LOCUS       NM_001163733            3073 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus USH1 protein network component harmonin (Ush1c),
            transcript variant b4, mRNA.
ACCESSION   NM_001163733
VERSION     NM_001163733.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3073)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 3073)
  AUTHORS   Wang,L., Kempton,J.B., Jiang,H., Jodelka,F.M., Brigande,A.M.,
            Dumont,R.A., Rigo,F., Lentz,J.J., Hastings,M.L. and Brigande,J.V.
  TITLE     Fetal antisense oligonucleotide therapy for congenital deafness and
            vestibular dysfunction
  JOURNAL   Nucleic Acids Res 48 (9), 5065-5080 (2020)
   PUBMED   32249312
REFERENCE   3  (bases 1 to 3073)
  AUTHORS   Collin,G.B., Gogna,N., Chang,B., Damkham,N., Pinkney,J., Hyde,L.F.,
            Stone,L., Naggert,J.K., Nishina,P.M. and Krebs,M.P.
  TITLE     Mouse Models of Inherited Retinal Degeneration with Photoreceptor
            Cell Loss
  JOURNAL   Cells 9 (4), 931 (2020)
   PUBMED   32290105
  REMARK    Review article
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3073)
  AUTHORS   Avan,P., Le Gal,S., Michel,V., Dupont,T., Hardelin,J.P., Petit,C.
            and Verpy,E.
  TITLE     Otogelin, otogelin-like, and stereocilin form links connecting
            outer hair cell stereocilia to each other and the tectorial
            membrane
  JOURNAL   Proc Natl Acad Sci U S A 116 (51), 25948-25957 (2019)
   PUBMED   31776257
REFERENCE   5  (bases 1 to 3073)
  AUTHORS   Dunbar,L.A., Patni,P., Aguilar,C., Mburu,P., Corns,L., Wells,H.R.,
            Delmaghani,S., Parker,A., Johnson,S., Williams,D., Esapa,C.T.,
            Simon,M.M., Chessum,L., Newton,S., Dorning,J., Jeyarajan,P.,
            Morse,S., Lelli,A., Codner,G.F., Peineau,T., Gopal,S.R.,
            Alagramam,K.N., Hertzano,R., Dulon,D., Wells,S., Williams,F.M.,
            Petit,C., Dawson,S.J., Brown,S.D., Marcotti,W., El-Amraoui,A. and
            Bowl,M.R.
  TITLE     Clarin-2 is essential for hearing by maintaining stereocilia
            integrity and function
  JOURNAL   EMBO Mol Med 11 (9), e10288 (2019)
   PUBMED   31448880
REFERENCE   6  (bases 1 to 3073)
  AUTHORS   Weil,D., El-Amraoui,A., Masmoudi,S., Mustapha,M., Kikkawa,Y.,
            Laine,S., Delmaghani,S., Adato,A., Nadifi,S., Zina,Z.B., Hamel,C.,
            Gal,A., Ayadi,H., Yonekawa,H. and Petit,C.
  TITLE     Usher syndrome type I G (USH1G) is caused by mutations in the gene
            encoding SANS, a protein that associates with the USH1C protein,
            harmonin
  JOURNAL   Hum Mol Genet 12 (5), 463-471 (2003)
   PUBMED   12588794
REFERENCE   7  (bases 1 to 3073)
  AUTHORS   Boeda,B., El-Amraoui,A., Bahloul,A., Goodyear,R., Daviet,L.,
            Blanchard,S., Perfettini,I., Fath,K.R., Shorte,S., Reiners,J.,
            Houdusse,A., Legrain,P., Wolfrum,U., Richardson,G. and Petit,C.
  TITLE     Myosin VIIa, harmonin and cadherin 23, three Usher I gene products
            that cooperate to shape the sensory hair cell bundle
  JOURNAL   EMBO J 21 (24), 6689-6699 (2002)
   PUBMED   12485990
  REMARK    GeneRIF: the shaping of the hair bundle relies on a functional unit
            composed of myosin VIIa, harmonin b and cadherin 23 that is
            essential to ensure the cohesion of the stereocilia
REFERENCE   8  (bases 1 to 3073)
  AUTHORS   Siemens,J., Kazmierczak,P., Reynolds,A., Sticker,M.,
            Littlewood-Evans,A. and Muller,U.
