LOCUS       NM_153385               3029 bp    mRNA    linear   ROD 09-FEB-2025
DEFINITION  Mus musculus clarin 1 (Clrn1), transcript variant 2, mRNA.
ACCESSION   NM_153385
VERSION     NM_153385.3
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 3029)
  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 3029)
  AUTHORS   Vona,B., Mazaheri,N., Lin,S.J., Dunbar,L.A., Maroofian,R.,
            Azaiez,H., Booth,K.T., Vitry,S., Rad,A., Ruschendorf,F.,
            Varshney,P., Fowler,B., Beetz,C., Alagramam,K.N., Murphy,D.,
            Shariati,G., Sedaghat,A., Houlden,H., Petree,C., VijayKumar,S.,
            Smith,R.J.H., Haaf,T., El-Amraoui,A., Bowl,M.R., Varshney,G.K. and
            Galehdari,H.
  TITLE     A biallelic variant in CLRN2 causes non-syndromic hearing loss in
            humans
  JOURNAL   Hum Genet 140 (6), 915-931 (2021)
   PUBMED   33496845
REFERENCE   3  (bases 1 to 3029)
  AUTHORS   Dulon,D., Papal,S., Patni,P., Cortese,M., Vincent,P.F.,
            Tertrais,M., Emptoz,A., Tlili,A., Bouleau,Y., Michel,V.,
            Delmaghani,S., Aghaie,A., Pepermans,E., Alegria-Prevot,O., Akil,O.,
            Lustig,L., Avan,P., Safieddine,S., Petit,C. and El-Amraoui,A.
  TITLE     Clarin-1 gene transfer rescues auditory synaptopathy in model of
            Usher syndrome
  JOURNAL   J Clin Invest 128 (8), 3382-3401 (2018)
   PUBMED   29985171
  REMARK    GeneRIF: results identify clarin-1 as a key organizer of IHC ribbon
            synapses, and suggest new treatment possibilities for USH3A
            patients.
REFERENCE   4  (bases 1 to 3029)
  AUTHORS   Geng,R., Omar,A., Gopal,S.R., Chen,D.H., Stepanyan,R., Basch,M.L.,
            Dinculescu,A., Furness,D.N., Saperstein,D., Hauswirth,W.,
            Lustig,L.R. and Alagramam,K.N.
  TITLE     Modeling and Preventing Progressive Hearing Loss in Usher Syndrome
            III
  JOURNAL   Sci Rep 7 (1), 13480 (2017)
   PUBMED   29044151
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3029)
  AUTHORS   Dickinson,M.E., Flenniken,A.M., Ji,X., Teboul,L., Wong,M.D.,
            White,J.K., Meehan,T.F., Weninger,W.J., Westerberg,H., Adissu,H.,
            Baker,C.N., Bower,L., Brown,J.M., Caddle,L.B., Chiani,F., Clary,D.,
            Cleak,J., Daly,M.J., Denegre,J.M., Doe,B., Dolan,M.E., Edie,S.M.,
            Fuchs,H., Gailus-Durner,V., Galli,A., Gambadoro,A., Gallegos,J.,
            Guo,S., Horner,N.R., Hsu,C.W., Johnson,S.J., Kalaga,S., Keith,L.C.,
            Lanoue,L., Lawson,T.N., Lek,M., Mark,M., Marschall,S., Mason,J.,
            McElwee,M.L., Newbigging,S., Nutter,L.M., Peterson,K.A.,
            Ramirez-Solis,R., Rowland,D.J., Ryder,E., Samocha,K.E.,
            Seavitt,J.R., Selloum,M., Szoke-Kovacs,Z., Tamura,M., Trainor,A.G.,
            Tudose,I., Wakana,S., Warren,J., Wendling,O., West,D.B., Wong,L.,
            Yoshiki,A., MacArthur,D.G., Tocchini-Valentini,G.P., Gao,X.,
            Flicek,P., Bradley,A., Skarnes,W.C., Justice,M.J., Parkinson,H.E.,
            Moore,M., Wells,S., Braun,R.E., Svenson,K.L., de Angelis,M.H.,
            Herault,Y., Mohun,T., Mallon,A.M., Henkelman,R.M., Brown,S.D.,
            Adams,D.J., Lloyd,K.C., McKerlie,C., Beaudet,A.L., Bucan,M. and
            Murray,S.A.
