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Set Analyses:

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CLN3 Gene

protein-coding GIFtS: 63
GCID: GC16M028488

Ceroid-Lipofuscinosis, Neuronal 3

(Previous names: Batten, Spielmeyer-Vogt disease)
(Previous symbol: BTS)

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Aliases
Ceroid-Lipofuscinosis, Neuronal 3¹ ²		Juvenile Neuronal Ceroid Lipofuscinosis¹
BTS¹ ² ³ ⁵		JNCL²
Batten Disease Protein² ³		battenin²
Batten, Spielmeyer-Vogt Disease¹		Protein CLN3³

External Ids:	HGNC: 2074¹	Entrez Gene: 1201²	Ensembl: ENSG00000188603⁷	OMIM: 607042⁵	UniProtKB: Q13286³

Export aliases for CLN3 gene to outside databases

Previous GC identifers: GC16P028406 GC16P028790 GC16P028559 GC16P028601 GC16M028396 GC16M026514

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CLN3 Gene:

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)

GeneCards Summary for CLN3 Gene:

CLN3 (ceroid-lipofuscinosis, neuronal 3) is a protein-coding gene. Diseases associated with CLN3 include neuronal ceroid lipofuscinosis, and spielmeyer-vogt disease. GO annotations related to this gene include unfolded protein binding. An important paralog of this gene is ENSG00000261832.

UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286

Function: Involved in microtubule-dependent, anterograde transport of late endosomes and lysosomes

Gene Wiki entry 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:

NC_000016.10 NC_018927.2 NT_187260.1

Regulatory elements:

Regulatory transcription factor binding sites in the CLN3 gene promoter:
AP-1 ATF-2 c-Jun IRF-1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: CLN3 promoter sequence

Search Chromatin IP Primers for CLN3

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing 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: 16p12

CLN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLN3 gene location

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

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286 (See protein sequence)

Recommended Name: Battenin precursor

Size: 438 amino acids; 47623 Da

Subunit: Interacts with DCTN1 and KIF3A. Interacts with RAB7A and RILP

Secondary accessions: B2R7J1 O00668 O95089 Q549S9 Q9UP09 Q9UP11 Q9UP12 Q9UP13 Q9UP14

Alternative splicing: 6 isoforms: Q13286-1 Q13286-2 Q13286-3 Q13286-4 Q13286-5 Q13286-6 (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

Explore proteomics data for CLN3 at MOPED

Post-translational modifications:

Highly glycosylated¹

Farnesylation is important for trafficking to lysosomes¹

Ubiquitination² at Lys262

Glycosylation² at Asn71, Thr80, Asn85, Asn310

Modification sites at PhosphoSitePlus

See CLN3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (6 alternative transcripts):

NP_000077.1 NP_001035897.1 NP_001273033.1 NP_001273034.1 NP_001273038.1 NP_001273039.1

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

CLN3 Human Recombinant Protein Products:

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	GenScript Custom Purified and Recombinant Proteins Services for CLN3
	Novus Biologicals CLN3 Protein Novus Biologicals CLN3 Lysates
	Browse Sino Biological Recombinant Proteins Browse Sino Biological Cell Lysates
	Browse ProSpec Recombinant Proteins
	Browse Proteins at Cloud-Clone Corp.

CLN3 Antibody Products:

	Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Browse R&D Systems for Antibodies
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	Novus Biologicals CLN3 Antibodies
	Abcam antibodies for CLN3
	Browse Antibodies at Cloud-Clone Corp.
	Search ThermoFisher Antibodies for CLN3
	LSBio Antibodies in human, mouse, rat for CLN3

CLN3 Assay Products:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Assay Services for CLN3
	Browse R&D Systems for biochemical assays
	GenScript Custom Assay Services for CLN3
	Browse Enzo Life Sciences for kits & assays
	Browse ELISAs at Cloud-Clone Corp. Browse CLIAs at Cloud-Clone Corp.

