LOCUS       NM_153299               1074 bp    mRNA    linear   ROD 30-MAR-2024
DEFINITION  Rattus norvegicus clarin 1 (Clrn1), mRNA.
ACCESSION   NM_153299 XM_346620
VERSION     NM_153299.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 1074)
  AUTHORS   Daiger,S.P., Sullivan,L.S. and Bowne,S.J.
  TITLE     Genes and mutations causing retinitis pigmentosa
  JOURNAL   Clin Genet 84 (2), 132-141 (2013)
   PUBMED   23701314
  REMARK    Review article
REFERENCE   2  (bases 1 to 1074)
  AUTHORS   Zallocchi,M., Meehan,D.T., Delimont,D., Askew,C., Garige,S.,
            Gratton,M.A., Rothermund-Franklin,C.A. and Cosgrove,D.
  TITLE     Localization and expression of clarin-1, the Clrn1 gene product, in
            auditory hair cells and photoreceptors
  JOURNAL   Hear Res 255 (1-2), 109-120 (2009)
   PUBMED   19539019
REFERENCE   3  (bases 1 to 1074)
  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
REFERENCE   4  (bases 1 to 1074)
  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
REFERENCE   5  (bases 1 to 1074)
  AUTHORS   Ebermann,I., Wilke,R., Lauhoff,T., Lubben,D., Zrenner,E. and
            Bolz,H.J.
  TITLE     Two truncating USH3A mutations, including one novel, in a German
            family with Usher syndrome
  JOURNAL   Mol Vis 13, 1539-1547 (2007)
   PUBMED   17893653
  REMARK    GeneRIF: First description of German family with Usher
            syndrome(USH) due to USH3A mutations, including one novel. Also in
            Central European population, USH3A mutations should be considered
            in cases of USH.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1074)
  AUTHORS   Plantinga,R.F., Kleemola,L., Huygen,P.L., Joensuu,T., Sankila,E.M.,
            Pennings,R.J. and Cremers,C.W.
  TITLE     Serial audiometry and speech recognition findings in Finnish Usher
            syndrome type III patients
  JOURNAL   Audiol Neurootol 10 (2), 79-89 (2005)
   PUBMED   15650299
REFERENCE   7  (bases 1 to 1074)
  AUTHORS   Aller,E., Jaijo,T., Oltra,S., Alio,J., Galan,F., Najera,C.,
            Beneyto,M. and Millan,J.M.
  TITLE     Mutation screening of USH3 gene (clarin-1) in Spanish patients with
            Usher syndrome: low prevalence and phenotypic variability
  JOURNAL   Clin Genet 66 (6), 525-529 (2004)
   PUBMED   15521980
REFERENCE   8  (bases 1 to 1074)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000002.1.
            
            On May 11, 2012 this sequence version replaced NM_153299.1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF482698.1, SRR26360190.3079853.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN06621351, SAMN14984043
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-297               JAXUCZ010000002.1  145280559-145280855 c
            298-477             JAXUCZ010000002.1  145253060-145253239 c
            478-1074            JAXUCZ010000002.1  145233941-145234537 c
FEATURES             Location/Qualifiers
     source          1..1074
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="2"
                     /map="2q26"
     gene            1..1074
                     /gene="Clrn1"
                     /gene_synonym="Ush3; Ush3a"
                     /note="clarin 1"
                     /db_xref="GeneID:261738"
                     /db_xref="RGD:628779"
     exon            1..297
                     /gene="Clrn1"
                     /gene_synonym="Ush3; Ush3a"
                     /inference="alignment:Splign:2.1.0"
     CDS             45..743
                     /gene="Clrn1"
                     /gene_synonym="Ush3; Ush3a"
                     /note="usher syndrome type-3 protein homolog; Usher
                     syndrome 3A homolog; Usher syndrome type III A"
                     /codon_start=1
                     /product="clarin-1"
                     /protein_id="NP_695211.2"
                     /db_xref="GeneID:261738"
                     /db_xref="RGD:628779"
                     /translation="MPSQQKKIIFCMAGVLSFLCALGVVTAVGTPLWVKATILCKTGA
                     LLVNASGKELDKFMGEMQYGLFHGEGVRQCGLGARPFRFSFFPDLVQAIPVSIHVNII
                     LFSMILVVLTMVGTAFFMYNAFGKPFETLHGPLGLYLVSFISGSCGCLVMILFASEVK
                     IHRLSEKIANFKEGTYAYKTQNENYTTSFWVVFICFFVHFLNGLLIRLAGFQFPFTKS
                     KETETTNVASDLMY"
     exon            298..477
                     /gene="Clrn1"
                     /gene_synonym="Ush3; Ush3a"
                     /inference="alignment:Splign:2.1.0"
     exon            478..1074
                     /gene="Clrn1"
                     /gene_synonym="Ush3; Ush3a"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 ggtctttgtt ttaaactttg ccttcaccga agccttttct catcatgcca agccagcaga
       61 agaagatcat cttttgcatg gctggcgtat tgagctttct ctgtgctctc ggagtggtga
      121 ccgcagtggg aaccccactg tgggtgaaag ccactatcct ctgcaaaaca ggggctctgc
      181 ttgtcaatgc gtcagggaag gagctggaca agttcatggg cgagatgcag tatggtcttt
      241 tccacggaga aggcgtaagg caatgcgggt taggagcaag gcctttccgg ttctcattct
      301 tcccagattt ggttcaagcc atccctgtaa gcatccacgt caatattatt ctcttctcca
      361 tgattcttgt cgtcttaacc atggtgggga cagccttctt catgtacaat gcttttggca
      421 agccctttga aactctgcat ggaccactgg ggctctatct ggtcagcttc atttcaggat
      481 cctgtggctg tcttgtcatg atactgtttg cctctgaagt gaaaatccac cgcctttcag
      541 agaaaattgc aaattttaaa gaagggacct atgcctacaa aacgcaaaac gaaaactata
      601 ccacctcatt ctgggttgtt ttcatttgct tttttgttca ttttttgaat gggctcctga
      661 tacgacttgc tggatttcag ttccctttca caaaatctaa agaaacagag accactaacg
      721 tagcttcaga tttaatgtac tgaaaagcaa atatcgccgt aatttctcaa taaggatatg
      781 gacttgcgtt ggccacattt agtctgtgcc tttagacttc ttaagcacca agccctcctt
      841 ctgttacatt tacagggcgt gtagtaagga ttcaggctga aaaataacgg gagcagaagg
      901 atggtttcag aagggtgctc tgtctagtgg gtaactgcca ccataggcag ttggctagat
      961 ggaccgatgg atggatggtc actccatgtc cttactgaac gataaagtac atgttctact
     1021 aaggagaact caacaagcac gtggcatata gtttaataaa atagatgtta tttc
//
