CLN3 Gene
protein-coding GIFtS: 62
GCID: GC16M028488
|
|
ceroid-lipofuscinosis, neuronal 3(Previous names: Batten, Spielmeyer-Vogt disease )
(Previous symbol: BTS)
| |
Aliases
for CLN3 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Ceroid-Lipofuscinosis, Neuronal 31 2 | | Batten, Spielmeyer-Vogt Disease1 | | BTS1 2 3 5 | | Battenin1 | | JNCL1 2 | | Protein CLN33 | | Batten Disease Protein2 3 | | |
Export aliases for CLN3 gene to outside databasesPrevious GC identifers: GC16P028406 GC16P028790 GC16P028559 GC16P028601 GC16M028396 GC16M026514 |
Summaries
for CLN3 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for CLN3:
This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronalceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectivelyknown as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have been found forthis gene. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286Function: Involved in microtubule-dependent, anterograde transport of late endosomes and lysosomes
Gene Wiki entry for CLN3
|
Genomic Views
for CLN3 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000016.9 NC_018927.1 NT_010393.16
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the CLN3 gene promoter:
AP-1 ATF-2 c-Jun IRF-1
Other transcription factors
Search SABiosciences Chromatin IP Primers for CLN3
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLN3 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 16p12.1 Ensembl cytogenetic band: 16p11.2 HGNC cytogenetic band: 16p12CLN3 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 16 GeneLoc Exon Structure GeneLoc location for GC16M028488: view genomic region
(about GC identifiers)
Start:
|
28,477,983 bp from pter |
End:
|
28,506,896 bp from pter |
Size:
|
28,914 bases |
Orientation:
|
minus strand |
|
Proteins
for CLN3 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286 (See
protein sequence)Recommended Name: Battenin Size: 438 amino acids; 47623 Da
Subunit: Interacts with DCTN1 and KIF3A. Interacts with RAB7A and RILP
Subcellular location: Lysosome membrane; Multi-pass membrane protein. Late endosome
Secondary accessions: B2R7J1 O00668 Q549S9 Q9UP09 Q9UP11 Q9UP12 Q9UP13 Q9UP14Alternative splicing: 5 isoforms: Q13286-1 Q13286-2 Q13286-3 Q13286-4 Q13286-5 (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)Explore the universe of human proteins at neXtProt for CLN3: NX_Q13286
Post-translational modifications:
Highly glycosylated1
Farnesylation is important for trafficking to lysosomes1
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q13286
CLN3 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (2 alternative transcripts):
NP_000077.1 NP_001035897.1
ENSEMBL proteins: ENSP00000454466 ENSP00000454229 ENSP00000329171 ENSP00000350457 ENSP00000350523 ENSP00000455387 ENSP00000379014 ENSP00000455549 ENSP00000456693 ENSP00000454680 ENSP00000456117 ENSP00000455342 ENSP00000455603 ENSP00000456414 ENSP00000456013 ENSP00000458015 ENSP00000456122 ENSP00000457615 ENSP00000454899 ENSP00000455365 ENSP00000353116 ENSP00000353073 ENSP00000346650 ENSP00000347660 ENSP00000443221 ENSP00000349586
Human Recombinant Protein Products:
Gene Ontology (GO): 5/21 cellular component terms (GO ID links to tree view) (see all 21): About this table
CLN3 for ontologies About GeneDecksing
CLN3 Antibody Products:
Assay Products for CLN3: |
Protein
Domains /
Families
for CLN3 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
CLN3 for domains About GeneDecksing
3 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q13286ProtoNet protein and cluster: Q13286 1 Blocks protein family: IPB003492 CLN3 Batten's disease protein (battenin) signature
UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286Similarity: Belongs to the battenin family |
Function
for CLN3 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Function Summary:
UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286Function: Involved in microtubule-dependent, anterograde transport of late endosomes and lysosomes Genatlas biochemistry entry for CLN3:integral lysosomal membrane protein battenin,highly conserved,with alternatively spliced forms,expressed inastrocytes,capillary endothelium and neurons of gray matter of the brain in peripheral nerve,pancreatic islet cellsand within the seminiferous tubules of the testis,involved in synaptic trafficking through the endoplasmic reticulumand Golgi,potentially protecting neurons from apoptosis mediated by ceramide,yeast BTN1 ortholog
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CLN3 (see all 5)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CLN3 (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector (see all 2): CLN3 (NM_001042432) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for CLN3 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLN3 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLN3 |
Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table
CLN3 for ontologies About GeneDecksing
2 GenomeRNAi human phenotypes for CLN3:
Animal Models:
Mouse knock-outs for CLN3: Cln3tm1Mkat Cln3tm1Mem Cln3tm1Nbm Cln3tm1.1Mem
10 MGI mutant phenotypes (inferred from 5 alleles ) (MGI details for Cln3):
CLN3 for phenotypes About GeneDecksing
|
Pathways & Interactions
for CLN3 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Unified GeneCards pathways About this table
See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | Lysosome | |
Pathway sources
See GeneCards unified pathways
Show all pathways
1 
Kegg Pathway (Kegg details for CLN3):
CLN3 for pathways About GeneDecksing
Interactions:
SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for CLN3
STRING Interaction
Network Preview (showing 5 interactants - click image to see 25)
5/674 Interacting proteins for CLN3 (Q132863 ENSP000003530734) via UniProtKB, MINT, STRING, and/or I2D (see all 674)About this table
Gene Ontology (GO): 5/32 biological process terms (GO ID links to tree view) (see all 32): About this table
CLN3 for ontologies About GeneDecksing
|
Drugs & Compounds
for CLN3 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
CLN3 for compounds About GeneDecksing
 Browse Tocris compounds for CLN3
8 Novoseek chemical compound relationships for CLN3 gene About this table
Search CenterWatch for drugs/clinical trials and news about CLN3
|
Transcripts
for CLN3 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for CLN3 gene (2 alternative transcripts): NM_000086.2 NM_001042432.1 Unigene Cluster for CLN3: Ceroid-lipofuscinosis, neuronal 3 Hs.534667 [show with all ESTs]Unigene Representative Sequence: AK09070918/41 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 41): ENST00000564091 ENST00000569430 ENST00000333496 ENST00000563874(uc002dqa.2 uc010vcx.1)
ENST00000357806(uc021tfs.1) ENST00000357857 ENST00000567963(uc002dpx.1)
ENST00000395653 ENST00000565354 ENST00000568422 ENST00000566057 ENST00000569030
ENST00000565316 ENST00000568452 ENST00000568076 ENST00000561689 ENST00000565140
ENST00000568558(uc002dpy.1)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CLN3 (see all 5)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CLN3 (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector (see all 2): CLN3 (NM_001042432) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for CLN3 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLN3 |
Additional cDNA sequence: AF015593.1 AF015594.1 AF015595.1 AF015596.1 AF015597.1 AF015598.1 AF015599.1 AF015600.1 AF015601.1 AF015602.1 AF077956.1 AF077957.1 AF077958.1 AF077959.1 AF077960.1 AF077961.1 AF077962.1 AF077966.1 AF077970.1 AF077971.1 AF077972.1 AF078168.1 AF078169.1 AK090709.1 AK294070.1 AK294250.1 AK295500.1 AK297690.1 AK302027.1 AK302138.1 AK313002.1 BC002394.2 BC004433.1 BC111068.1 U32680.1 24/37 DOTS entries (see all 37): DT.87018129 DT.100867986 DT.95239976 DT.100831826 DT.95368403 DT.100868011 DT.92457282 DT.95368415 DT.92457287 DT.92457300 DT.97860083 DT.100868007 DT.100868000 DT.120696604 DT.120696706 DT.92457289 DT.92457297 DT.100868006 DT.120696247 DT.100844156 DT.120695125 DT.91867272 DT.100868014 DT.102843670 24/260 AceView cDNA sequences (see all 260): BU619787 CR620473 CR605499 AI355261 BM781749 BM739110 CR591558 CA453983 BQ963046 BI870454 CR613621 BM741475 BX402900 BM772581 BX384288 BQ929206 AX746584 AF078168 CR601899 BM917287 AI393924 BM753441 AL555221 T08995