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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3 InterPro protein domains:

IPR018460 Battenin_disease_Cln3_subgr

IPR003492 Battenin_disease_Cln3

IPR016196 MFS_dom_general_subst_transpt

Graphical View of Domain Structure for InterPro Entry Q13286

ProtoNet protein and cluster: Q13286

1 Blocks protein domain: IPB003492 CLN3 Batten's disease protein (battenin) signature

UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286

Similarity: Belongs to the battenin family

CLN3 for domains About GeneDecksing

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: CLN3_HUMAN, Q13286

Function: 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 in

astrocytes,capillary endothelium and neurons of gray matter of the brain in peripheral nerve,pancreatic islet

cells and within the seminiferous tubules of the testis,involved in synaptic trafficking through the endoplasmic

reticulum and Golgi,potentially protecting neurons from apoptosis mediated by ceramide,yeast BTN1 ortholog

Gene Ontology (GO): 2 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	IPI	12134079
GO:0051082	unfolded protein binding	TAS	8980123

CLN3 for ontologies About GeneDecksing

Phenotypes:
2 GenomeRNAi human phenotypes for CLN3:

Decreased Tat-dependent transc

Decreased p24 protein expressi

10 MGI mutant phenotypes (inferred from 5 alleles) (MGI details for Cln3):

behavior/neurological	cellular	homeostasis/metabolism	liver/biliary system	mortality/aging
nervous system	no phenotypic analysis	renal/urinary system	reproductive system	vision/eye

CLN3 for phenotypes About GeneDecksing

Animal Models:
MGI mouse knock-outs for CLN3: Cln3^tm1Mkat Cln3^tm1Mem Cln3^tm1Nbm Cln3^tm1.1Mem

inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CLN3

inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CLN3

genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CLN3

genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CLN3

miRNA Products:		miRTarBase miRNAs that target CLN3: hsa-mir-7-5p (MIRT025765), hsa-mir-877-3p (MIRT037057)

		Block miRNA regulation of human, mouse, rat CLN3 using miScript Target Protectors
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Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for CLN3
		Predesigned siRNA for gene silencing in human, mouse, rat CLN3

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for CLN3

Clone Products:		OriGene clones in human, mouse for CLN3 (see all 11) OriGene ORF clones in mouse, rat for CLN3 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

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for CLN3
		Browse ESI BIO Cell Lines and PureStem Progenitors for CLN3

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLN3

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

CLN3_HUMAN, Q13286: Lysosome membrane; Multi-pass membrane protein. Late endosome

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
endoplasmic reticulum	5
endosome	5
golgi apparatus	5
lysosome	5
nucleus	5
plasma membrane	5
vacuole	5
mitochondrion	4

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Gene Ontology (GO): Selected cellular component terms (see all 21): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000139	Golgi membrane	IDA	10191111
GO:0005634	nucleus	IDA	10191116
GO:0005737	cytoplasm	IDA	10191116
GO:0005739	mitochondrion	TAS	8980123
GO:0005764	lysosome	IDA	10924275

CLN3 for ontologies About GeneDecksing

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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SuperPaths for CLN3 About

See pathways by source

SuperPath

Contained pathways About

Lysosome

Lysosome

Pathways by source See SuperPaths
Show all pathways

1 Kegg Pathway (Kegg details for CLN3):

Lysosome

CLN3 for pathways About GeneDecksing

Pathway & Disease-focused RT² Profiler PCR Arrays including CLN3:

GABA & Glutamate in human mouse rat

Autophagy in human mouse rat

Prostate Cancer in human mouse rat

Interactions:

GeneGlobe Interaction Network for CLN3

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for CLN3 (Q13286³ ENSP00000353073⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 715)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
HIST1H4A	P62805³	I2D: score=1
HIST1H4B	P62805³	I2D: score=1
HIST1H4C	P62805³	I2D: score=1
HIST1H4D	P62805³	I2D: score=1
HIST1H4E	P62805³	I2D: score=1

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Gene Ontology (GO): Selected biological process terms (see all 32): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000046	autophagic vacuole fusion	ISS	--
GO:0001508	action potential	ISS	--
GO:0001575	globoside metabolic process	IMP	15240864
GO:0006457	protein folding	TAS	8980123
GO:0006520	cellular amino acid metabolic process	ISS	--

