LOCUS       NM_152311               1146 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens clarin 3 (CLRN3), mRNA.
ACCESSION   NM_152311
VERSION     NM_152311.5
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 1146)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   2  (bases 1 to 1146)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   3  (bases 1 to 1146)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Paulo,J.A., Cannon,J.R., Ting,L.,
            Baltier,K., Colby,G., Gebreab,F., Gygi,M.P., Parzen,H., Szpyt,J.,
            Tam,S., Zarraga,G., Pontano-Vaites,L., Swarup,S., White,A.E.,
            Schweppe,D.K., Rad,R., Erickson,B.K., Obar,R.A., Guruharsha,K.G.,
            Li,K., Artavanis-Tsakonas,S., Gygi,S.P. and Harper,J.W.
  TITLE     Architecture of the human interactome defines protein communities
            and disease networks
  JOURNAL   Nature 545 (7655), 505-509 (2017)
   PUBMED   28514442
REFERENCE   4  (bases 1 to 1146)
  AUTHORS   Chung,S.J., Armasu,S.M., Biernacka,J.M., Anderson,K.J.,
            Lesnick,T.G., Rider,D.N., Cunningham,J.M., Eric Ahlskog,J.,
            Frigerio,R. and Maraganore,D.M.
  TITLE     Genomic determinants of motor and cognitive outcomes in Parkinson's
            disease
  JOURNAL   Parkinsonism Relat Disord 18 (7), 881-886 (2012)
   PUBMED   22658654
  REMARK    GeneRIF: The SNP rs6482992 in the CLRN3 gene had the smallest p
            value in analyses of the cognitive outcome.
REFERENCE   5  (bases 1 to 1146)
  AUTHORS   Gonzales,P.A., Pisitkun,T., Hoffert,J.D., Tchapyjnikov,D.,
            Star,R.A., Kleta,R., Wang,N.S. and Knepper,M.A.
  TITLE     Large-scale proteomics and phosphoproteomics of urinary exosomes
  JOURNAL   J Am Soc Nephrol 20 (2), 363-379 (2009)
   PUBMED   19056867
REFERENCE   6  (bases 1 to 1146)
  AUTHORS   Grupe,A., Li,Y., Rowland,C., Nowotny,P., Hinrichs,A.L., Smemo,S.,
            Kauwe,J.S., Maxwell,T.J., Cherny,S., Doil,L., Tacey,K., van
            Luchene,R., Myers,A., Wavrant-De Vrieze,F., Kaleem,M.,
            Hollingworth,P., Jehu,L., Foy,C., Archer,N., Hamilton,G.,
            Holmans,P., Morris,C.M., Catanese,J., Sninsky,J., White,T.J.,
            Powell,J., Hardy,J., O'Donovan,M., Lovestone,S., Jones,L.,
            Morris,J.C., Thal,L., Owen,M., Williams,J. and Goate,A.
  TITLE     A scan of chromosome 10 identifies a novel locus showing strong
            association with late-onset Alzheimer disease
  JOURNAL   Am J Hum Genet 78 (1), 78-88 (2006)
   PUBMED   16385451
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   7  (bases 1 to 1146)
  AUTHORS   Oh,J.H., Yang,J.O., Hahn,Y., Kim,M.R., Byun,S.S., Jeon,Y.J.,
            Kim,J.M., Song,K.S., Noh,S.M., Kim,S., Yoo,H.S., Kim,Y.S. and
            Kim,N.S.
