLLQGGD
                     EKKVNLVLGDGRSLGLTIRGGAEYGLGIYITGVDPGSEAEGSGLKVGDQILEVNGRSF
                     LNILHDEAVRLLKSSRHLILTVKDVGRLPHARTTVDETKWIASSRIRETMANSAGFLG
                     DLTTEGINKPGFYKGPAGSQVTLSSLGNQTRVLLEEQARHLLNEQEHATMAYYLDEYR
                     GGSVSVEALVMALFKLLNTHAKFSLLSEVRGTISPQDLERFDHLVLRREIESMKARQP
                     PGPGAGDTYSMVSYSDTGSSTGSHGTSTTVSSARNTLDLEETGEAVQGNINALPDVSV
                     DDVRSTSQGLSSFKPLPRPPPLAQGNDLPLGQPRKLGREDLQPPSSMPSCSGTVFSAP
                     QNRSPPAGTAPTPGTSSAQDLPSSPIYASVSPANPSSKRPLDAHLALVNQHPIGPFPR
                     VQSPPHLKSPSAEATVAGGCLLPPSPSGHPDQTGTNQHFVMVEVHRPDSEPDVNEVRA
                     LPQTRTASTLSQLSDSGQTLSEDSGVDAGEAEASAPGRGRQSVSTKSRSSKELPRNER
                     PTDGANKPPGLLEPTSTLVRVKKSAATLGIAIEGGANTRQPLPRIVTIQRGGSAHNCG
                     QLKVGHVILEVNGLTLRGKEHREAARIIAEAFKTKDRDYIDFLVTEFNVML"
     exon            1291..1509
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            1510..1635
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            1636..1838
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            1839..1875
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            1876..2088
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            2089..2298
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            2299..2370
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            2371..2908
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            2909..3090
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            3091..3213
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     exon            3214..4070
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4047..4052
                     /regulatory_class="polyA_signal_sequence"
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /note="hexamer: AATAAA"
     polyA_site      4070
                     /gene="WHRN"
                     /gene_synonym="CIP98; DFNB31; PDZD7B; USH2D; WI"
                     /note="major polyA site"
ORIGIN      
        1 agactcggcc cgggtggctc aacagttcgc aaagtccggg cttgcggccg ggcggcgcag
       61 aggcgcggag gctccccggg cggctgcatc ccggggctgc cccggacatg ccccgcaccc
      121 cttgtcggac gcccgcgccg cttcaccggc tgccactccc cggagtgctc tgggactaga
      181 gcgccctccg ccccaacttc tgactttggg gtcccccagc cctagaggaa cgggcgcccg
      241 gctgggggag ccccgggcat ggtgtgacgg ggcagtcagg tcagctttgc ggcgccccca
      301 aactccagcc acccgtcgtc tccgtgccct ccagaatgta gctgctgacc ccgcgccccc
      361 cggactccag cagcagtctc cgccacctcc gggctccagc agccaactct tgtgtctctc
      421 aggaacccgc cgacgtctcc gcgtcccccg gattccaggt tcgcgacccc cgccgtcttc
      481 gcgcctccgg gactctagca gcggtctccg cgacccccta ggatccagcc actgtacccg
      541 tgctccccaa acccaggctc cagccgtcgt ctccgcgctc ccggggatcc agctgtcgcg
      601 ccagtacccg cgaggacagc ggcaccgccc acaccccgcg cgctcagagc ccggccgggc
      661 ctcggcgtgg agatgaacgc gccgctggac ggcctgtcgg tgagctcgtc ctccaccggc
      721 tcgctgggct cggcggccgg ggcgggcggc ggcgggggcg cggggctgcg gttactgtct
      781 gccaacgtgc gccagctgca ccaagcgctg accgcgctgc tgagcgaggc ggagcgggag
      841 cagttcaccc actgcctgaa cgcttaccac gcgcgccgca acgtcttcga cctggtgcgc
      901 accctgcgcg tgctgctgga cagtccggtc aagcggcgcc tgctgcccat gcttcgtctg
      961 gtcatcccgc gctccgacca gctgctcttc gaccaataca cggccgaggg cctctacctg
     1021 cccgccacca ccccctacag gcagcccgcc tggggcggcc ccgacagcgc ggggccaggg
     1081 gaggtgcgcc tggtgagttt gcggcgtgcc aaggcccacg agggcttggg cttcagcatc
     1141 cgtgggggct cggagcacgg cgtgggcatc tacgtgtctc tggtggaacc aggctctcta