CLN3 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for CLN3

8 Novoseek inferred chemical compound relationships for CLN3 gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
mannose 6-phosphate	42.5	2	17286803 (1), 9878558 (1)
ceramide	33.6	7	10191118 (3), 16151633 (2)
atp	10.8	2	11589015 (1), 10356317 (1)
arginine	4.06	3	14660799 (2), 17896996 (1)
glutamate	1.58	2	9490299 (1), 9450775 (1)
lysine	0	1	9450775 (1)
lipid	0	4	17896996 (1), 18317235 (1), 17237713 (1), 15094366 (1)
serine	0	1	9878558 (1)

CLN3 for compounds About GeneDecksing

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for CLN3 gene (6 alternative transcripts):

NM_000086.2 NM_001042432.1 NM_001286104.1 NM_001286105.1 NM_001286109.1 NM_001286110.1

Unigene Cluster for CLN3:

Ceroid-lipofuscinosis, neuronal 3

Hs.534667 [show with all ESTs]

Unigene Representative Sequence: AK090709

Selected 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)

miRNA Products:		Block miRNA regulation of human, mouse, rat CLN3 using miScript Target Protectors
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		Predesigned siRNA for gene silencing in human, mouse, rat CLN3

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		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

Primer Products:		OriGene qPCR primer pairs and template standards for CLN3 OriGene qSTAR qPCR primer pairs in human, mouse for CLN3
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat CLN3
		QuantiTect SYBR Green Assays in human, mouse, rat CLN3
		QuantiFast Probe-based Assays in human, mouse, rat CLN3

Additional mRNA 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

Selected 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

Selected AceView cDNA sequences (see all 260):

BI761771 BQ067057 AL536863 CA444377 BM726882 CR613621 AL555221 AU121777

CR605499 BM923971 BI490061 AK090709 T08995 BM795168 BG696720 BU150620

CR597053 AF077971 CR601899 AU099671 BX393642 AI355261 BU619787 CB117283

GeneLoc Exon Structure

Selected 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

(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™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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CLN3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: CCTTCTGAAT

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CLN3 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

CLN3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.534667

Pathway & Disease-focused RT² Profiler PCR Arrays including CLN3:

GABA & Glutamate in human mouse rat

Autophagy in human mouse rat

Prostate Cancer in human mouse rat

Primer Products:		OriGene qPCR primer pairs and template standards for CLN3 OriGene qSTAR qPCR primer pairs in human, mouse for CLN3
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat CLN3
		QuantiTect SYBR Green Assays in human, mouse, rat CLN3
		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 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)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for CLN3 gene from Selected species (see all 19) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Cln3^{1 , 5}	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, more^{1, 5}	82.91(n)¹ 86.04(a)¹		7 (69.16 cM)⁵ 12752¹ NM_009907.3¹ NP_034037.3¹ 126571207⁵
lizard (Anolis carolinensis)	Reptilia	--	Uncharacterized protein	56(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	cln3¹	40(a)³ 52.67(n)¹ 46.26(a)¹		75A4³ 39981¹ NM_140754.2¹ NP_649011.1¹
worm (Caenorhabditis elegans)	Secernentea	cln-3.1³ cln-3.2¹	Human CLN3 protein like³ cln-3.2¹	40(a) (best of 3)³ 48.94(n)¹ 45.8(a)¹		V(11266193-11268210)³ 172171¹ NM_059155.6¹ NP_491556.1¹
baker's yeast (Saccharomyces cerevisiae)	Saccharomycetes	YHC3(YJL059W)⁴ YHC3¹	Vacuolar membrane protein involved in the ATP-dependent more⁴ YHC3¹	46.35(n)¹ 44.32(a)¹		10(324964-326190)⁴ 853387^{1, 4} NP_012476.1^{1, 4}

ENSEMBL Gene Tree for CLN3 (if available)
TreeFam Gene Tree for CLN3 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for CLN3 gene