  TITLE     The Usher syndrome proteins cadherin 23 and harmonin form a complex
            by means of PDZ-domain interactions
  JOURNAL   Proc Natl Acad Sci U S A 99 (23), 14946-14951 (2002)
   PUBMED   12407180
  REMARK    GeneRIF: forms a complex with cadherin 23 by means of PDZ-domain
            interactions
REFERENCE   9  (bases 1 to 3073)
  AUTHORS   Bolz,H., von Brederlow,B., Ramirez,A., Bryda,E.C., Kutsche,K.,
            Nothwang,H.G., Seeliger,M., del C-Salcedo Cabrera,M., Vila,M.C.,
            Molina,O.P., Gal,A. and Kubisch,C.
  TITLE     Mutation of CDH23, encoding a new member of the cadherin gene
            family, causes Usher syndrome type 1D
  JOURNAL   Nat Genet 27 (1), 108-112 (2001)
   PUBMED   11138009
REFERENCE   10 (bases 1 to 3073)
  AUTHORS   Verpy,E., Leibovici,M., Zwaenepoel,I., Liu,X.Z., Gal,A., Salem,N.,
            Mansour,A., Blanchard,S., Kobayashi,I., Keats,B.J., Slim,R. and
            Petit,C.
  TITLE     A defect in harmonin, a PDZ domain-containing protein expressed in
            the inner ear sensory hair cells, underlies Usher syndrome type 1C
  JOURNAL   Nat Genet 26 (1), 51-55 (2000)
   PUBMED   10973247
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AF228925.1, BP775197.1, AY246556.1, AC120135.7 and BY708209.1.
            
            Transcript Variant: This variant (b4) has an additional segment in
            the 3' coding region, resulting in frame-shift, as compared to
            variant b3. The resulting isoform (b4) is shorter and has a
            different C-terminus, as compared to isoform b3.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: AY246556.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849376 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-811               AF228925.1         1-811
            812-1236            BP775197.1         111-535             c
            1237-1273           AY246556.1         1211-1247
            1274-1381           AF228925.1         1274-1381
            1382-1439           AC120135.7         30852-30909
            1440-1556           AC120135.7         32088-32204
            1557-2039           AC120135.7         32736-33218
            2040-2159           AC120135.7         36755-36874
            2160-2681           AF228925.1         2160-2681
            2682-2793           AY246556.1         2656-2767
            2794-3067           AF228925.1         2786-3059
            3068-3073           BY708209.1         705-710
FEATURES             Location/Qualifiers
     source          1..3073
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="7"
                     /map="7 29.66 cM"
     gene            1..3073
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /note="USH1 protein network component harmonin"
                     /db_xref="GeneID:72088"
                     /db_xref="MGI:MGI:1919338"
     exon            1..62
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     CDS             27..2702
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /note="isoform b4 is encoded by transcript variant b4; PDZ
                     domain-containing protein; usher syndrome type-1C protein
                     homolog; Usher syndrome 1C homolog"
                     /codon_start=1
                     /product="harmonin isoform b4"
                     /protein_id="NP_001157205.1"
                     /db_xref="CCDS:CCDS52250.1"
                     /db_xref="GeneID:72088"
                     /db_xref="MGI:MGI:1919338"
                     /translation="MDRKVAREFRHKVDFLIENDAEKDYLYDVLRMYHQTMDVAVLVG