  CONSRTM   International Mouse Phenotyping Consortium; Jackson Laboratory;
            Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris
            (ICS); Charles River Laboratories; MRC Harwell; Toronto Centre for
            Phenogenomics; Wellcome Trust Sanger Institute; RIKEN BioResource
            Center
  TITLE     High-throughput discovery of novel developmental phenotypes
  JOURNAL   Nature 537 (7621), 508-514 (2016)
   PUBMED   27626380
  REMARK    Erratum:[Nature. 2017 Nov 16;551(7680):398. doi:
            10.1038/nature24643.. PMID: 29144450]
REFERENCE   6  (bases 1 to 3029)
  AUTHORS   Geng,R., Geller,S.F., Hayashi,T., Ray,C.A., Reh,T.A.,
            Bermingham-McDonogh,O., Jones,S.M., Wright,C.G., Melki,S.,
            Imanishi,Y., Palczewski,K., Alagramam,K.N. and Flannery,J.G.
  TITLE     Usher syndrome IIIA gene clarin-1 is essential for hair cell
            function and associated neural activation
  JOURNAL   Hum Mol Genet 18 (15), 2748-2760 (2009)
   PUBMED   19414487
  REMARK    GeneRIF: Clrn1 is necessary for hair cell function and associated
            neural activation.
REFERENCE   7  (bases 1 to 3029)
  AUTHORS   Tian,G., Zhou,Y., Hajkova,D., Miyagi,M., Dinculescu,A.,
            Hauswirth,W.W., Palczewski,K., Geng,R., Alagramam,K.N.,
            Isosomppi,J., Sankila,E.M., Flannery,J.G. and Imanishi,Y.
  TITLE     Clarin-1, encoded by the Usher Syndrome III causative gene, forms a
            membranous microdomain: possible role of clarin-1 in organizing the
            actin cytoskeleton
  JOURNAL   J Biol Chem 284 (28), 18980-18993 (2009)
   PUBMED   19423712
  REMARK    GeneRIF: clarin-1 has a role in the regulation and homeostasis of
            actin filaments
REFERENCE   8  (bases 1 to 3029)
  AUTHORS   Aarnisalo,A.A., Pietola,L., Joensuu,J., Isosomppi,J., Aarnisalo,P.,
            Dinculescu,A., Lewin,A.S., Flannery,J., Hauswirth,W.W.,
            Sankila,E.M. and Jero,J.
  TITLE     Anti-clarin-1 AAV-delivered ribozyme induced apoptosis in the mouse
            cochlea
  JOURNAL   Hear Res 230 (1-2), 9-16 (2007)
   PUBMED   17493778
  REMARK    GeneRIF: Clarin-1 ribozyme induced apoptosis of cochlear hair cells
            and cells of stria vascularis. Suggest role for apoptosis in
            progressin of Usher syndrome type 3.
REFERENCE   9  (bases 1 to 3029)
  AUTHORS   Fields,R.R., Zhou,G., Huang,D., Davis,J.R., Moller,C.,
            Jacobson,S.G., Kimberling,W.J. and Sumegi,J.
  TITLE     Usher syndrome type III: revised genomic structure of the USH3 gene
            and identification of novel mutations
  JOURNAL   Am J Hum Genet 71 (3), 607-617 (2002)
   PUBMED   12145752
REFERENCE   10 (bases 1 to 3029)
  AUTHORS   Adato,A., Vreugde,S., Joensuu,T., Avidan,N., Hamalainen,R.,
            Belenkiy,O., Olender,T., Bonne-Tamir,B., Ben-Asher,E., Espinos,C.,
            Millan,J.M., Lehesjoki,A.E., Flannery,J.G., Avraham,K.B.,
            Pietrokovski,S., Sankila,E.M., Beckmann,J.S. and Lancet,D.
  TITLE     USH3A transcripts encode clarin-1, a four-transmembrane-domain
            protein with a possible role in sensory synapses
  JOURNAL   Eur J Hum Genet 10 (6), 339-350 (2002)
   PUBMED   12080385
  REMARK    GeneRIF: a role for clarin-1 in hair cell and photoreceptor cell
            synapses, as well as a common pathophysiological pathway for
            different Usher syndromes
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AF495719.1, AC112998.15 and AK037267.1.
            
            On Nov 14, 2013 this sequence version replaced NM_153385.2.
            
            Transcript Variant: This variant (2) lacks an in-frame exon in the
            5' coding region compared to isoform 1. The encoded protein
            (isoform 2) is shorter than isoform 1.