     1201 gctgagaagg aaggactgcg ggtcggggac cagattctgc gcgtcaacga caaatccctg
     1261 gcccgggtga cccacgcgga ggccgtcaag gctctgaagg gctccaagaa gctggtgctg
     1321 tctgtgtact cagcagggcg catccctggg ggctacgtca ccaaccacat ctacacctgg
     1381 gtggacccgc agggccgcag catctcccca ccctcgggcc tgccccagcc ccacggtggt
     1441 gccctgaggc agcaggaggg tgaccggagg agcaccctgc acctcctgca aggaggggat
     1501 gagaaaaagg tgaacctggt gctgggggac ggccggtccc tgggcctcac gatccgtggg
     1561 ggagctgagt acggccttgg catttacatc actggcgtgg acccaggctc tgaagcagaa
     1621 ggcagcgggc tcaaggttgg ggaccagatt ctagaagtga atgggcggag ctttctcaac
     1681 atcctacacg acgaggctgt caggctgctt aagtcatctc ggcacctcat cctgacagtg
     1741 aaggacgtcg ggaggctgcc ccatgcccgc accactgtgg acgagaccaa gtggatcgcc
     1801 agttcccgga tcagggagac catggcgaac tcggcagggt ttcttggcga tctcacaaca
     1861 gaaggaataa acaagccagg attttacaag ggcccagccg gctcccaggt gaccctgagc
     1921 agcctgggga accagacacg agtgctgctg gaggagcagg ctcggcacct gctgaacgag
     1981 caggaacacg ccaccatggc ctactacctg gatgagtacc gtggtggcag cgtctctgtg
     2041 gaggccctcg tcatggccct gttcaagctg ctcaacaccc acgccaagtt ctcactcctc
     2101 tctgaggtga gaggcaccat ttccccgcaa gacctagaac gcttcgacca cctggtgctg
     2161 aggcgtgaga ttgagtccat gaaggcgcgg cagcccccag gccccggggc tggggacacc
     2221 tactccatgg tctcctacag tgacacgggt tcatccacag gcagccacgg cacctccacc
     2281 accgtcagct cggccaggaa cactctggac ctggaggaaa ctggcgaggc tgtccagggc
     2341 aatatcaacg ccctcccaga tgtgtccgtg gatgatgtca gatccacctc ccaggggctg
     2401 tcaagcttca agccactgcc tcgcccacca cctctggccc aaggcaacga cctcccacta
     2461 ggccagccaa ggaagctggg gagagaggac ctccagccac cttcctccat gccttcctgc
     2521 tcgggcactg tcttctcggc tccacagaac cgcagcccgc cagcgggcac cgcacccacc
     2581 ccagggacct cctctgcaca ggacttgccc tcttccccca tctatgcctc cgtctcccct
     2641 gccaacccca gctccaagag gccgctggac gcccatctgg ccctggtcaa ccaacacccc
     2701 atcggcccct tcccacgggt ccagtcaccc ccgcacctga aaagcccctc tgcagaggcc
     2761 acagtggctg ggggctgcct tctgccccca tcaccctctg gccacccaga ccagacaggc
     2821 acaaaccagc actttgtcat ggtggaggtc caccgccccg acagcgagcc agacgtcaat
     2881 gaagtgaggg cgctgcccca gacgcgcaca gcctctacgc tctcccagct ctcggacagc
     2941 gggcagactc taagcgagga cagtggtgtg gatgctggcg aggcagaggc cagcgcccca
     3001 ggccgaggaa ggcagtcggt gtccaccaag agcaggagta gcaaggagct gcctcggaac
     3061 gagaggccca cagatggggc caacaaaccg cctggacttc tggagcccac gtccactctg
     3121 gtccgtgtga agaaaagtgc ggccaccctg ggcatcgcca tcgagggtgg cgccaacacc
     3181 cgccagcccc tgcctaggat tgtcactatt cagagaggcg gctcagctca caactgtggg
     3241 cagctcaagg tgggccacgt gattctggaa gtgaatgggc tgacgcttcg gggcaaggag
     3301 caccgggagg ccgcccgcat tatcgccgag gccttcaaga ctaaggaccg tgactacatt
     3361 gactttctgg tcactgagtt caatgtgatg ctctagaggc caaggcctga gggcctccca
     3421 ccactgccca gcccctggtc ccagtccctt tccaccgttg gcttcatcaa gctccttgcg
     3481 gggttggggc tgcatggcca gggtggcagg aagacatccc ccctccatcc cagcccactg
     3541 gaccagaact gggagaggaa gagagcagga caaggcagac agaaggtcag gtcaggaact
     3601 ggtgctgtac tgggtacaca gtaggcgccc aggacaagtg ggttgcaaga caggaagaaa
     3661 ggaaaaggaa gggcagagtg ctggtttctc caggttgggt tgggggcact gctgtccccc
     3721 ctccagctag gacccagccc atccccagat gcctgagcct ttgtccaaag tgaggtcact
     3781 cgagaattca tggacacggc ccccagtcag ggggcatctt gcaagacctt tagtgccaca
     3841 aataagcatc gagcacctcc ccattcacac ccccattcct cctggctcct tatcccccat
     3901 ggtgtttatt atttatttcc ctccccatgc ccctggggac cccaaggccc cagcttccct
     3961 ctgcaccccc agcctatccc agaggccttg caggtgacca gcagtgtcat tgtatttata
     4021 tacagagctt atgactttaa tttttcaata aagaaatctg aacaaggtta
//