                     DLKLVINEPNRLPLFDAIRPLIPLKHQVEYDQLTPRRSRKLKEVRLDRLHPEGLGLSV
                     RGGLEFGCGLFISHLIKGGQADSVGLQVGDEIVRINGYSISSCTHEEVINLIRTKKTV
                     SIKVRHIGLIPVKSSPEESLKWQYVDQFVSESGGVRGGLGSPGNRTTKEKKVFISLVG
                     SRGLGCSISSGPIQKPGIFVSHVKPGSLSAEVGLETGDQIVEVNGIDFTNLDHKEAVN
                     VLKSSRSLTISIVAGAGRELFMTDRERLEEARQRELQRQELLMQKRLAMESNKILQEQ
                     QEMERQRRKEIAQKAAEENERYRKEMEQISEEEEKFKKQWKEDWGSKEQLILPKTITA
                     EVHPVPLRKPKSFGWFYRYDGKFPTIRKKAKEKKKAKYDSLQDLRKNKKELEFEQKLY
                     KEKEEMLEKEKQLKINRLAQEVSETEREDLEESEKTQYWVERLCQTRLEQISSAENEI
                     PEMTTGPPPPPPSVSPLAPPLRRFAGGIHLHTTDLDDIPLDMFYYPPKTPSALPVMPH
                     PPSVNPPSKVPAPPVLPSSGHVSSSSSPWVQRTPPPIPIPPPPSIPTQDLTPTRPLPS
                     ALEEALGNHPFRTGDPGHPADDWEANTHSGKPSSSPTTERSFPPAPKTFCPSPQPPRG
                     PGVSTISKPVMVHQEHNFVYRPAVKSEVLPQEMLKRMVVYQTAFRQDFRKYEEGFDPY
                     SMFSPEQIAGKDVRLLRIKKEGSLDLALEGGVDSPVGKVVVSAVYEGGAAERHGGVVK
                     GDEIMAINGKIVTDYTLAEAEAALQKAWNQGGDWIDLVVAVCPPKEYDDELSSLPSSA
                     AESPQLARKQLEAYEPVCRHGFFLQLEPTVTRTFF"
     exon            63..130
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            131..274
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            275..413
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            414..522
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            523..547
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            548..605
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            606..700
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            701..785
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            786..845
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            846..902
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            903..1045
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            1046..1111
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            1112..1236
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            1237..1286
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            1287..1439
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            1440..1556
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            1557..2039
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            2040..2159
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            2160..2210
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            2211..2252
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            2253..2306
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            2307..2406
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            2407..2516
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            2517..2572
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            2573..2689
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     exon            2690..3073
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3049..3054
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /note="hexamer: AATAAA"
     polyA_site      3070
                     /gene="Ush1c"
                     /gene_synonym="2010016F01Rik; harmonin"
                     /note="major polyA site"
ORIGIN      
        1 gcaaagcaac tggatcaggc tcagtcatgg accggaaggt ggcccgagaa ttccgacaca
       61 aggtggattt tctcattgaa aatgacgcag agaaggacta tctttatgat gtgctgcgga
      121 tgtatcacca gaccatggat gtggctgtgc tcgtgggaga cctgaagctg gtcatcaatg