  TITLE     Transcriptome analysis of human gastric cancer
  JOURNAL   Mamm Genome 16 (12), 942-954 (2005)
   PUBMED   16341674
REFERENCE   8  (bases 1 to 1146)
  AUTHORS   Deloukas,P., Earthrowl,M.E., Grafham,D.V., Rubenfield,M.,
            French,L., Steward,C.A., Sims,S.K., Jones,M.C., Searle,S.,
            Scott,C., Howe,K., Hunt,S.E., Andrews,T.D., Gilbert,J.G.,
            Swarbreck,D., Ashurst,J.L., Taylor,A., Battles,J., Bird,C.P.,
            Ainscough,R., Almeida,J.P., Ashwell,R.I., Ambrose,K.D.,
            Babbage,A.K., Bagguley,C.L., Bailey,J., Banerjee,R., Bates,K.,
            Beasley,H., Bray-Allen,S., Brown,A.J., Brown,J.Y., Burford,D.C.,
            Burrill,W., Burton,J., Cahill,P., Camire,D., Carter,N.P.,
            Chapman,J.C., Clark,S.Y., Clarke,G., Clee,C.M., Clegg,S., Corby,N.,
            Coulson,A., Dhami,P., Dutta,I., Dunn,M., Faulkner,L., Frankish,A.,
            Frankland,J.A., Garner,P., Garnett,J., Gribble,S., Griffiths,C.,
            Grocock,R., Gustafson,E., Hammond,S., Harley,J.L., Hart,E.,
            Heath,P.D., Ho,T.P., Hopkins,B., Horne,J., Howden,P.J., Huckle,E.,
            Hynds,C., Johnson,C., Johnson,D., Kana,A., Kay,M., Kimberley,A.M.,
            Kershaw,J.K., Kokkinaki,M., Laird,G.K., Lawlor,S., Lee,H.M.,
            Leongamornlert,D.A., Laird,G., Lloyd,C., Lloyd,D.M., Loveland,J.,
            Lovell,J., McLaren,S., McLay,K.E., McMurray,A.,
            Mashreghi-Mohammadi,M., Matthews,L., Milne,S., Nickerson,T.,
            Nguyen,M., Overton-Larty,E., Palmer,S.A., Pearce,A.V., Peck,A.I.,
            Pelan,S., Phillimore,B., Porter,K., Rice,C.M., Rogosin,A.,
            Ross,M.T., Sarafidou,T., Sehra,H.K., Shownkeen,R., Skuce,C.D.,
            Smith,M., Standring,L., Sycamore,N., Tester,J., Thorpe,A.,
            Torcasso,W., Tracey,A., Tromans,A., Tsolas,J., Wall,M., Walsh,J.,
            Wang,H., Weinstock,K., West,A.P., Willey,D.L., Whitehead,S.L.,
            Wilming,L., Wray,P.W., Young,L., Chen,Y., Lovering,R.C.,
            Moschonas,N.K., Siebert,R., Fechtel,K., Bentley,D., Durbin,R.,
            Hubbard,T., Doucette-Stamm,L., Beck,S., Smith,D.R. and Rogers,J.
  TITLE     The DNA sequence and comparative analysis of human chromosome 10
  JOURNAL   Nature 429 (6990), 375-381 (2004)
   PUBMED   15164054
REFERENCE   9  (bases 1 to 1146)
  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 1146)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BC029478.1, BM830163.1, BX640823.1 and AI289873.1.
