LOCUS       NM_001042432            1685 bp    mRNA    linear   PRI 09-FEB-2025
DEFINITION  Homo sapiens CLN3 lysosomal/endosomal transmembrane protein,
            battenin (CLN3), transcript variant 1, mRNA.
ACCESSION   NM_001042432
VERSION     NM_001042432.2
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 1685)
  AUTHORS   Yasa,S., Butz,E.S., Colombo,A., Chandrachud,U., Montore,L.,
            Tschirner,S., Prestel,M., Sheridan,S.D., Muller,S.A., Groh,J.,
            Lichtenthaler,S.F., Tahirovic,S. and Cotman,S.L.
  TITLE     Loss of CLN3 in microglia leads to impaired lipid metabolism and
            myelin turnover
  JOURNAL   Commun Biol 7 (1), 1373 (2024)
   PUBMED   39438652
  REMARK    GeneRIF: Loss of CLN3 in microglia leads to impaired lipid
            metabolism and myelin turnover.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1685)
  AUTHORS   Zhang,H.Y., Minnis,C., Gustavsson,E., Ryten,M. and Mole,S.E.
  TITLE     CLN3 transcript complexity revealed by long-read RNA sequencing
            analysis
  JOURNAL   BMC Med Genomics 17 (1), 244 (2024)
   PUBMED   39367445
  REMARK    GeneRIF: CLN3 transcript complexity revealed by long-read RNA
            sequencing analysis.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1685)
  AUTHORS   Wunkhaus,D., Tang,R., Nyame,K., Laqtom,N.N., Schweizer,M., Scotto
            Rosato,A., Krogsaeter,E.K., Wollnik,C., Abu-Remaileh,M., Grimm,C.,
            Hermey,G., Kuhn,R., Gruber-Schoffnegger,D. and Markmann,S.
  TITLE     TRPML1 activation ameliorates lysosomal phenotypes in CLN3
            deficient retinal pigment epithelial cells
  JOURNAL   Sci Rep 14 (1), 17469 (2024)
   PUBMED   39080379
  REMARK    GeneRIF: TRPML1 activation ameliorates lysosomal phenotypes in CLN3
            deficient retinal pigment epithelial cells.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1685)
  AUTHORS   Heins-Marroquin,U., Singh,R.R., Perathoner,S., Gavotto,F., Merino
            Ruiz,C., Patraskaki,M., Gomez-Giro,G., Kleine Borgmann,F.,
            Meyer,M., Carpentier,A., Warmoes,M.O., Jager,C., Mittelbronn,M.,
            Schwamborn,J.C., Cordero-Maldonado,M.L., Crawford,A.D.,
            Schymanski,E.L. and Linster,C.L.
  TITLE     CLN3 deficiency leads to neurological and metabolic perturbations
            during early development
  JOURNAL   Life Sci Alliance 7 (3), e202302057 (2024)
   PUBMED   38195117
  REMARK    GeneRIF: CLN3 deficiency leads to neurological and metabolic
            perturbations during early development.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1685)
  AUTHORS   Janes,R.W., Munroe,P.B., Mitchison,H.M., Gardiner,R.M., Mole,S.E.
            and Wallace,B.A.
  TITLE     A model for Batten disease protein CLN3: functional implications
            from homology and mutations
  JOURNAL   FEBS Lett 399 (1-2), 75-77 (1996)
   PUBMED   8980123
REFERENCE   6  (bases 1 to 1685)
  AUTHORS   Jarvela,I., Mitchison,H.M., Munroe,P.B., O'Rawe,A.M., Mole,S.E. and
            Syvanen,A.C.
  TITLE     Rapid diagnostic test for the major mutation underlying Batten
            disease
  JOURNAL   J Med Genet 33 (12), 1041-1042 (1996)
   PUBMED   9004140
REFERENCE   7  (bases 1 to 1685)
  AUTHORS   Taschner,P.E., de Vos,N., Thompson,A.D., Callen,D.F., Doggett,N.,
            Mole,S.E., Dooley,T.P., Barth,P.G. and Breuning,M.H.
