LOCUS       NM_001191794            1958 bp    mRNA    linear   ROD 31-MAR-2024
DEFINITION  Rattus norvegicus CLN6, transmembrane ER protein (Cln6), mRNA.
ACCESSION   NM_001191794 XM_236325
VERSION     NM_001191794.1
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 1958)
  AUTHORS   Brandenstein,L., Schweizer,M., Sedlacik,J., Fiehler,J. and
            Storch,S.
  TITLE     Lysosomal dysfunction and impaired autophagy in a novel mouse model
            deficient for the lysosomal membrane protein Cln7
  JOURNAL   Hum Mol Genet 25 (4), 777-791 (2016)
   PUBMED   26681805
REFERENCE   2  (bases 1 to 1958)
  AUTHORS   Arsov,T., Smith,K.R., Damiano,J., Franceschetti,S., Canafoglia,L.,
            Bromhead,C.J., Andermann,E., Vears,D.F., Cossette,P.,
            Rajagopalan,S., McDougall,A., Sofia,V., Farrell,M., Aguglia,U.,
            Zini,A., Meletti,S., Morbin,M., Mullen,S., Andermann,F., Mole,S.E.,
            Bahlo,M. and Berkovic,S.F.
  TITLE     Kufs disease, the major adult form of neuronal ceroid
            lipofuscinosis, caused by mutations in CLN6
  JOURNAL   Am J Hum Genet 88 (5), 566-573 (2011)
   PUBMED   21549341
REFERENCE   3  (bases 1 to 1958)
  AUTHORS   Ghosh,D., Lippert,D., Krokhin,O., Cortens,J.P. and Wilkins,J.A.
  TITLE     Defining the membrane proteome of NK cells
  JOURNAL   J Mass Spectrom 45 (1), 1-25 (2010)
   PUBMED   19946888
REFERENCE   4  (bases 1 to 1958)
  AUTHORS   Lyly,A., von Schantz,C., Heine,C., Schmiedt,M.L., Sipila,T.,
            Jalanko,A. and Kyttala,A.
  TITLE     Novel interactions of CLN5 support molecular networking between
            Neuronal Ceroid Lipofuscinosis proteins
  JOURNAL   BMC Cell Biol 10, 83 (2009)
   PUBMED   19941651
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1958)
  AUTHORS   Rusyn,E., Mousallem,T., Persaud-Sawin,D.A., Miller,S. and
            Boustany,R.M.
  TITLE     CLN3p impacts galactosylceramide transport, raft morphology, and
            lipid content
  JOURNAL   Pediatr Res 63 (6), 625-631 (2008)
   PUBMED   18317235
REFERENCE   6  (bases 1 to 1958)
  AUTHORS   Mole,S.E., Michaux,G., Codlin,S., Wheeler,R.B., Sharp,J.D. and
            Cutler,D.F.
  TITLE     CLN6, which is associated with a lysosomal storage disease, is an
            endoplasmic reticulum protein
  JOURNAL   Exp Cell Res 298 (2), 399-406 (2004)
   PUBMED   15265688
REFERENCE   7  (bases 1 to 1958)
  AUTHORS   Heine,C., Koch,B., Storch,S., Kohlschutter,A., Palmer,D.N. and
            Braulke,T.
  TITLE     Defective endoplasmic reticulum-resident membrane protein CLN6
            affects lysosomal degradation of endocytosed arylsulfatase A
  JOURNAL   J Biol Chem 279 (21), 22347-22352 (2004)
   PUBMED   15010453
REFERENCE   8  (bases 1 to 1958)
  AUTHORS   Gao,H., Boustany,R.M., Espinola,J.A., Cotman,S.L., Srinidhi,L.,
            Antonellis,K.A., Gillis,T., Qin,X., Liu,S., Donahue,L.R.,
            Bronson,R.T., Faust,J.R., Stout,D., Haines,J.L., Lerner,T.J. and
            MacDonald,M.E.
  TITLE     Mutations in a novel CLN6-encoded transmembrane protein cause
            variant neuronal ceroid lipofuscinosis in man and mouse
  JOURNAL   Am J Hum Genet 70 (2), 324-335 (2002)
   PUBMED   11791207
REFERENCE   9  (bases 1 to 1958)
  AUTHORS   Holopainen,J.M., Saarikoski,J., Kinnunen,P.K. and Jarvela,I.
  TITLE     Elevated lysosomal pH in neuronal ceroid lipofuscinoses (NCLs)
  JOURNAL   Eur J Biochem 268 (22), 5851-5856 (2001)
   PUBMED   11722572
REFERENCE   10 (bases 1 to 1958)
  AUTHORS   Bronson,R.T., Donahue,L.R., Johnson,K.R., Tanner,A., Lane,P.W. and
            Faust,J.R.
  TITLE     Neuronal ceroid lipofuscinosis (nclf), a new disorder of the mouse
            linked to chromosome 9
  JOURNAL   Am J Med Genet 77 (4), 289-297 (1998)
   PUBMED   9600738
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAXUCZ010000008.1.
            
            On Jul 17, 2010 this sequence version replaced XM_236325.5.
            
            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.
            
