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    CLN3 CLN3, battenin [ Homo sapiens (human) ]

    Gene ID: 1201, updated on 12-Aug-2018

    Summary

    Official Symbol
    CLN3provided by HGNC
    Official Full Name
    CLN3, batteninprovided by HGNC
    Primary source
    HGNC:HGNC:2074
    See related
    Ensembl:ENSG00000188603 Ensembl:ENSG00000261832 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; BTN1; JNCL
    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]
    Expression
    Ubiquitous expression in placenta (RPKM 23.0), colon (RPKM 17.0) and 25 other tissues See more
    Orthologs

    Genomic context

    See CLN3 in Genome Data Viewer
    Location:
    16p12.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (28466653..28492302, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28488600..28505897, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 3 subunit C like Neighboring gene microRNA 6862-1 Neighboring gene uncharacterized LOC112268171 Neighboring gene cell division cycle 37 pseudogene 2 Neighboring gene nuclear pore complex interacting protein family member B7 Neighboring gene apolipoprotein B receptor Neighboring gene interleukin 27

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Juvenile neuronal ceroid lipofuscinosis
    MedGen: C0751383 OMIM: 204200 GeneReviews: Neuronal Ceroid-Lipofuscinoses
    Compare labs

    NHGRI GWAS Catalog

    Description
    Common variants at five new loci associated with early-onset inflammatory bowel disease.
    NHGRI GWA Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    NHGRI GWA Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of ceroid-lipofuscinosis, neuronal 3 (CLN3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Genome-wide shRNA screening identifies CLN3, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

    Go to the HIV-1, Human Interaction Database

    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...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC102840

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    unfolded protein binding TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    action potential ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    amyloid precursor protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    arginine transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    arginine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    associative learning ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    autophagosome maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular amino acid metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    ceramide metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    lysosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    macroautophagy NAS
    Non-traceable Author Statement
    more info
    PubMed 
    membrane organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 neuron apoptotic process 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 processing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cytosolic calcium ion concentration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of intracellular pH IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sphingomyelin metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    vesicle transport along microtubule IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 
    autophagosome 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 
    early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    late endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    lysosomal membrane HDA PubMed 
    lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    lysosome 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
    batten disease protein
    ceroid-lipofuscinosis, neuronal 3

    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_008654.2 RefSeqGene

      Range
      5001..30650
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_689

    mRNA and Protein(s)

    1. NM_000086.2NP_000077.1  battenin isoform a

      See identical proteins and their annotated locations for NP_000077.1

      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 isoform (a).
      Source sequence(s)
      AF077962, AI138575, AU105965, DA869025, U32680
      Consensus CDS
      CCDS10632.1
      UniProtKB/Swiss-Prot
      Q13286
      UniProtKB/TrEMBL
      A0A024QZB8
      Related
      ENSP00000353073.9, OTTHUMP00000122517, ENST00000359984.12, OTTHUMT00000214115
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein
    2. NM_001042432.1NP_001035897.1  battenin isoform a

      See identical proteins and their annotated locations for NP_001035897.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same isoform (a).
      Source sequence(s)
      AF077957, AI138575, DA552461, DB101039
      Consensus CDS
      CCDS10632.1
      UniProtKB/Swiss-Prot
      Q13286
      UniProtKB/TrEMBL
      A0A024QZB8
      Related
      ENSP00000490105.1, OTTHUMP00000282216, ENST00000636147.1, OTTHUMT00000489689
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein
    3. NM_001286104.1NP_001273033.1  battenin isoform b

      See identical proteins and their annotated locations for NP_001273033.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AK302027, DA703317
      Consensus CDS
      CCDS73855.1
      UniProtKB/Swiss-Prot
      Q13286
      Related
      ENSP00000353116.3, OTTHUMP00000254078, ENST00000360019.8, OTTHUMT00000430940
      Conserved Domains (1) summary
      pfam02487
      Location:40413
      CLN3; CLN3 protein
    4. NM_001286105.1NP_001273034.1  battenin isoform c

      See identical proteins and their annotated locations for NP_001273034.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and lacks two exons compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (c) with a shorter and distinct N-terminus compared to isoform a.
      Source sequence(s)
      AK297690, AK302027, BP252176
      UniProtKB/Swiss-Prot
      Q13286
      UniProtKB/TrEMBL
      B4DMY6
      Conserved Domains (1) summary
      pfam02487
      Location:27337
      CLN3; CLN3 protein
    5. NM_001286109.1NP_001273038.1  battenin isoform d

      See identical proteins and their annotated locations for NP_001273038.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence, the 3' UTR, and lacks an alternate in-frame exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (d) with a shorter N-terminus and missing an alternate internal segment compared to isoform a.
      Source sequence(s)
      BC111068, BP252176, DA869025
      Consensus CDS
      CCDS73853.1
      UniProtKB/TrEMBL
      Q2TA70
      Related
      ENSP00000454253.1, OTTHUMP00000254076, ENST00000568224.4, OTTHUMT00000430938
      Conserved Domains (1) summary
      pfam02487
      Location:1359
      CLN3; CLN3 protein
    6. NM_001286110.1NP_001273039.1  battenin isoform e

      See identical proteins and their annotated locations for NP_001273039.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (e) with a shorter N-terminus and missing an alternate internal segment compared to isoform a.
      Source sequence(s)
      AK294070, BP252176, DA869025
      Consensus CDS
      CCDS73854.1
      UniProtKB/TrEMBL
      B4DFF3
      Related
      ENSP00000350523.9, OTTHUMP00000254080, ENST00000357857.14, OTTHUMT00000430943
      Conserved Domains (1) summary
      pfam02487
      Location:1383
      CLN3; CLN3 protein

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

      Range
      28466653..28492302 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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