            
            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 :: AF495719.1, BC145202.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849383, SAMN01164136
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-27                AF495719.1         1-27
            28-28               AC112998.15        114418-114418
            29-1043             AF495719.1         29-1043
            1044-1874           AK037267.1         762-1592
            1875-2182           AC112998.15        154421-154728
            2183-3025           AK037267.1         1893-2735
            3026-3029           AC112998.15        155572-155575
FEATURES             Location/Qualifiers
     source          1..3029
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="3"
                     /map="3 28.78 cM"
     gene            1..3029
                     /gene="Clrn1"
                     /gene_synonym="A130002D11Rik; clarin-1; USH3; Ush3a"
                     /note="clarin 1"
                     /db_xref="GeneID:229320"
                     /db_xref="MGI:MGI:2388124"
     exon            1..425
                     /gene="Clrn1"
                     /gene_synonym="A130002D11Rik; clarin-1; USH3; Ush3a"
                     /inference="alignment:Splign:2.1.0"
     CDS             173..871
                     /gene="Clrn1"
                     /gene_synonym="A130002D11Rik; clarin-1; USH3; Ush3a"
                     /note="isoform 2 is encoded by transcript variant 2; usher
                     syndrome type-3 protein homolog; Usher syndrome 3A
                     homolog"
                     /codon_start=1
                     /product="clarin-1 isoform 2"
                     /protein_id="NP_700434.1"
                     /db_xref="CCDS:CCDS38438.1"
                     /db_xref="GeneID:229320"
                     /db_xref="MGI:MGI:2388124"
                     /translation="MPSQQKKIIFCMAGVLSFLCALGVVTAVGTPLWVKATILCKTGA
                     LLVNASGKELDKFMGEMQYGLFHGEGVRQCGLGARPFRFSFFPDLVQAIPVSIHINII
                     LFSMILVVLTMVGTAFFMYNAFGKPFETLHGPLGLYLVSFISGSCGCLVMILFASEVK
                     VHRLSEKIANFKEGTYAYRTQNENYTTSFWVVFICFFVHFLNGLLIRLAGFQFPFTKS
                     KETETTNVASDLMY"
     exon            426..605
                     /gene="Clrn1"
                     /gene_synonym="A130002D11Rik; clarin-1; USH3; Ush3a"
                     /inference="alignment:Splign:2.1.0"
     exon            606..3029
                     /gene="Clrn1"
                     /gene_synonym="A130002D11Rik; clarin-1; USH3; Ush3a"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1630..1635
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Clrn1"
                     /gene_synonym="A130002D11Rik; clarin-1; USH3; Ush3a"
                     /note="hexamer: AATAAA"
     polyA_site      1649
                     /gene="Clrn1"
                     /gene_synonym="A130002D11Rik; clarin-1; USH3; Ush3a"
                     /note="major polyA site"
     regulatory      1825..1830
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Clrn1"
                     /gene_synonym="A130002D11Rik; clarin-1; USH3; Ush3a"
                     /note="hexamer: AAGAAA"
     polyA_site      1846
                     /gene="Clrn1"
                     /gene_synonym="A130002D11Rik; clarin-1; USH3; Ush3a"
                     /note="major polyA site"
ORIGIN      
        1 agtgggtgag gaaggatgct tcacggactg gcgttctgcc tggtggaacc actgtaagga
       61 agggcagtgt ttttcagctg ctgtgataaa tgcagccgac ggggcagtcg ctacttgatg
      121 ctcacaaagg tctttgtttt caagtttgtc tttaccgaag ccttttctcg tcatgccaag
