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    CLN3 ceroid-lipofuscinosis, neuronal 3 [ Homo sapiens ]

    Gene ID: 1201, updated on 11-May-2012

    Summary

    Official Symbol
    CLN3provided by HGNC
    Official Full Name
    ceroid-lipofuscinosis, neuronal 3provided by HGNC
    Primary source
    HGNC:2074
    See related
    Ensembl:ENSG00000188603; Ensembl:ENSG00000261832; HPRD:08450; MIM:607042; Vega:OTTHUMG00000097024; Vega:OTTHUMG00000175737
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BTS; JNCL; MGC102840
    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]

    Genomic context

    Location :
    16p12.1
    Sequence :
    Chromosome: 16; NC_000016.9 (28488600..28503623, complement)
    See CLN3 in Epigenomics, MapViewer

    Chromosome 16 - NC_000016.9Genomic Context describing neighboring genes Neighboring gene cell division cycle 37 homolog (S. cerevisiae) pseudogene 2 Neighboring gene nuclear pore complex interacting protein-like 1 Neighboring gene apolipoprotein B receptor Neighboring gene interleukin 27

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    BioGRID:107612 BioGRID:111783 ABCD3    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116139 AFG3L2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:115787 ATG7    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:107031 AUP1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:120937 CAND1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:121318 CCDC47    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116167 CKAP4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:107747 COX15    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:107765 CPT1A    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:107917 CYC1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:108017 DDOST    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116387 DDX20    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:121556 ESYT2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:120511 FANCI    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116802 GANAB    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116181 GCN1L1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:119102 GEMIN4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:119328 HSD17B12    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116190 ILVBL    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116185 IMMT    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:109863 IRAK1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116966 KIAA0368    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:114897 NPEPPS    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116777 NUP205    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:115041 NUP93    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:111264 PHB    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:111577 PRKDC    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:120482 RIF1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:112100 RPN2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:119307 SBDS    BioGRID  PubMed Two-hybrid 
    BioGRID:107612 BioGRID:120475 SEC61A2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:125645 SFXN4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:115569 SIGMAR1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:107850 SLC25A10    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:113990 SLC25A11    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:122862 SLC25A22    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:115223 TELO2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:112967 TMPO    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:114730 TRIP13    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:120986 UNC45A    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:113260 VDAC2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:113348 XPO1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107612 BioGRID:116420 XPOT    BioGRID  PubMed Affinity Capture-MS 

    General gene information

    Markers

    Homology

    • Homologs of the CLN3 gene: The CLN3 gene is conserved in dog, cow, mouse, rat, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, , S.pombe, , and N.crassa.
    • Map Viewer (Mouse, Rat)

    Pathways from BioSystems

    • Lysosome, organism-specific biosystem (from KEGG)
      Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
    • Lysosome, conserved biosystem (from KEGG)
      Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    calcium-dependent protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    unfolded protein binding TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    amino acid transport IEA
    Inferred from Electronic Annotation
    more info
     
    amyloid precursor protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    arginine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    associative learning ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    autophagic vacuole fusion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell death IEA
    Inferred from Electronic Annotation
    more info
     
    cellular amino acid metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular membrane organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    ceramide metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosolic calcium ion homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    galactosylceramide metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    globoside metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    glucosylceramide metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ionotropic glutamate receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    lysosomal lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lysosomal lumen pH elevation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lysosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    macroautophagy NAS
    Non-traceable Author Statement
    more info
    PubMed 
    negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of catalytic activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of macroautophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of neuron apoptosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of proteolysis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    neuromuscular process controlling balance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    neurotransmitter metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein catabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    protein folding TAS
    Traceable Author Statement
    more info
    PubMed 
    protein processing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of action potential ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    sphingomyelin metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    vacuolar transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Golgi membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Golgi stack IDA
    Inferred from Direct Assay
    more info
    PubMed 
    autophagic vacuole ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    caveola IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasmic vesicle part IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral to endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral to membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    late endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    membrane fraction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitochondrion TAS
    Traceable Author Statement
    more info
    PubMed 
    neuron projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    synaptic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    battenin
    Names
    battenin
    batten disease protein

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008654.1 RefSeqGene

      Range
      5001..20024
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000086.2NP_000077.1  battenin

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AF077962, AI138575, AU105965, DA869025, U32680
      Consensus CDS
      CCDS10632.1
      UniProtKB/Swiss-Prot
      Q13286
      UniProtKB/TrEMBL
      Q549S9
      Related
      ENSP00000353073, ENST00000359984
      Conserved Domains (1) summary
      pfam02487
      Location:37438
      Blast Score: 1241
      CLN3; CLN3 protein
    2. NM_001042432.1NP_001035897.1  battenin