            
            On Nov 22, 2018 this sequence version replaced NM_152311.4.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC029478.1, BM789465.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA2153932,
                                           SAMEA2153946 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000368671.4/ ENSP00000357660.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-267               BC029478.1         7-273
            268-871             BM830163.1         27-630
            872-1096            BC029478.1         878-1102
            1097-1136           BX640823.1         1383-1422
            1137-1146           AI289873.1         9-18                c
FEATURES             Location/Qualifiers
     source          1..1146
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /map="10q26.2"
     gene            1..1146
                     /gene="CLRN3"
                     /gene_synonym="TMEM12; USH3AL1"
                     /note="clarin 3"
                     /db_xref="GeneID:119467"
                     /db_xref="HGNC:HGNC:20795"
                     /db_xref="MIM:620256"
     exon            1..386
                     /gene="CLRN3"
                     /gene_synonym="TMEM12; USH3AL1"
                     /inference="alignment:Splign:2.1.0"
     CDS             158..838
                     /gene="CLRN3"
                     /gene_synonym="TMEM12; USH3AL1"
                     /note="transmembrane protein 12; usher syndrome
                     type-3A-like protein 1"
                     /codon_start=1
                     /product="clarin-3"
                     /protein_id="NP_689524.1"
                     /db_xref="CCDS:CCDS7656.1"
                     /db_xref="GeneID:119467"
                     /db_xref="HGNC:HGNC:20795"
                     /db_xref="MIM:620256"
                     /translation="MPTTKKTLMFLSSFFTSLGSFIVICSILGTQAWITSTIAVRDSA
                     SNGSIFITYGLFRGESSEELSHGLAEPKKKFAVLEILNNSSQKTLHSVTILFLVLSLI
                     TSLLSSGFTFYNSISNPYQTFLGPTGVYTWNGLGASFVFVTMILFVANTQSNQLSEEL
                     FQMLYPATTSKGTTHSYGYSFWLILLVILLNIVTVTIIIFYQKARYQRKQEQRKPMEY
                     APRDGILF"
     exon            387..566
                     /gene="CLRN3"
                     /gene_synonym="TMEM12; USH3AL1"
                     /inference="alignment:Splign:2.1.0"
     exon            567..1146
                     /gene="CLRN3"
                     /gene_synonym="TMEM12; USH3AL1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1119..1124
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLRN3"
                     /gene_synonym="TMEM12; USH3AL1"
                     /note="hexamer: AATAAA"
     polyA_site      1146
                     /gene="CLRN3"
                     /gene_synonym="TMEM12; USH3AL1"
                     /note="major polyA site"
ORIGIN      
        1 cattagcata acccttcctc aggaagagtg agattttata tttgacaata aagtgttaga
       61 ctccatttct aaataccaga cttcaaaaga taaggttcaa aagtgttata agaagatatt
      121 cctttttttg tcctagagaa cttattttcc tgtgaaaatg cctaccacaa agaagacatt
      181 gatgttctta tcaagctttt tcaccagcct tgggtccttc attgtaattt gctctattct
      241 tgggacacaa gcatggatca ccagtacaat tgctgttaga gactctgctt caaatgggag
      301 cattttcatc acttacggac tttttcgtgg ggagagtagt gaagaattga gtcacggact
      361 tgcagaacca aagaaaaagt ttgcagtttt agagatactg aataattctt cccaaaaaac
      421 tctgcattcg gtgactatcc tgttcctggt cctgagtttg atcacgtcgc tgctgagctc
      481 tgggtttacc ttctacaaca gcatcagcaa cccttaccag acattcctgg ggccgacggg
      541 ggtgtacacc tggaacgggc tcggtgcatc cttcgttttt gtgaccatga tactgtttgt
      601 ggcgaacacg cagtccaacc aactctccga agagttgttc caaatgcttt acccggcaac
      661 caccagtaaa ggaacgaccc acagttacgg atactcgttc tggctcatac tgctcgtcat
      721 tcttctaaat atagtcactg taaccatcat cattttctac cagaaggcca gataccagcg
      781 gaagcaggag cagagaaagc caatggaata tgctccaagg gacggaattt tattctgaat
      841 tctctttcat ctcattttgg cgttgcatct attgtacatc agccctgagt agtaactggt
      901 tagcttctct ggacaattca gcatggtaac gtgactgtca tctgtgacag catttgtgtt
      961 tcatgacact gtgttcttca ttgatgctgt actcctgaaa atttttccca caaggttggg
     1021 gaaatgaatg ggaaatgtcg ctggtctgtg tggtattcaa agcagtagta tcatgatgag
     1081 cgtaacgacc cttctgacct ggtctcacga tctgaaataa taaaaggctg tgtcatgttt
     1141 cttttc
//
