LOCUS       NM_001033175            2142 bp    mRNA    linear   ROD 02-MAY-2024
DEFINITION  Mus musculus ceroid-lipofuscinosis, neuronal 6 (Cln6), mRNA.
ACCESSION   NM_001033175 XM_134858
VERSION     NM_001033175.3
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 2142)
  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 2142)
  AUTHORS   Tuermer,A., Mausbach,S., Kaade,E., Damme,M., Sylvester,M.,
            Gieselmann,V. and Thelen,M.
  TITLE     CLN6 deficiency causes selective changes in the lysosomal protein
            composition
  JOURNAL   Proteomics 21 (19), e2100043 (2021)
   PUBMED   34432360
  REMARK    GeneRIF: CLN6 deficiency causes selective changes in the lysosomal
            protein composition.
REFERENCE   3  (bases 1 to 2142)
  AUTHORS   Best,H.L., Clare,A.J., McDonald,K.O., Wicky,H.E. and Hughes,S.M.
  TITLE     An altered secretome is an early marker of the pathogenesis of CLN6
            Batten disease
  JOURNAL   J Neurochem 157 (3), 764-780 (2021)
   PUBMED   33368303
  REMARK    GeneRIF: An altered secretome is an early marker of the
            pathogenesis of CLN6 Batten disease.
REFERENCE   4  (bases 1 to 2142)
  AUTHORS   Bajaj,L., Sharma,J., di Ronza,A., Zhang,P., Eblimit,A., Pal,R.,
            Roman,D., Collette,J.R., Booth,C., Chang,K.T., Sifers,R.N.,
            Jung,S.Y., Weimer,J.M., Chen,R., Schekman,R.W. and Sardiello,M.
  TITLE     A CLN6-CLN8 complex recruits lysosomal enzymes at the ER for Golgi
            transfer
  JOURNAL   J Clin Invest 130 (8), 4118-4132 (2020)
   PUBMED   32597833
  REMARK    GeneRIF: A CLN6-CLN8 complex recruits lysosomal enzymes at the ER
            for Golgi transfer.
REFERENCE   5  (bases 1 to 2142)
  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   6  (bases 1 to 2142)
  AUTHORS   Chang,B., Hawes,N.L., Hurd,R.E., Davisson,M.T., Nusinowitz,S. and
            Heckenlively,J.R.
  TITLE     Retinal degeneration mutants in the mouse
  JOURNAL   Vision Res 42 (4), 517-525 (2002)
   PUBMED   11853768
  REMARK    Review article
REFERENCE   7  (bases 1 to 2142)
  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   8  (bases 1 to 2142)
  AUTHORS   Wheeler,R.B., Sharp,J.D., Schultz,R.A., Joslin,J.M., Williams,R.E.
            and Mole,S.E.
  TITLE     The gene mutated in variant late-infantile neuronal ceroid
            lipofuscinosis (CLN6) and in nclf mutant mice encodes a novel
            predicted transmembrane protein
  JOURNAL   Am J Hum Genet 70 (2), 537-542 (2002)
   PUBMED   11727201
REFERENCE   9  (bases 1 to 2142)
  AUTHORS   Pantaleon,M., Kanai-Azuma,M., Mattick,J.S., Kaibuchi,K., Kaye,P.L.
            and Wood,S.A.
  TITLE     FAM deubiquitylating enzyme is essential for preimplantation mouse
            embryo development
  JOURNAL   Mech Dev 109 (2), 151-160 (2001)
   PUBMED   11731229
REFERENCE   10 (bases 1 to 2142)
  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     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC164614.3.
            
            On Jun 20, 2018 this sequence version replaced NM_001033175.2.
