Human Gene CLN3 (uc002dpr.1)
  Description: Homo sapiens ceroid-lipofuscinosis, neuronal 3 (CLN3), transcript variant 2, mRNA.
RefSeq Summary (NM_000086): 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 (Including UTRs)
   Position: hg19 chr16:28,488,785-28,503,156 Size: 14,372 Total Exon Count: 14 Strand: -


Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionOther SpeciesmRNA DescriptionsPathwaysOther Names
GeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:28,488,785-28,503,156)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSEnsemblExonPrimerGeneNetworkH-INVHGNC
LynxMalacardsPubMedTreefamWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CLN3
CDC HuGE Published Literature: CLN3
Positive Disease Associations: Crohn Disease , inflammatory bowel disease (early onset)
Related Studies:
  1. Crohn Disease
    Andre Franke et al. Nature genetics 2010, Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci., Nature genetics. [PubMed 21102463]
  2. inflammatory bowel disease (early onset)
    Imielinski ,et al. 2009, Common variants at five new loci associated with early-onset inflammatory bowel disease, Nature genetics 2009 41- 12 : 1335-40. [PubMed 19915574]

-  MalaCards Disease Associations
  MalaCards Gene Search: CLN3
Diseases sorted by gene-association score: ceroid lipofuscinosis, neuronal, 3* (1725), neuronal ceroid-lipofuscinoses* (108), neuronal ceroid lipofuscinosis (31), peripheral retinal degeneration (19), ceroid lipofuscinosis, neuronal, 2 (15), ceroid lipofuscinosis, neuronal, 1 (14), retinal degeneration (13), lysosomal storage disease (11), secondary corneal edema (11), epilepsy, progressive myoclonic 2b (9), bladder neck obstruction (8), ceroid lipofuscinosis, neuronal, 10 (8), phelan-mcdermid syndrome (6), lipid storage disease (6), epileptic encephalopathy, childhood-onset (5), wolfram syndrome 2 (5), ceroid lipofuscinosis, neuronal, 11 (5), inherited metabolic disorder (5), unverricht-lundborg syndrome (4), retinitis pigmentosa (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.16 RPKM in Colon - Transverse
Total median expression: 109.35 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  BC111068 - Homo sapiens ceroid-lipofuscinosis, neuronal 3, mRNA (cDNA clone MGC:102840 IMAGE:5764535), complete cds.
BC002394 - Homo sapiens ceroid-lipofuscinosis, neuronal 3, mRNA (cDNA clone MGC:8415 IMAGE:2820893), complete cds.
BC004433 - Homo sapiens ceroid-lipofuscinosis, neuronal 3, mRNA (cDNA clone MGC:3974 IMAGE:2820893), complete cds.
U32680 - Homo sapiens CLN3 protein (CLN3) mRNA, complete cds.
AK294070 - Homo sapiens cDNA FLJ60087 complete cds, highly similar to Protein CLN3.
AK302027 - Homo sapiens cDNA FLJ58551 complete cds, highly similar to Protein CLN3.
AK090709 - Homo sapiens cDNA FLJ33390 fis, clone BRACE2006900, highly similar to CLN3 PROTEIN.
AX746584 - Sequence 109 from Patent EP1308459.
AK297690 - Homo sapiens cDNA FLJ59353 complete cds, highly similar to Protein CLN3.
JD099989 - Sequence 81013 from Patent EP1572962.
AF015593 - Homo sapiens CLN3 protein (CLN3) mRNA, complete cds.
AF015595 - Homo sapiens CLN3 protein (CLN3) mRNA, complete cds.
JD280455 - Sequence 261479 from Patent EP1572962.
AF015598 - Homo sapiens CLN3 protein (CLN3) mRNA, complete cds.
AF077956 - Homo sapiens clone 412 CLN3 protein (CLN3) mRNA, complete cds.
AF077957 - Homo sapiens clone 313 CLN3 protein (CLN3) mRNA, complete cds.
AF077958 - Homo sapiens clone 301 CLN3 protein (CLN3) mRNA, complete cds.
AF077959 - Homo sapiens clone 305 CLN3 protein (CLN3) mRNA, complete cds.
AF077960 - Homo sapiens clone 318 CLN3 protein (CLN3) mRNA, complete cds.
AF077961 - Homo sapiens clone 327 CLN3 protein (CLN3) mRNA, complete cds.
AF077962 - Homo sapiens clone 333 CLN3 protein (CLN3) mRNA, complete cds.
AF077963 - Homo sapiens clone 324 CLN3 protein (CLN3) mRNA, complete cds.
AF077964 - Homo sapiens clone 326 CLN3 protein (CLN3) mRNA, complete cds.
AF077965 - Homo sapiens clone 319 CLN3 protein (CLN3) mRNA, complete cds.
AF077966 - Homo sapiens clone 506 CLN3 protein (CLN3) mRNA, complete cds.
AF077967 - Homo sapiens clone 509 CLN3 protein (CLN3) mRNA, complete cds.
AF077968 - Homo sapiens clone 503 CLN3 protein (CLN3) mRNA, complete cds.
AF077969 - Homo sapiens clone 515 CLN3 protein (CLN3) mRNA, complete cds.
AF077970 - Homo sapiens clone 517 CLN3 protein (CLN3) mRNA, complete cds.
AF077971 - Homo sapiens clone 21 CLN3 protein (CLN3) mRNA, complete cds.
AF077972 - Homo sapiens clone 32 CLN3 protein (CLN3) mRNA, complete cds.
AF077973 - Homo sapiens clone 36 CLN3 protein (CLN3) mRNA, complete cds.
AF078169 - Homo sapiens CLN3 protein (CLN3) mRNA, complete cds.
AK313002 - Homo sapiens cDNA, FLJ93467, highly similar to Homo sapiens ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) (CLN3), mRNA.
AF015594 - Homo sapiens CLN3 protein (CLN3) mRNA, partial cds.
AF015600 - Homo sapiens CLN3 protein (CLN3) mRNA, partial cds.
AK302138 - Homo sapiens cDNA FLJ59098 complete cds, highly similar to Protein CLN3.
EF587244 - Homo sapiens mutant CLN3 (CLN3) mRNA, partial cds, alternatively spliced.
AF015601 - Homo sapiens CLN3 protein (CLN3) mRNA, partial cds.
AF015597 - Homo sapiens CLN3 protein (CLN3) mRNA, partial cds.
AK294250 - Homo sapiens cDNA FLJ59870 complete cds, highly similar to Protein CLN3.
AK295500 - Homo sapiens cDNA FLJ59896 complete cds, highly similar to Protein CLN3.
AF015599 - Homo sapiens CLN3 protein (CLN3) mRNA, partial cds.
AF015602 - Homo sapiens CLN3 protein (CLN3) mRNA, partial cds.
EF587245 - Homo sapiens mutant CLN3 (CLN3) mRNA, partial cds, alternatively spliced.
AF015596 - Homo sapiens CLN3 protein (CLN3) mRNA, partial cds.
AF078168 - Homo sapiens CLN3 protein (CLN3) mRNA, alternative splice product, partial cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04142 - Lysosome

-  Other Names for This Gene
  Alternate Gene Symbols: AF077968
UCSC ID: uc002dpr.1
RefSeq Accession: NM_000086

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CLN3:
dystonia-ov (Hereditary Dystonia Overview)

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: yes RNA accession: AF077968.1
exon count: 14CDS single in 3' UTR: no RNA size: 1225
ORF size: 0CDS single in intron: no Alignment % ID: 99.92
txCdsPredict score: 876.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.