GeneLoc Exon Structure
5/25 Alternative Splicing Database (ASD) splice patterns (SP) for CLN3 (see all 25) About this scheme
| ExUns: | 1 | ^ | 2 | ^ | 3a | · | 3b | · | 3c | ^ | 4a | · | 4b | · | 4c | · | 4d | · | 4e | · | 4f | · | 4g | · | 4h | ^ | 5 | ^ | 6 | ^ | 7a | · | 7b | ^ | 8 | ^ | 9 | ^ | 10a | · | 10b | ^ | 11 | ^ | 12 | ^ | 13a | · | 13b | · | 13c | ^ |
|---|
|
| SP1: | | | | | | | | | | | - | | - | | - | | - | | - | | | | | | | | | | - | | | | | | | | | | | | | | | | | | - | | | | | | |
| SP2: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | | | | | | | | | | | | | | | | | - | | | | | | |
| SP3: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | | | | | | | - | | | | | | | | | | - | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | | | | | | | | | | | | | | | | | - | | | | | | |
| SP5: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | | | | | | | | | | | | | | | | | - | | | | | |
| ExUns: | 14a | · | 14b | ^ | 15a | · | 15b | ^ | 16 | ^ | 17a | · | 17b | · | 17c | ^ | 18 | ^ | 19a | · | 19b | · | 19c | · | 19d | · | 19e |
|---|
|
| SP1: | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP3: | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP4: | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | - | | - | | | | | | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for CLN3
|
Expression
for CLN3 gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| CLN3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CCTTCTGAAT
About this image
See CLN3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CLN3
SOURCE GeneReport for Unigene cluster: Hs.534667
SABiosciences Expression via Pathway-Focused PCR Arrays including CLN3:
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for CLN3
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat CLN3 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CLN3 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CLN3 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLN3 |
Orthologs
for CLN3 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of animals and fungi.
Orthologs for CLN3 gene from 7/27 species (see all 27) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
mouse
(Mus musculus) |
Mammalia |
Cln31 , 5 |
ceroid lipofuscinosis, neuronal 3, juvenile (Batten, more1, 5 |
82.91(n)1
86.04(a)1 |
|
7 (69.16 cM)5
127521 NM_001146311.11 NP_001139783.11
1265712075 |
lizard
(Anolis carolinensis) |
Reptilia |
CLN36 |
-- |
57(a) |
1 → many |
GL343287.1(735505-750833) |
African clawed frog
(Xenopus laevis) |
Amphibia |
Xl.152912 |
Xenopus laevis transcribed sequence with weak similarity more |
76.05(n) |
|
48012878 |
zebrafish
(Danio rerio) |
Actinopterygii |
Dr.31672 |
Transcribed sequence with weak similarity to protein more |
72.42(n) |
|
57057328 |
fruit fly
(Drosophila melanogaster) |
Insecta |
CG55823
cln31 |
CG5582-PA1 |
40(a)3
52.33(n)1
45.38(a)1 |
|
75A43
399811 NM_140754.11 NP_649011.11 |
worm
(Caenorhabditis elegans) |
Secernentea |
cln-3.13
cln-3.21 |
Human CLN3 protein like3
Protein CLN-3.21 |
40(a)
(best of 3)3
48.94(n)1
45.55(a)1 |
|
V(11266193-11268210)3
1721711 NM_059155.51 NP_491556.11 |
baker's yeast
(Saccharomyces cerevisiae) |
Saccharomycetes |
YHC3(YJL059W)4
YHC31 |
Vacuolar membrane protein involved in the ATP-dependent more4
Yhc3p1 |
45.75(n)1
41.37(a)1 |
|
10(324964-326190)4
8533871, 4 NP_012476.11, 4 |
ENSEMBL Gene Tree for CLN3 (if available)
TreeFam Gene Tree for CLN3 (if available) |
Paralogs
for CLN3 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for CLN3 gene
- ENSG000002618322
CLN3 for paralogs About GeneDecksing
|
Genomic Variants
for CLN3 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 16 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
|
|
|