  TITLE     Chromosome 16 microdeletion in a patient with juvenile neuronal
            ceroid lipofuscinosis (Batten disease)
  JOURNAL   Am J Hum Genet 56 (3), 663-668 (1995)
   PUBMED   7887420
REFERENCE   8  (bases 1 to 1685)
  AUTHORS   Mole,S.E. and Williams,R.E.
  TITLE     Neuronal Ceroid-Lipofuscinoses - RETIRED CHAPTER, FOR HISTORICAL
            REFERENCE ONLY
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301601
REFERENCE   9  (bases 1 to 1685)
  AUTHORS   Klein,C., Lohmann,K., Marras,C. and Munchau,A.
  TITLE     Hereditary Dystonia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301334
REFERENCE   10 (bases 1 to 1685)
  AUTHORS   Barnett,T.R., Pickle,W. 2nd and Elting,J.J.
  TITLE     Characterization of two new members of the pregnancy-specific beta
            1-glycoprotein family from the myeloid cell line KG-1 and
            suggestion of two distinct classes of transcription unit
  JOURNAL   Biochemistry 29 (44), 10213-10218 (1990)
   PUBMED   2271648
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA552461.1, DB101039.1,
            AF077957.1 and AI138575.1.
            
            On Nov 21, 2019 this sequence version replaced NM_001042432.1.
            
            Summary: This gene encodes a protein that is involved in lysosomal
            function. Mutations in this, as well as other neuronal
            ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases
            commonly known as Batten disease or collectively known as neuronal
            ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript
            variants have been found for this gene. [provided by RefSeq, Jul
            2008].
            
            Transcript Variant: This variant (1) represents the longest
            transcript. Both variants 1 and 2 encode the same isoform (a).
            
            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 :: BC002394.2, AK313002.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000636147.2/ ENSP00000490105.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-50                DA552461.1         229-278
            51-131              DB101039.1         279-359
            132-1448            AF077957.1         1-1317
            1449-1685           AI138575.1         3-239               c
FEATURES             Location/Qualifiers
     source          1..1685
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16p12.1"
     gene            1..1685
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /note="CLN3 lysosomal/endosomal transmembrane protein,
                     battenin"
                     /db_xref="GeneID:1201"
                     /db_xref="HGNC:HGNC:2074"
                     /db_xref="MIM:607042"
     exon            1..55
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            56..177
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     CDS             132..1448
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /note="isoform a is encoded by transcript variant 1;
                     battenin; CLN3, battenin; batten disease protein;
                     ceroid-lipofuscinosis, neuronal 3"
                     /codon_start=1
                     /product="battenin isoform a"
                     /protein_id="NP_001035897.1"
                     /db_xref="CCDS:CCDS10632.1"
                     /db_xref="GeneID:1201"
                     /db_xref="HGNC:HGNC:2074"
                     /db_xref="MIM:607042"
                     /translation="MGGCAGSRRRFSDSEGEETVPEPRLPLLDHQGAHWKNAVGFWLL
                     GLCNNFSYVVMLSAAHDILSHKRTSGNQSHVDPGPTPIPHNSSSRFDCNSVSTAAVLL
                     ADILPTLVIKLLAPLGLHLLPYSPRVLVSGICAAGSFVLVAFSHSVGTSLCGVVFASI
                     SSGLGEVTFLSLTAFYPRAVISWWSSGTGGAGLLGALSYLGLTQAGLSPQQTLLSMLG
