CLN3 (CLN3 lysosomal/endosomal transmembrane protein, battenin) - Rat Genome Database

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Gene: CLN3 (CLN3 lysosomal/endosomal transmembrane protein, battenin) Sus scrofa
Analyze
Symbol: CLN3
Name: CLN3 lysosomal/endosomal transmembrane protein, battenin
RGD ID: 14257289
Description: ENCODES a protein that exhibits glycolipid binding (ortholog); INVOLVED IN actin cytoskeleton organization (ortholog); action potential (ortholog); amino acid transport (ortholog); ASSOCIATED WITH cone-rod dystrophy (ortholog); Disease Progression (ortholog); epilepsy (ortholog); FOUND IN autophagosome (ortholog); cytoplasm (ortholog); cytoplasmic vesicle (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: battenin; ceroid-lipofuscinosis, neuronal 3, juvenile; CLN3, battenin
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl318,433,559 - 18,450,293 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1318,433,564 - 18,450,296 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin cytoskeleton organization  (IEA,ISO)
action potential  (IEA,ISO)
amino acid transport  (ISO)
amyloid precursor protein catabolic process  (IEA)
arginine transport  (IBA,IEA)
associative learning  (IEA,ISO)
autophagosome maturation  (IEA,ISO)
autophagosome-lysosome fusion  (IEA)
cell migration  (IEA,ISO)
cellular water homeostasis  (IEA)
endocytosis  (ISO)
glycerophospholipid biosynthetic process  (IEA)
glycolipid transport  (IEA)
Golgi to lysosome transport  (IEA)
ionotropic glutamate receptor signaling pathway  (IEA,ISO)
learning or memory  (ISO)
lysosomal lumen acidification  (IBA,IEA)
lysosomal lumen pH elevation  (IEA)
lysosomal protein catabolic process  (IEA)
lysosome organization  (IBA,ISO)
macroautophagy  (ISO)
membrane organization  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of catalytic activity  (IEA,ISO)
negative regulation of neuron apoptotic process  (IEA,ISO)
negative regulation of proteolysis  (IEA,ISO)
neuromuscular process controlling balance  (IEA,ISO)
neurotransmitter metabolic process  (IEA,ISO)
phagosome-lysosome docking  (IEA)
phagosome-lysosome fusion  (IEA)
plasma membrane raft organization  (IEA)
positive regulation of caveolin-mediated endocytosis  (IEA)
positive regulation of Golgi to plasma membrane protein transport  (IEA)
positive regulation of pinocytosis  (IEA)
positive regulation of protein phosphorylation  (IEA,ISO)
protein localization to membrane  (ISO)
protein localization to plasma membrane  (IEA,ISO)
protein processing  (IEA,ISO)
receptor-mediated endocytosis  (IEA)
regulation of arginine biosynthetic process  (IEA)
regulation of autophagosome maturation  (IEA)
regulation of autophagosome size  (IEA)
regulation of autophagy  (ISO)
regulation of cellular response to osmotic stress  (IEA)
regulation of cytoskeleton organization  (IEA)
regulation of cytosolic calcium ion concentration  (IEA,ISO)
regulation of fibroblast migration  (IEA)
regulation of filopodium assembly  (IEA,ISO)
regulation of intracellular pH  (IBA)
regulation of modification of synaptic structure  (IEA)
regulation of phagosome maturation  (IEA)
regulation of protein localization to plasma membrane  (ISO)
regulation of protein processing  (IEA)
regulation of short-term neuronal synaptic plasticity  (IEA)
regulation of synaptic transmission, GABAergic  (IEA)
regulation of synaptic transmission, glutamatergic  (IEA)
renal potassium excretion  (IEA)
vesicle transport along microtubule  (IEA)

Molecular Function

References
Additional References at PubMed
PMID:14681463   PMID:17145712  


Genomics

Comparative Map Data
CLN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl318,433,559 - 18,450,293 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1318,433,564 - 18,450,296 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CLN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1628,474,111 - 28,495,575 (-)EnsemblGRCh38hg38GRCh38
GRCh381628,466,653 - 28,492,082 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371628,477,974 - 28,503,403 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361628,396,101 - 28,411,124 (-)NCBINCBI36hg18NCBI36
Build 341628,396,101 - 28,410,717NCBI
Celera1627,700,143 - 27,715,170 (+)NCBI
Cytogenetic Map16p12.1NCBI
HuRef1626,514,259 - 26,529,549 (-)NCBIHuRef
CHM1_11629,500,208 - 29,515,233 (-)NCBICHM1_1
Cln3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397126,170,379 - 126,184,989 (-)NCBIGRCm39mm39
GRCm39 Ensembl7126,170,379 - 126,184,989 (-)Ensembl
GRCm387126,571,207 - 126,585,817 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7126,571,207 - 126,585,817 (-)EnsemblGRCm38mm10GRCm38
MGSCv377133,714,914 - 133,727,794 (-)NCBIGRCm37mm9NCBIm37
MGSCv367126,362,548 - 126,374,368 (-)NCBImm8
Celera7126,395,665 - 126,433,408 (-)NCBICelera
Cytogenetic Map7F3NCBI
cM Map769.16NCBI
Cln3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21181,156,071 - 181,169,458 (-)NCBI
Rnor_6.0 Ensembl1197,986,385 - 197,997,664 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01197,986,384 - 197,999,726 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01204,965,144 - 204,978,485 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,713,096 - 185,724,375 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11185,862,977 - 185,874,256 (-)NCBI
Celera1178,814,090 - 178,825,369 (-)NCBICelera
Cytogenetic Map1q36NCBI
Cln3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554936,696,241 - 6,707,849 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554936,696,520 - 6,707,849 (-)NCBIChiLan1.0ChiLan1.0
CLN3
(Pan paniscus - bonobo/pygmy chimpanzee)
No map positions available.
CLN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1618,252,543 - 18,266,033 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl618,254,139 - 18,266,033 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha619,832,816 - 19,844,709 (+)NCBI
ROS_Cfam_1.0618,390,161 - 18,402,054 (+)NCBI
UMICH_Zoey_3.1618,189,180 - 18,201,073 (+)NCBI
UNSW_CanFamBas_1.0618,104,266 - 18,116,159 (+)NCBI
UU_Cfam_GSD_1.0618,420,341 - 18,432,234 (+)NCBI
Cln3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344123,857,474 - 123,870,439 (-)NCBI
SpeTri2.0NW_00493650111,955,334 - 11,967,338 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1526,320,132 - 26,343,009 (-)NCBI
ChlSab1.1 Ensembl526,320,061 - 26,337,402 (-)Ensembl
Vero_WHO_p1.0NW_0236660683,236,192 - 3,251,867 (+)NCBI
Cln3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478212,995,277 - 13,004,980 (-)NCBI