      181 ccagcagaag aagatcatct tttgcatggc tggcgtactg agctttctct gtgctcttgg
      241 agtggtgaca gcagtgggca ccccactgtg ggttaaagcc actatcctct gcaaaacagg
      301 ggctctgctt gtcaacgcgt cagggaagga gctggacaag ttcatgggcg agatgcagta
      361 tggccttttc cacggagaag gcgtaaggca atgtgggtta ggagcaaggc ctttccggtt
      421 ctcattcttc ccagatttgg tccaagccat ccccgtaagc atccacatca atattattct
      481 cttctccatg attcttgtcg tcttaaccat ggtggggaca gccttcttca tgtacaatgc
      541 ttttggcaag ccctttgaaa ctcttcatgg accactgggg ctctatctgg tcagcttcat
      601 ttcaggctcc tgtggctgtc ttgtcatgat attgtttgcc tctgaagtga aagtccaccg
      661 cctttcagag aaaattgcaa attttaaaga agggacctat gcctacagaa cacaaaacga
      721 aaactatacc acctcattct gggttgtttt catttgcttt tttgttcatt ttttgaatgg
      781 gctcctgata cgacttgctg gatttcagtt ccctttcaca aaatctaaag aaacagagac
      841 cactaatgta gcttcagatt taatgtactg aaaagcaaat atcttcataa tttctcaata
      901 aggatatgga cttcctttgg ccacttttaa tatgggtgat ttcatctgtg catttagact
      961 tcttaagtac caagccctcc ttatgttatg tttacagagc atgtagtaag gattcaggct
     1021 ggaaaataac agaagcagga ggatggtttc actgggaaga cgttcttcct gatgggtaat
     1081 ggcctgcata gttagtccaa agcagttggc tagatggacg gatggttact ccatgtcctt
     1141 actgaccgat aagatgcacg ttctcccaag cagaactcaa caggcacatg acatacagtt
     1201 ttgtaagact ccagggagcc ttaacttacc agggaccccc tgagtggacc acgtggagct
     1261 gggatcaatg caaaaagcaa gaggaattta ttgttccagt gcactggggt tgtcccagat
     1321 caacagtgct ggcagcgacc cccagcacct tttcagtgag tttttatacg gtttctaggg
     1381 gcagaataga gcatcagcaa ctaggcacaa tatgattgat ggaacagtgc accctttaaa
     1441 ctgattggtc tttaaggaat gaggtgacaa ggacttccgt tgtctgatgg tggaggtcct
     1501 gtggagtgtg tccccacaca caggtcagtt cctgtccttt agtctgagaa atgttaatta
     1561 gcctctccct tccagagggg gacgtattcc atgaccttcc caaagttctt gagctgacct
     1621 attcagttaa ataaaacaga cgttatttct aattgtccac atagtcacag atcccagaaa
     1681 acagaggtga aattggtgtc ttaaactgac agtgcaccga atcattgcaa accttcaagt
     1741 tctttgtaag tttgcttaga gcatgatgtc attatgtctg gtggtcaaaa ccagaaaagt
     1801 ttataagcaa acaagcaagc tagcaagaaa ggaagaaaaa ggaaaggaag aaaggaagaa
     1861 aggaagaaag gaagaaagga aggaaggaag gaaggaagga aggaaggaag gaaggaagac
     1921 ggaaagaagc agatcaatgg tttctttcct tatgcatctg agttcataac aatggtactt
     1981 acagtggaca gaatccctac tagacaagtt ggtgagagaa acccactggg aactgtttcc
     2041 agcttggtgt ctttggcact aatgagctcc aaatcatgaa aattcagaat tgaggtggga
     2101 ttgcagtgtg tcatgggaga catgaagcat ggcccaagtc aaatctttct ccttgaatta
     2161 ttcaccaaat gaatctgctg gagaccagag gccacaagtg agcctgaaac tgacactcct
     2221 taactctcaa tgtgttaccc tcaggaaaga acaaaggaca aagacattat ggtgccctgg
     2281 ccacaaacac cagagatcat agagtttgga aatgctccag aaaaccaatc tggaactagg
     2341 aagatggctc agttgataaa gggctgcctc aaaagcttga gagcctgagt tcagattccc
     2401 cagcacccat gagaaacgca tgggtttcat acatgtctgt gatcccagca ctgggaaggc
     2461 agagctaggc aagtcttaaa gctcaccagc aagccaagtc aaacctaatc agtgcactcc
     2521 aaggtcagtg agagaccctg actcaaaaca aaaaaacgga ggtgatggag aaaggcacca
     2581 tcagcctcca tgaaccccct catgaacaca cacattttca tttgggaaca atttacatac
     2641 aaggaaggag agactgcaca cctgaaatat aaccagctct ggtgatggcc tgctggttac
     2701 tctcagacat cagaacatac ttgcttttct caggatggag tcctttcacc ttaattcagg
     2761 acactggaag tttctagaag cccaccagct agtctgtcca ggagctggtg catgctttgg
     2821 tgatgggcta gtagtgccct gacctggagg tcagaccctg aaattctcaa gcacaaaagg
     2881 ctgtgttagg agggaaaggg agggagttga aggctggagg atgaatcccc ctcctctggc
     2941 ctccatctac ctctttcctc tctgctcaga ggtctgaaaa ctttctgtaa taccaagcct
     3001 tttttaaaaa aaaattctgt agaaaacaa
//