                     IPALLLASYFLLLTSPEAQDPGGEEEAESAARQPLIRTEAPESKPGSSSSLSLRERWT
                     VFKGLLWYIVPLVVVYFAEYFINQGLFELLFFWNTSLSHAQQYRWYQMLYQAGVFASR
                     SSLRCCRIRFTWALALLQCLNLVFLLADVWFGFLPSIYLVFLIILYEGLLGGAAYVNT
                     FHNIALETSDEHREFAMAATCISDTLGISLSGLLALPLHDFLCQLS"
     exon            178..256
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            257..353
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            354..425
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            426..505
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            506..591
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            592..664
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            665..808
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            809..921
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            922..968
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            969..1037
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            1038..1093
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            1094..1187
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            1188..1328
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     exon            1329..1685
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1661..1666
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /note="hexamer: AATAAA"
     polyA_site      1685
                     /gene="CLN3"
                     /gene_synonym="BTN1; BTS; JNCL; SLC29B1"
                     /note="major polyA site"
ORIGIN      
        1 acgtgatccg acaaacggcc tctgcatagt gcagaacatt ctgctgctct taaagaccct
       61 catccctccc gtgggagccc cctttggaca ctctatgacc ctggaccctc gggggacctg
      121 aacttgatgc gatgggaggc tgtgcaggct cgcggcggcg cttttcggat tccgaggggg
      181 aggagaccgt cccggagccc cggctccctc tgttggacca tcagggcgcg cattggaaga
      241 acgcggtggg cttctggctg ctgggccttt gcaacaactt ctcttatgtg gtgatgctga
      301 gtgccgccca cgacatcctt agccacaaga ggacatcggg aaaccagagc catgtggacc
      361 caggcccaac gccgatcccc cacaacagct catcacgatt tgactgcaac tctgtctcta
      421 cggctgctgt gctcctggcg gacatcctcc ccacactcgt catcaaattg ttggctcctc
      481 ttggccttca cctgctgccc tacagccccc gggttctcgt cagtgggatt tgtgctgctg
      541 gaagcttcgt cctggttgcc ttttctcatt ctgtggggac cagcctgtgt ggtgtggtct
      601 tcgctagcat ctcatcaggc cttggggagg tcaccttcct ctccctcact gccttctacc
      661 ccagggccgt gatctcctgg tggtcctcag ggactggggg agctgggctg ctgggggccc
      721 tgtcctacct gggcctcacc caggccggcc tctcccctca gcagaccctg ctgtccatgc
      781 tgggtatccc tgccctgctg ctggccagct atttcttgtt gctcacatct cctgaggccc
      841 aggaccctgg aggggaagaa gaagcagaga gcgcagcccg gcagcccctc ataagaaccg
      901 aggccccgga gtcgaagcca ggctccagct ccagcctctc ccttcgggaa aggtggacag
      961 tgttcaaggg tctgctgtgg tacattgttc ccttggtcgt agtttacttt gccgagtatt
     1021 tcattaacca gggacttttt gaactcctct ttttctggaa cacttccctg agtcacgctc
     1081 agcaataccg ctggtaccag atgctgtacc aggctggcgt ctttgcctcc cgctcttctc
     1141 tccgctgctg tcgcatccgt ttcacctggg ccctggccct gctgcagtgc ctcaacctgg
     1201 tgttcctgct ggcagacgtg tggttcggct ttctgccaag catctacctc gtcttcctga
     1261 tcattctgta tgaggggctc ctgggaggcg cagcctacgt gaacaccttc cacaacatcg
     1321 ccctggagac cagtgatgag caccgggagt ttgcaatggc ggccacctgc atctctgaca
     1381 cactggggat ctccctgtcg gggctcctgg ctttgcctct gcatgacttc ctctgccagc
     1441 tctcctgata ctcgggatcc tcaggacgca ggtcacattc acctgtgggc agagggacag
     1501 gtcagacacc caggcccacc ccagagaccc tccatgaact gtgctcccag ccttcccggc
     1561 aggtctggga gtagggaagg gctgaagcct tgtttccctt gcaggggggc cagccattgt
     1621 ctcccacttg gggagtttct tcctggcatc atgccttctg aataaatgcc gattttatcc
     1681 atgga
//