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 1 1
Low 10 4 3 4 2 23 2 2 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000041904   ⟹   ENSSSCP00000049546
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl318,433,836 - 18,450,293 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000058141   ⟹   ENSSSCP00000057536
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl318,433,559 - 18,450,293 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000068715   ⟹   ENSSSCP00000060511
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl318,433,559 - 18,450,293 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000069009   ⟹   ENSSSCP00000067756
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl318,433,836 - 18,450,035 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000086294   ⟹   ENSSSCP00000072004
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl318,433,559 - 18,450,293 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000086437   ⟹   ENSSSCP00000061618
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl318,433,836 - 18,448,183 (+)Ensembl
RefSeq Acc Id: NM_001113051   ⟹   NP_001106522
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1318,435,478 - 18,450,035 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021085539   ⟹   XP_020941198
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1318,433,913 - 18,450,296 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021085540   ⟹   XP_020941199
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1318,433,841 - 18,450,296 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021085541   ⟹   XP_020941200
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1318,433,913 - 18,450,296 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021085542   ⟹   XP_020941201
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1318,433,913 - 18,450,296 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021085543   ⟹   XP_020941202
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1318,433,564 - 18,450,296 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021085544   ⟹   XP_020941203
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1318,433,913 - 18,450,296 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021085545   ⟹   XP_020941204
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1318,433,913 - 18,450,296 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_020941202   ⟸   XM_021085543
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_020941199   ⟸   XM_021085540
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_020941198   ⟸   XM_021085539
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_020941201   ⟸   XM_021085542
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_020941204   ⟸   XM_021085545
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_020941200   ⟸   XM_021085541
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_020941203   ⟸   XM_021085544
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: NP_001106522   ⟸   NM_001113051
- UniProtKB: A9UHP2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000057536   ⟸   ENSSSCT00000058141
RefSeq Acc Id: ENSSSCP00000060511   ⟸   ENSSSCT00000068715
RefSeq Acc Id: ENSSSCP00000049546   ⟸   ENSSSCT00000041904
RefSeq Acc Id: ENSSSCP00000067756   ⟸   ENSSSCT00000069009
RefSeq Acc Id: ENSSSCP00000072004   ⟸   ENSSSCT00000086294
RefSeq Acc Id: ENSSSCP00000061618   ⟸   ENSSSCT00000086437


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000036603 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00000049546 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00000057536 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00000060511 UniProtKB/TrEMBL
  ENSSSCP00000061618 UniProtKB/TrEMBL
  ENSSSCP00000067756 UniProtKB/TrEMBL
  ENSSSCP00000072004 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000041904 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00000058141 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00000068715 UniProtKB/TrEMBL
  ENSSSCT00000069009 UniProtKB/TrEMBL
  ENSSSCT00000086294 UniProtKB/TrEMBL
  ENSSSCT00000086437 UniProtKB/TrEMBL
InterPro Battenin_disease_Cln3 UniProtKB/TrEMBL
  Battenin_disease_Cln3_subgr UniProtKB/TrEMBL
  MFS_trans_sf UniProtKB/TrEMBL
KEGG Report ssc:100127354 UniProtKB/TrEMBL
NCBI Gene CLN3 ENTREZGENE
PANTHER PTHR10981 UniProtKB/TrEMBL
Pfam CLN3 UniProtKB/TrEMBL
PIRSF CLN3_BTN1 UniProtKB/TrEMBL
PRINTS BATTENIN UniProtKB/TrEMBL
Superfamily-SCOP SSF103473 UniProtKB/TrEMBL
UniProt A0A287AZH5_PIG UniProtKB/TrEMBL
  A0A287BN79_PIG UniProtKB/TrEMBL
  A0A5G2QEQ8_PIG UniProtKB/TrEMBL
  A0A5G2QHZ5_PIG UniProtKB/TrEMBL
  A0A5G2R0M6_PIG UniProtKB/TrEMBL
  A0A5G2RJH0_PIG UniProtKB/TrEMBL
  A9UHP2 ENTREZGENE, UniProtKB/TrEMBL