            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 :: SRR22582424.799709.1,
                                           SRR26360190.1630693.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760383, SAMEA5760386
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-90                JAXUCZ010000008.1  72198823-72198912
            91-205              JAXUCZ010000008.1  72205652-72205766
            206-304             JAXUCZ010000008.1  72207131-72207229
            305-493             JAXUCZ010000008.1  72208095-72208283
            494-549             JAXUCZ010000008.1  72208791-72208846
            550-672             JAXUCZ010000008.1  72210352-72210474
            673-1958            JAXUCZ010000008.1  72212492-72213777
FEATURES             Location/Qualifiers
     source          1..1958
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="8"
                     /map="8q24"
     gene            1..1958
                     /gene="Cln6"
                     /note="CLN6, transmembrane ER protein"
                     /db_xref="GeneID:315746"
                     /db_xref="RGD:1309714"
     exon            1..90
                     /gene="Cln6"
                     /inference="alignment:Splign:2.1.0"
     CDS             17..943
                     /gene="Cln6"
                     /note="ceroid-lipofuscinosis, neuronal 6, late infantile"
                     /codon_start=1
                     /product="ceroid-lipofuscinosis neuronal protein 6"
                     /protein_id="NP_001178723.1"
                     /db_xref="GeneID:315746"
                     /db_xref="RGD:1309714"
                     /translation="MEAAARRRQLPGAAGGPGVAFLQARHGSAKAEDKDRTAPFHFDL
                     WFYFTLQNWVLDFGRPIAMLVFPIQWFPLNKPSVGDYFHMAYNIITPFLLLKLMERSP
                     RTLPRSIIYVSIITFIMGASIHLVGDSVNHRLLFSGYQHHLSVRENPIIKNLKPETLI
                     DSFELLYYYDEYLGHCMWYIPFFLILFMYFSGCFTTSKAESHMPGPALLLVVPSGIYY
                     WYLVTEGQIFILFIFTFFAMLALVLHQKRRRLLLDSNGLFLFCSFALTLLLVALWVAW
                     LWNDPVLRKKYPGVIYVPEPWAFYTLHVSNQQ"
     exon            91..205
                     /gene="Cln6"
                     /inference="alignment:Splign:2.1.0"
     exon            206..304
                     /gene="Cln6"
                     /inference="alignment:Splign:2.1.0"
     exon            305..493
                     /gene="Cln6"
                     /inference="alignment:Splign:2.1.0"
     exon            494..549
                     /gene="Cln6"
                     /inference="alignment:Splign:2.1.0"
     exon            550..672
                     /gene="Cln6"
                     /inference="alignment:Splign:2.1.0"
     exon            673..1958
                     /gene="Cln6"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gccgagcgtg gcggccatgg aggcggcggc gcggaggcgg cagctccccg gagcggctgg
       61 cggccccggt gtcgcgttct tgcaggccag gcatggctcc gcgaaggctg aggacaaaga
      121 ccgcacagcc cccttccact ttgacctctg gttctacttc acactgcaga actgggttct
      181 ggactttggc cgccctattg ccatgctggt attcccgatc cagtggtttc ctctcaacaa
      241 gccgagtgtt ggggactact tccacatggc ctacaatatc atcacaccat tccttctgct
      301 aaagctgatg gagcggtccc cccgaacgct gccgcggtcg ataatctatg tcagcatcat
      361 cacattcatc atgggagcca gcatccacct ggtgggcgac tcagtcaacc accgcttgct
      421 cttcagcggg taccagcacc acttgtctgt cagagagaac cccataatca agaatctcaa
      481 gccggagact ctgatcgact cctttgagct gctgtactac tatgacgagt acctgggcca
      541 ctgcatgtgg tacatcccct tcttcctcat cctcttcatg tacttcagtg gctgttttac
      601 tacctccaag gccgagagcc acatgccagg gcctgccctg ctcctggtgg tgcccagtgg
      661 tatatactac tggtacctgg tgaccgaggg ccagatcttc atcctcttca tcttcacctt
      721 cttcgccatg ctggctctcg ttttgcacca gaagcgtagg cgcctgttac tggacagcaa
      781 tggcctcttc ctcttctgtt ccttcgcgct caccctctta ctggtggctc tgtgggttgc
      841 ctggctgtgg aatgaccctg tgctcagaaa gaagtaccct ggtgtcatct atgttcctga
      901 gccctgggcc ttctacacac tccatgttag caaccaacag tgaggctcag tgggggcaac
      961 aggccatggt atttgtatgt gtgcatacgt gcactgtggt aatatgaact atgcattggg
     1021 ggcagagatt ggcagagtgt gttgttgaga gactcaactg ttctggtcag gttttgggtt
     1081 tgtttgtttg ttttgctttg gacttaagat ggagtttatt ttggcgaagt atatgaaggc
     1141 caagatcgcc cctgccctcc cctgtatttc actaccatta gaggtgcccg aaacatccct
     1201 atctctcagc actgggctgg ccttatggag atgtcttctg gtggcatgca ggtgagggct
     1261 gggcaggaca gaaacaagag actcggctac ttgcctggct cctggcacct gaaactgctt
     1321 acccctgggc cctaggtttc tgggtcacaa cttcttttgt gctttaaaca gagcaattcc
     1381 aactctgggc ttcatttgtt ctggacggct cctatggttc caagtggctc tggggactgg
     1441 tggttactga ttcccttgga gcagcagcag cagcaaggaa gagctgttct tttactatat
     1501 cccccacccc tcctcctggt cacactgtca gtgaagctct tggagctggc ctgggttctg
     1561 agctgcatgg aaggcagaat tctcaagccc ttgttttata gattccctga gacccattgt
     1621 aagggtctga gacattacaa gtcagtctct tgagacagtg cagccagaat ctttcaccac
     1681 ctgccttgtg cctttgttcc cagcatggtg gctcctgcct ttccccagcc cacctcctcc
     1741 taggcctcag atataggtct ccttggcacg aggtgccatc accttattta gcagccagca
     1801 ttgagtggtc tgtgctgtga gtcttgggga tactccatgc atggctctgc ctcttttctg
     1861 ctgctctcag ggactaggcc tcagttttct ctagtagact ttctatgggc tagcccatgc
     1921 tggggtggag gtctgaataa aggctgattt gaagccca
//
