LOCUS       NM_001146311            3013 bp    mRNA    linear   ROD 06-AUG-2024
DEFINITION  Mus musculus CLN3 lysosomal/endosomal transmembrane protein,
            battenin (Cln3), transcript variant 1, mRNA.
ACCESSION   NM_001146311
VERSION     NM_001146311.3
KEYWORDS    RefSeq.
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 3013)
  AUTHORS   Nyame,K., Hims,A., Aburous,A., Laqtom,N.N., Dong,W., Medoh,U.N.,
            Heiby,J.C., Xiong,J., Ori,A. and Abu-Remaileh,M.
  TITLE     Glycerophosphodiesters inhibit lysosomal phospholipid catabolism in
            Batten disease
  JOURNAL   Mol Cell 84 (7), 1354-1364 (2024)
   PUBMED   38447580
REFERENCE   2  (bases 1 to 3013)
  AUTHORS   Kovacs,A.D., Gonzalez Hernandez,J.L. and Pearce,D.A.
  TITLE     Acidified drinking water improves motor function, prevents tremors
            and changes disease trajectory in Cln2R207X mice, a model of late
            infantile Batten disease
  JOURNAL   Sci Rep 13 (1), 19229 (2023)
   PUBMED   37932327
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3013)
  AUTHORS   Sleat,D.E., Banach-Petrosky,W., Larrimore,K.E., Nemtsova,Y.,
            Wiseman,J.A., Najafi,A., Johnson,D., Poole,T.A., Takahashi,K.,
            Cooper,J.D. and Lobel,P.
  TITLE     A mouse mutant deficient in both neuronal ceroid
            lipofuscinosis-associated proteins CLN3 and TPP1
  JOURNAL   J Inherit Metab Dis 46 (4), 720-734 (2023)
   PUBMED   37078466
  REMARK    GeneRIF: A mouse mutant deficient in both neuronal ceroid
            lipofuscinosis-associated proteins CLN3 and TPP1.
REFERENCE   4  (bases 1 to 3013)
  AUTHORS   Johnson,T.B., Brudvig,J.J., Likhite,S., Pratt,M.A., White,K.A.,
            Cain,J.T., Booth,C.D., Timm,D.J., Davis,S.S., Meyerink,B.,
            Pineda,R., Dennys-Rivers,C., Kaspar,B.K., Meyer,K. and Weimer,J.M.
  TITLE     Early postnatal administration of an AAV9 gene therapy is safe and
            efficacious in CLN3 disease
  JOURNAL   Front Genet 14, 1118649 (2023)
   PUBMED   37035740
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3013)
  AUTHORS   Mole,S.E. and Cotman,S.L.
  TITLE     Genetics of the neuronal ceroid lipofuscinoses (Batten disease)
  JOURNAL   Biochim Biophys Acta 1852 (10 Pt B), 2237-2241 (2015)
   PUBMED   26026925
  REMARK    Review article
REFERENCE   6  (bases 1 to 3013)
  AUTHORS   Rakheja,D., Narayan,S.B. and Bennett,M.J.
  TITLE     The function of CLN3P, the Batten disease protein
  JOURNAL   Mol Genet Metab 93 (3), 269-274 (2008)
   PUBMED   18688960
  REMARK    Review article
            Erratum:[Mol Genet Metab. 2008 Jun;94(2):270]
REFERENCE   7  (bases 1 to 3013)
  AUTHORS   Puranam,K.L., Guo,W.X., Qian,W.H., Nikbakht,K. and Boustany,R.M.
  TITLE     CLN3 defines a novel antiapoptotic pathway operative in
            neurodegeneration and mediated by ceramide
  JOURNAL   Mol Genet Metab 66 (4), 294-308 (1999)
   PUBMED   10191118
REFERENCE   8  (bases 1 to 3013)
  AUTHORS   Zhong,N., Wisniewski,K.E., Kaczmarski,A.L., Ju,W., Xu,W.M.,
            Xu,W.W., Mclendon,L., Liu,B., Kaczmarski,W., Sklower Brooks,S.S.
            and Brown,W.T.
  TITLE     Molecular screening of Batten disease: identification of a missense
            mutation (E295K) in the CLN3 gene
  JOURNAL   Hum Genet 102 (1), 57-62 (1998)
   PUBMED   9490299
REFERENCE   9  (bases 1 to 3013)
  AUTHORS   Taschner,P.E., de Vos,N. and Breuning,M.H.
  TITLE     Cross-species homology of the CLN3 gene
  JOURNAL   Neuropediatrics 28 (1), 18-20 (1997)
   PUBMED   9151313
REFERENCE   10 (bases 1 to 3013)
  AUTHORS   Lee,R.L., Johnson,K.R. and Lerner,T.J.
  TITLE     Isolation and chromosomal mapping of a mouse homolog of the Batten
            disease gene CLN3
  JOURNAL   Genomics 35 (3), 617-619 (1996)
   PUBMED   8812504
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC125169.4.