      181 aacccaaccg cctgccgctg tttgatgcca ttcgacccct gatcccactg aagcaccagg
      241 tggagtatga ccagctgaca ccccgacgct ccaggaaact gaaggaggta cgcttggacc
      301 gtctgcaccc agaaggtctc ggcctcagcg tgcgtggagg cctggaattt ggctgtggac
      361 tctttatctc ccacctcatc aaaggtggcc aggcagacag cgttgggctt caggtagggg
      421 atgaaattgt ccggatcaac ggctattcca tctcttcctg tacccatgag gaagtcatca
      481 acctgatccg caccaagaag accgtgtcca tcaaagtgag acacatcgga ctgatccctg
      541 tgaagagctc tcctgaggag tccctcaaat ggcagtatgt ggatcagttc gtgtcggaat
      601 ctgggggtgt gcgaggtggc ttgggctcac ctggcaatcg gacaaccaag gagaagaagg
      661 tgtttatcag tctagtgggc tctcggggcc tgggctgcag catctccagt ggccccatcc
      721 agaagcctgg catcttcgtc agccacgtga agcctggctc cctgtctgca gaggtggggt
      781 tagagacagg agaccagatt gtggaagtca acggcataga cttcaccaac ctggaccaca
      841 aggaggctgt gaatgtcctg aagagcagcc gcagcctgac catctccatc gttgctggag
      901 ccggccggga gctgttcatg acggaccggg aacggctgga ggaggcacgg cagcgtgagc
      961 tgcaacggca ggaactcctc atgcagaagc ggctggccat ggagtccaac aagatcctcc
     1021 aggagcagca ggagatggag cgccagagga gaaaggagat cgcccagaag gctgccgagg
     1081 agaatgagag ataccggaag gagatggaac agatctcgga ggaggaagag aagtttaaga
     1141 agcagtggaa agaagactgg ggttcaaagg agcagctcat tctgcctaag accatcaccg
     1201 cagaggtgca cccggtgccc cttcgcaagc ccaagtcttt tgggtggttt taccgttacg
     1261 atggcaaatt cccaaccatc cggaagaaag caaaagagaa gaagaaagcc aagtacgata
     1321 gcctgcagga cctgaggaag aacaagaagg aactcgagtt tgaacaaaag ctctacaaag
     1381 agaaggaaga gatgctggag aaggagaagc agctcaagat caaccggctg gcccaggagg
     1441 tgtctgagac tgagcgggaa gaccttgagg aatcggaaaa gactcagtat tgggtggaga
     1501 ggctctgtca gacgcgcctc gagcagattt cctctgcaga gaatgagatt cctgagatga
     1561 ccacagggcc cccacctccc ccaccttctg tgtctcctct ggccccaccc ttgagacgat
     1621 tcgctggtgg gatccacctc cacaccactg acctggatga catccccttg gacatgttct
     1681 actacccccc caagactccc tcagcactgc ccgtgatgcc ccaccctcca tctgtcaacc
     1741 caccttccaa ggtccccgcg ccccctgtgc ttccctcatc aggtcacgtg agcagctcat
     1801 cctcaccatg ggtgcaacgc actcctcccc caatccccat tcctccgcct ccatccattc
     1861 ccacccaaga cctcactcct acccgcccat tgccctcagc actggaagag gccctgggca
     1921 accacccctt ccgcactggg gacccaggcc atccagcaga tgactgggag gcaaacaccc
     1981 acagtgggaa gccctccagc tcccccacca ctgagcggag cttcccacct gccccaaaga
     2041 cattctgccc aagcccacag cctccacgag gccctggcgt gtccaccatc tccaaacccg
     2101 tcatggtcca ccaggaacac aacttcgtct acaggcctgc tgtgaagtcc gaggttctgc
     2161 cgcaggagat gctgaagagg atggtggtat atcagacagc attcagacaa gattttcgaa
     2221 aatacgaaga aggctttgat ccctactcca tgttctcgcc agagcagatc gcagggaagg
     2281 acgtccggct tctgcgaatc aagaaggagg ggtctttaga cttggccctg gagggaggcg
     2341 tggactcccc cgtggggaag gtggtcgtct ctgctgttta tgaaggggga gctgcggaga
     2401 ggcatggtgg cgttgtgaaa ggggatgaga tcatggccat caatggcaag attgtgacgg
     2461 actacaccct ggctgaggcc gaggctgccc tacagaaggc ctggaatcag ggcggggact
     2521 ggatagacct tgtggttgct gtctgtcccc ctaaggagta tgatgacgag ctctcttctc
     2581 ttccctcctc tgcagccgaa agcccccagc tggcccgaaa gcagcttgaa gcctatgagc
     2641 ccgtgtgtag acacgggttt ttcctgcagc tggagcccac ggtgactaga accttctttt
     2701 aaagtccaga gagagaaacc agacagaccc atcctggagg ccggcgagct ccgcacccag
     2761 cccctgagct caacctgaga gacaccagat gtagaaagtc tccctggaag ctgacccaca
     2821 aagccctgtg acctggcccc tcctctgaag gccagcaaga ggtggagcaa ggatcaactg
     2881 ctgttctgga gtagggttcc atctcccatt tcttccagct ctgccaagtt ggccctccct
     2941 gctctcgagt gttcctttct tgagacctca gggtgcccag gtcctgcatc tctctattgc
     3001 cccacttcct gctataatcc ctgatgaaaa cctgacggtg aactcactaa taaacaagac
     3061 tgactccttc ttc
//