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AF077957, AI138575, DA552461, DB101039
      Consensus CDS
      CCDS10632.1
      UniProtKB/Swiss-Prot
      Q13286
      UniProtKB/TrEMBL
      Q549S9
      Related
      ENSP00000353116, ENST00000360019
      Conserved Domains (1) summary
      pfam02487
      Location:37438
      Blast Score: 1241
      CLN3; CLN3 protein

    RefSeqs of Annotated Genomes: Build 37.3

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000016.9 Reference GRCh37.p5 Primary Assembly

      Range
      28488600..28503623, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000148.1 Alternate HuRef

      Range
      26514259..26529549, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AC002425.1 AAC05337.1
    genomic AC002544.1 AAC27430.1
    genomic AC138894.2 (38089..52704) None
    genomic CH471279.1 EAW52281.1
      EAW52282.1
      EAW52283.1
      EAW52284.1
      EAW52285.1
      EAW52286.1
      EAW52287.1
      EAW52288.1
      EAW52289.1
      EAW52290.1
      EAW52291.1
      EAW52292.1
      EAW52293.1
      EAW52294.1
      EAW52295.1
      EAW52296.1
      EAW52297.1
      EAW52298.1
      EAW52299.1
    genomic CQ834698.1 CAH05564.1
    genomic X99832.1 CAA68148.1
    mRNA AF015593.1 AAD01555.1
    mRNA AF015594.1 AAD01556.1
    mRNA AF015595.1 AAD01557.1
    mRNA AF015596.1 AAD01558.1
    mRNA AF015597.1 AAD01559.1
    mRNA AF015598.1 AAD01560.1
    mRNA AF015599.1 AAD01561.1
    mRNA AF015600.1 AAD01562.1
    mRNA AF015601.1 AAD01563.1
    mRNA AF015602.1 AAD01564.1
    mRNA AF077956.1 AAD51478.1
    mRNA AF077957.1 AAD51479.1
    mRNA AF077958.1 AAD51480.1
    mRNA AF077959.1 AAD51481.1
    mRNA AF077960.1 AAD51482.1
    mRNA AF077961.1 AAD51483.1
    mRNA AF077962.1 AAD51484.1
    mRNA AF077963.1 AAD51485.1
    mRNA AF077964.1 AAD51486.1
    mRNA AF077965.1 AAD51487.1
    mRNA AF077966.1 AAD51488.1
    mRNA AF077967.1 AAD51489.1
    mRNA AF077968.1 AAD51490.1
    mRNA AF077969.1 AAD51491.1
    mRNA AF077970.1 AAD51492.1
    mRNA AF077971.1 AAD51493.1
    mRNA AF077972.1 AAD51494.1
    mRNA AF077973.1 AAD51495.1
    mRNA AF078168.1 AAD48542.1
    mRNA AF078169.1 AAD48543.1
    mRNA AI138575.1 None
    mRNA AK090709.1 None
    mRNA AK294070.1 BAG57414.1
    mRNA AK294250.1 BAG57546.1
    mRNA AK295500.1 BAG58420.1
    mRNA AK297690.1 BAG60048.1
    mRNA AK302027.1 BAG63425.1
    mRNA AK302138.1 BAG63512.1
    mRNA AK313002.1 BAG35838.1
    mRNA AU105965.1 None
    mRNA BC002394.2 AAH02394.1
    mRNA BC004433.1 AAH04433.1
    mRNA BC111068.1 AAI11069.1
    mRNA BK001540.1 DAA02067.1
    mRNA DA552461.1 None
    mRNA DA869025.1 None
    mRNA DB101039.1 None
    mRNA EF587244.1 ABW04812.1
    mRNA EF587245.1 ABW04813.1
    mRNA U32680.1 AAB51075.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95085 GenPept UniProtKB/TrEMBL:O95085
    O95086 GenPept UniProtKB/TrEMBL:O95086
    O95087 GenPept UniProtKB/TrEMBL:O95087
    O95088 GenPept UniProtKB/TrEMBL:O95088
    O95089 GenPept UniProtKB/TrEMBL:O95089
    O95090 GenPept UniProtKB/TrEMBL:O95090
    O95091 GenPept UniProtKB/TrEMBL:O95091
    O95092 GenPept UniProtKB/TrEMBL:O95092
    O95093 GenPept UniProtKB/TrEMBL:O95093
    Q13286.1 GenPept UniProtKB/Swiss-Prot:Q13286
    Q2TA70 GenPept UniProtKB/TrEMBL:Q2TA70
    Q549S9 GenPept UniProtKB/TrEMBL:Q549S9
    Q5XFT9 GenPept UniProtKB/TrEMBL:Q5XFT9
    Q9UBD8 GenPept UniProtKB/TrEMBL:Q9UBD8
    Q9UBH5 GenPept UniProtKB/TrEMBL:Q9UBH5
    Q9UP05 GenPept UniProtKB/TrEMBL:Q9UP05
    Q9UP08 GenPept UniProtKB/TrEMBL:Q9UP08
    Q9UP10 GenPept UniProtKB/TrEMBL:Q9UP10

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