            
            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 :: AK154414.1, AK154551.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-170               AC164614.3         68400-68569         c
            171-285             AC164614.3         62670-62784         c
            286-384             AC164614.3         61302-61400         c
            385-573             AC164614.3         60200-60388         c
            574-629             AC164614.3         59714-59769         c
            630-752             AC164614.3         58123-58245         c
            753-2142            AC164614.3         55348-56737         c
FEATURES             Location/Qualifiers
     source          1..2142
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="9"
                     /map="9 33.89 cM"
     gene            1..2142
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /note="ceroid-lipofuscinosis, neuronal 6"
                     /db_xref="GeneID:76524"
                     /db_xref="MGI:MGI:2159324"
     exon            1..170
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /inference="alignment:Splign:2.1.0"
     CDS             97..1023
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /codon_start=1
                     /product="ceroid-lipofuscinosis neuronal protein 6"
                     /protein_id="NP_001028347.1"
                     /db_xref="CCDS:CCDS23267.1"
                     /db_xref="GeneID:76524"
                     /db_xref="MGI:MGI:2159324"
                     /translation="MEAATRRRQLLGAAGGPGVAFVQARHGSVKAEDKDRTAPFHLDL
                     WFYFTLQNWVLDFGRPIAMLVFPIQWFPLNKPSVGDYFHMTYNIITPFLLLKLIERSP
                     RTLPRSIVYVSIITFIMGASIHLVGDSVNHRLLFSGYQHHLSVRENPIIKNLKPETLI
                     DSFELLYYYDEYLGHCMWYIPFFLILFMYFSGCFTTCKAESHMPGPALLLVVPSGLYY
                     WYLVTEGQIFILFIFTFFAMLALVLHQKRRRLFLDSNGLFLLYSFALTLSLVALWVAW
                     LWNDPVLRKKYPGVIYVPEPWAFYTLHVSSQQ"
     exon            171..285
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            286..384
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            385..573
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            574..629
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            630..752
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            753..2142
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2117..2122
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /note="hexamer: AATAAA"
     polyA_site      2139
                     /gene="Cln6"
                     /gene_synonym="1810065L06Rik; D9Bwg1455e; nclf"
                     /note="major polyA site"
ORIGIN      
        1 ctctcccgcc cagccttccc cgcgttgggc gccgaggctc cgcgcggccc gcgcagccgt
       61 ctctcctccc ggaaggcgag gccgagcgtg gcggccatgg aggcggcgac gcggaggcgg
      121 cagctcctcg gagcggcggg cggccccggt gtcgcgttcg tgcaggccag gcatggctct
      181 gtgaaggccg aggacaaaga ccgcacagcc cccttccatc ttgacctctg gttctacttc
      241 acactgcaga actgggttct ggactttggc cgccccattg ccatgctggt attcccgatc
      301 cagtggtttc ctctcaacaa gccaagtgtc ggggactact ttcacatgac ctacaacatc
      361 atcacgccct tcctgctgct aaagcttatt gagcggtccc cccgaacgct gccgcggtct
      421 atagtctatg tcagcatcat cactttcatc atgggagcca gcatccacct ggtgggagac
      481 tcagtcaacc atcgcctgct cttcagtggg taccagcacc acctgtccgt cagagagaac
      541 cccattatca agaacctcaa gccggagact ctgatcgact cctttgagct gttgtactac
      601 tatgacgagt acctgggcca ctgcatgtgg tacatcccct tcttcctcat cctcttcatg
      661 tacttcagtg gctgtttcac cacctgcaag gctgagagcc acatgccagg acctgccctg
      721 ctcctggtgg tgcccagtgg tctgtactac tggtacctgg tcaccgaggg ccagatcttc
      781 atcctcttca tcttcacctt cttcgccatg ctggctctcg tcttgcacca gaagcgcagg
      841 cgcctcttcc tggacagcaa cggcctcttc ctcttgtatt ccttcgcgct caccctctca
      901 ctggtggctc tgtgggtggc ttggctgtgg aatgaccctg tactcagaaa gaagtaccct
      961 ggtgtcatct atgttcctga gccctgggcc ttctacacac tccacgttag cagtcaacag
     1021 tgaggcttac tgggggcacc aggccatggt gtttgtacat gtgtgcatac atgcaccgtg
     1081 gtaatgtgaa ctatgcactg gtggcaggga tggacagagt gtgctgttga gagactcaac
     1141 tgttctggtc aggttctgag tttgtttttt tcttttcttt ttttcccccc tttggactta
     1201 agatggaatt tagtttgggg aagtatatga aggccaagat cccggcccct gccctcccct
     1261 gtatttcatt actattagag gtgcctgaat aacaccccta tctctcagga ctgggctggc
     1321 cttatggaga tatcttctgg tgacaagcgg gtgagggctg ctcagggcag aagcaggaga
     1381 ctctgctacc tgtccctggg ccctaggttt ctgggtcaca acttcttttg tgctttaaac
     1441 agagcagttc catctctggg cttcttttgc tgtggtgggc tccatagttt atgtggctct
     1501 ggggactggt ggttgctgat tcccttaggg agcggcagca cggaagagtg gttcttttac
     1561 tgtgcccccg cccccaccct cagcctaggg gtatgtttct cccagcctct tgtccaactt
     1621 cacaccccat ttatatgctg ttgagaaccc agtctccagg gagccagagg cccccactcc
     1681 cagtctctct cagctaagct ctctaagctg gcctgggttc tgagctacat ggaaggcaga
     1741 gttctcaagc ccttgtttta tagtttcccc cgaaacccct tgtaagggtc tgagacaata
     1801 caagtcagac tcttgagaca gcacatctca gcctgaatct ctcaccacct gcctggtgcc
     1861 tttgttccca gcatggtggc tcctccccag cccacttcct cccaggcctc agatataggt
     1921 ctccttggca caaggcgcca ccacctcatt tggcagccag cactgactga cctgtgctgt
     1981 gagtcttgga gacactccat gcatggccct gcctcttttc tgctgttctc agggactttg
     2041 cctcagtttc cccttgtgat ctttctgtgg gttagcccat gctggggtag gggtggtgac
     2101 aggggtgaga ggcttaaata aaggctgttt tgaagcccag ca
//