ENSG00000261832²

CLN3 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr 16 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
VAR_005134⁴		Ceroid lipofuscinosis, neuronal, 3 (CLN3)⁴	--	see VAR_005134	2	V F	mis⁴		0	--	--	--	--
VAR_005132⁴		Ceroid lipofuscinosis, neuronal, 3 (CLN3)⁴	--	see VAR_005132	2	L P	mis⁴		0	--	--	--	--
VAR_005131⁴		Ceroid lipofuscinosis, neuronal, 3 (CLN3)⁴	--	see VAR_005131	2	L P	mis⁴		0	--	--	--	--
VAR_005135⁴		Ceroid lipofuscinosis, neuronal, 3 (CLN3)⁴	--	see VAR_005135	2	R C	mis⁴		0	--	--	--	--
VAR_066894⁴		Ceroid lipofuscinosis, neuronal, 3 (CLN3)⁴	--	see VAR_066894	2	G R	mis⁴		0	--	--	--	--
VAR_066893⁴		Ceroid lipofuscinosis, neuronal, 3 (CLN3)⁴	--	see VAR_066893	2	G A	mis⁴		0	--	--	--	--
VAR_005136⁴		Ceroid lipofuscinosis, neuronal, 3 (CLN3)⁴	--	see VAR_005136	2	R H	mis⁴		0	--	--	--	--
VAR_005133⁴		Ceroid lipofuscinosis, neuronal, 3 (CLN3)⁴	--	see VAR_005133	2	E K	mis⁴		0	--	--	--	--
VAR_066892⁴		Ceroid lipofuscinosis, neuronal, 3 (CLN3)⁴	--	see VAR_066892	2	C R	mis⁴		0	--	--	--	--
rs138665362^1,2	C	--	26531542(+)	`TGGCT-/GGGTGGC`	1	--	us2k¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for CLN3 (28477983 - 28506896 bp)

Structural Variations
Database of Genomic Variants (DGV) 8 variations for CLN3: About this table

Variant ID	Type	Subtype	PubMed ID
esv2673092	CNV	Deletion	23128226
nsv509608	CNV	Insertion	20534489
nsv103376	CNV	Loss	16902084
nsv833180	CNV	Loss	17160897
nsv9415	CNV	Gain	18304495
nsv905688	CNV	Gain	21882294
dgv842e1	CNV	Complex	17122850
dgv843e1	CNV	Complex	17122850

Human Gene Mutation Database (HGMD): CLN3
Locus Specific Mutation Databases (LSDB): CLN3

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing CLN3

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 607042
OMIM disorders: 204200
UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286

Ceroid lipofuscinosis, neuronal, 3 (CLN3) [MIM:204200]: A form of neuronal ceroid lipofuscinosis.

Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by

intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual

loss, and/or cerebral atrophy. The hallmark of CLN3 is the ultrastructural pattern of lipopigment with a

fingerprint profile, which can have 3 different appearances: pure within a lysosomal residual body; in

conjunction with curvilinear or rectilinear profiles; and as a small component within large membrane-bound

lysosomal vacuoles. The combination of fingerprint profiles within lysosomal vacuoles is a regular feature of

blood lymphocytes from patients with neuronal ceroid lipofuscinosis type 3. Note=The disease is caused by

mutations affecting the gene represented in this entry

Selected diseases for CLN3 (see all 37):
About MalaCards

neuronal ceroid lipofuscinosis spielmeyer-vogt disease blue toe syndrome batten disease

juvenile batten disease northern epilepsy neuroretinitis neuronal ceroid-lipofuscinoses

lafora disease neuronitis peripheral retinal degeneration blue cone monochromacy

late-infantile neuronal ceroid lipofuscinosis progressive myoclonus epilepsy myoclonus epilepsy cerebral atrophy

myoclonus epilepsy syndrome retinal degeneration lysosomal storage disease

3 diseases from the University of Copenhagen DISEASES database for CLN3:

Neuronal ceroid lipofuscinosis Neurodegenerative disease Blindness

CLN3 for disorders About GeneDecksing

Congresses - knowledge worth sharing:
The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

Selected Novoseek inferred disease relationships for CLN3 gene (see all 12) About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
batten disease	98.3	95	10527801 (4), 11590129 (4), 10916181 (3), 14699076 (3) (see all 55)
neuronal ceroid lipofuscinoses	96	9	15032383 (2), 11001812 (1), 17896996 (1), 18552385 (1) (see all 6)
lincl	92.4	8	11339651 (2), 9097964 (1), 9458173 (1), 10446748 (1) (see all 6)
neurodegenerative diseases	79.3	17	14644441 (2), 11589015 (1), 20015955 (1), 17896996 (1) (see all 16)
lysosomal storage diseases	73.2	1	18314010 (1)
lafora disease	58.5	1	11579433 (1)
neurodegeneration	55.7	2	10191118 (1), 11921051 (1)
retinal degeneration	53.9	2	10964839 (1), 18265413 (1)
chromosome deletion	53.2	2	9490299 (1), 9450775 (1)
visual loss	46.4	1	16720047 (1)