            
            On Mar 21, 2022 this sequence version replaced NM_001146311.2.
            
            Summary: This gene encodes a transmembrane protein called battenin
            that is involved in lysosomal function. Mutations in this, as well
            as other neuronal ceroid-lipofuscinosis genes, cause a number of
            neurodegenerative diseases collectively known as neuronal ceroid
            lipofuscinoses, the most common of which is juvenile neuronal
            ceroid-lipofuscinosis (Batten disease). Alternate splicing results
            in multiple transcript variants. [provided by RefSeq, Aug 2016].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1). Both variants 1 and
            2 encode the same protein.
            
            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 :: AK134036.1, SRR13861859.1949778.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164135 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-525               AC125169.4         82490-83014
            526-632             AC125169.4         84029-84135
            633-777             AC125169.4         84862-85006
            778-874             AC125169.4         85213-85309
            875-953             AC125169.4         85467-85545
            954-1050            AC125169.4         86567-86663
            1051-1122           AC125169.4         87445-87516
            1123-1202           AC125169.4         87897-87976
            1203-1288           AC125169.4         88080-88165
            1289-1361           AC125169.4         88836-88908
            1362-1505           AC125169.4         88993-89136
            1506-1618           AC125169.4         90388-90500
            1619-1665           AC125169.4         92773-92819
            1666-1734           AC125169.4         92897-92965
            1735-1790           AC125169.4         93051-93106
            1791-1884           AC125169.4         93222-93315
            1885-2025           AC125169.4         95698-95838
            2026-3013           AC125169.4         95923-96910
FEATURES             Location/Qualifiers
     source          1..3013
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="7"
                     /map="7 69.16 cM"
     gene            1..3013
                     /gene="Cln3"
                     /note="CLN3 lysosomal/endosomal transmembrane protein,
                     battenin"
                     /db_xref="GeneID:12752"
                     /db_xref="MGI:MGI:107537"
     exon            1..525
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            526..632
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            633..777
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            778..874
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     CDS             829..2145
                     /gene="Cln3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     battenin; ceroid lipofuscinosis, neuronal 3, juvenile
                     (Batten, Spielmeyer-Vogt disease)"
                     /codon_start=1
                     /product="battenin isoform 1"
                     /protein_id="NP_001139783.1"
                     /db_xref="CCDS:CCDS21833.1"
                     /db_xref="GeneID:12752"
                     /db_xref="MGI:MGI:107537"
                     /translation="MGSSAGSWRRLEDSEREETDSEPQAPRLDSRSVLWKNAVGFWIL
                     GLCNNFSYVVMLSAAHDILKQEQASGNQSHVEPGPTPTPHNSSSRFDCNSISTAAVLL
                     ADILPTLVIKLLAPLGLHLLPYSPRVLVSGVCSAGSFVLVAFSQSVGLSLCGVVLASI
                     SSGLGEVTFLSLTAFYPSAVISWWSSGTGGAGLLGSLSYLGLTQAGLSPQHTLLSMLG
                     IPVLLLASYFLLLTSPEPLDPGGENEAETAARQPLIGTETPESKPGASWDLSLQERWT
                     VFKGLLWYIIPLVLVYFAEYFINQGLFELLFFRNTSLSHAQQYRWYQMLYQAGVFASR
                     SSLQCCRIRFTWVLALLQCLNLALLLADVCLNFLPSIYLIFIIILYEGLLGGAAYVNT
                     FHNIALETSDKHREFAMEAACISDTLGISLSGVLALPLHDFLCHLP"
     exon            875..953
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            954..1050
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1051..1122
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1123..1202
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1203..1288
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1289..1361
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1362..1505
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1506..1618
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1619..1665
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1666..1734
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1735..1790
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1791..1884
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            1885..2025
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     exon            2026..3013
                     /gene="Cln3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2304..2309
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Cln3"
                     /note="hexamer: AATAAA"
     polyA_site      2326
                     /gene="Cln3"
                     /note="major polyA site"
     regulatory      2984..2989
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Cln3"
                     /note="hexamer: TATAAA"
     polyA_site      3013
                     /gene="Cln3"
ORIGIN      
        1 acaggttctc agaggctccc cactgcttgc ttcctcttca ccgtgctccc agatctcctg
       61 ggctgtatta ctgctcctgt ctctgtgagt cccaggctct gcctcaggct tcagtgggac
      121 acttggctcc tggcccctgg catcctcagc tgccttccag gacccagtgt cctgcctttc
      181 tgcttggggc cttgcagagc tatctgctct ccacccccag gtctgttcac cagctaaact
      241 tccttcttgg catcttctag tctcttcggg tgcttctacc ccctcactct ggccacttct
      301 aagtccctcc agtacctcct gggcttcctc tcctacaacc ttcccctcag tcacctctcc
      361 cagttcctca gctgcctgtg tctgcctctc tactgtgggg actgtgtctc ctacgaggta
      421 ggacacaaac gcactgaagg agtcctagaa gagaagaaag aagagtgaag gcactcaggg
      481 gaggtctaac cacttcccca ggagtacact gttaacaaag cccaggtggt tgaaaagacc
      541 cgggagaagt gggcagaggc tgctggaatc catagcagag gaataggctt gatgaagaat
      601 ggtcaagatg ctgccctgcc atcgagtgga agtttgagaa gtccaaaggc gaaaaagaga
      661 aaaaaggacc cggaagtaag aagcaaccct caagcacgtg atggaaggct cacgggtact
      721 gtcacgtgac ccccaacctg ctcgtctacc ttgcggagag ttcagctgct cttaaagctc
      781 ggaacacacg ctgactttgg gccctttggg ggacccgaac tcaatgttat gggaagttct
      841 gcgggctcgt ggaggcgcct tgaggattct gagagggagg agaccgactc agagccccag
      901 gcccctcggt tggatagtcg gagtgtcctt tggaagaatg cagtgggttt ctggatcttg
      961 ggtctttgca acaatttctc atatgtggtg atgctgagcg ctgcccatga catcctcaag
     1021 caggagcagg cgtctggaaa ccagagccat gtggaaccag gcccaacacc cacaccccac
     1081 aacagctcat ctcgatttga ctgcaactcc atctccacag ctgcggtgct cctagcagac
     1141 atccttccca cccttgtcat caaactcctg gcgcctcttg gccttcactt gctgccttac
     1201 agcccccggg tgctcgtcag tggagtttgt tctgctggga gctttgttct ggttgccttc
     1261 tctcagtcag tggggttaag cctgtgtgga gtggttttgg ccagcatctc ctcagggcta
     1321 ggggaggtca ccttcctctc actgactgcc ttctacccca gtgctgtgat ctcatggtgg
     1381 tcttcgggta ccgggggtgc agggcttctt ggatcgctgt cttacctggg actcacccag
     1441 gctggcctct ccccgcagca caccctactt tctatgttgg ggatccctgt tctgctgcta
     1501 gccagctatt tcttgttgct cacgtctcct gaacccctgg accctggagg ggaaaacgag
     1561 gcagagactg ctgcccggca gcctctcata ggcaccgaga ccccagagtc aaagccaggt
     1621 gccagctggg acctctccct ccaggaaagg tggacagtgt tcaagggtct cttgtggtac
     1681 atcatccctc tggtgctggt ctactttgca gaatacttta tcaaccaggg acttttcgag
     1741 ctcctgtttt tccggaacac ttccctaagc catgctcagc agtaccgatg gtaccagatg
     1801 ctataccagg ctggtgtgtt cgcctcccgc tcttctctcc aatgttgccg aatacggttc
     1861 acctgggtcc tagccctgct ccagtgcctc aacctggccc tcctgctggc agatgtctgc
     1921 ttgaacttct tgcccagcat ctacctcatc ttcatcatca ttctgtacga agggctcctg
     1981 ggtggggccg cttacgtgaa taccttccac aacattgctc tggagaccag tgacaagcac
     2041 cgagagtttg ccatggaagc tgcctgtatc tctgacacct tgggaatctc cctgtcgggg
     2101 gtcctggccc tgcctctgca tgacttcctc tgtcacctcc cttgacagga gttgctcgac
     2161 acacactgat ctgcaggcac atgagcagat cacacatctt cgagctctgc cacagccttt
     2221 ccctgcccca ctgcagcaag gagcccctga tgtttcccac tcctgagctg gcctcagagt
     2281 tttctcctac cctctgccct tctaataaat gcttatttta acagtttcct ttttgtgcag
     2341 tctctgaaac ggaaagttta cataagccca ctgtgaaaga tatatgtatt tatgaatgta
     2401 taaagtattt cagacaaggt gtggcacaca cctgtaattc cagcactcag cagactggag
     2461 aatccaagtt cacgtctgac tgggatatac ggtgagaccc tgaggactag ggctatagtt
     2521 cagtggtaga gtacttgccc aggatgtcct gggctctcag ttttatccct ggaaaacaat
     2581 tcaaaagcag cgtatgctaa tataagcctg tagtcccagg attggggagg tagagacagg
     2641 aggatccaga gttcatggtc ctcagctaca taggaaacca aggtcagcct ggcctacata
     2701 agatcttgtt ttacaataat tacattgtgt atttctggct tctttataaa aaaaaatcaa
     2761 atgtccatag gtatgtagat ttatatctgg gtcttcgatt ccattgatca acttgtctgt
     2821 ttttatgcca atactgtgtg ggttttatta ctataactct gtagtagtgc ttgaaataag
     2881 gatggtgata cctccaggag ttctattact gtacagagtt gttttagcaa tcctgtgttt
     2941 cttgtttttt tcatatgaaa ttgagtattg ttctttcaag gtctataaag aattgtgttg
     3001 gaattttgat gga
//