Genatlas disease: CLN3

ceroid-lipofuscinosis,neuronal 3,juvenile,Batten (Spielmeyer-Vogt-Sjogren) disease,progressive neurodegenerative

disease with an onset between 5 and 10 years,characterized by retinitis pigmentosa and a rapid loss of vision

with macular and peripheral retinal degeneration,cognitive and motor dysfunction,seizures in childhood,a fatal

outcome within a decade,and a characteristic fingerprint profile inclusions in different cells,including the

variant form with granular osmiophilic deposits (GROD)

GeneTests: CLN3
GeneReviews: CLN3
Genetic Association Database (GAD): CLN3
Human Genome Epidemiology (HuGE) Navigator: CLN3 (2 documents)

Export disorders for CLN3 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for CLN3 gene, integrated from 10 sources (see all 178):
(articles sorted by number of sources associating them with CLN3)

Utopia: connect your pdf to the dynamic
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Expression studies of CLN3 protein (battenin) in fusion with the green fluorescent protein in mammalian cells in vitro. (PubMed id 10191115)^{1, 2, 9} Golabek A.A....Wisniewski K.E. (Mol. Genet. Metab. 1999)
Genomic structure and complete nucleotide sequence of the Batten disease gene, CLN3. (PubMed id 9119403)^{1, 2, 9} Mitchison H.M.... Mole S.E. (Genomics 1997)
C-terminal prenylation of the CLN3 membrane glycoprotein is required for efficient endosomal sorting to lysosomes. (PubMed id 17286803)^{1, 2, 9} Storch S.... Braulke T. (Traffic 2007)
Spectrum of mutations in the Batten disease gene, CLN3. (PubMed id 9311735)^{1, 2, 9} Munroe P.B.... Mole S.E. (Am. J. Hum. Genet. 1997)
Molecular screening of Batten disease: identification of a missense mutation (E295K) in the CLN3 gene. (PubMed id 9490299)^{1, 2, 9} Zhong N.... Brown W.T. (Hum. Genet. 1998)
Isolation of a novel gene underlying Batten disease, CLN3. (PubMed id 7553855)^{1, 2, 9} Lerner T.J.... Mole S.E. (Cell 1995)
CLN3p impacts galactosylceramide transport, raft morphology, and lipid content. (PubMed id 18317235)^{1, 3, 9} Rusyn E....Boustany R.M. (Pediatr. Res. 2008)
Neuronal ceroid lipofuscinosis protein CLN3 interacts with motor proteins and modifies location of late endosomal compartments. (PubMed id 22261744)^{1, 2} Uusi-Rauva K.... Jalanko A. (Cell. Mol. Life Sci. 2012)
Genotype does not predict severity of behavioural phenotype in juvenile neuronal ceroid lipofuscinosis (Batten disease). (PubMed id 20187884)^{1, 4} Adams H.R....Mink J.W. (Dev Med Child Neurol 2010)
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. (PubMed id 21102463)^{1, 4} Franke A....Parkes M. (Nat. Genet. 2010)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 1201	HGNC: 2074	AceView: CLN3	Ensembl:ENSG00000188603	euGenes: HUgn1201
ECgene: CLN3	Kegg: 1201	H-InvDB: CLN3

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for CLN3	Pharmacogenomics, SNPs, Pathways
NCL CLN3	http://www.ucl.ac.uk/ncl/cln3.shtml
Mutations of the CLN3 gene	http://www.retina-international.org/files/sci-news/cln3mut.htm
GeneReviews	http://www.ncbi.nlm.nih.gov/books/NBK1116/?term=CLN3[genesymbol]

Intellectual Property for CLN3 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for CLN3 gene:
Search GeneIP for patents involving CLN3

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

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CLN3 Gene

Ceroid-Lipofuscinosis, Neuronal 3

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CLN3 Gene

Ceroid-Lipofuscinosis, Neuronal 3

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