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

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Gene: CLN3 (CLN3 lysosomal/endosomal transmembrane protein, battenin) Chlorocebus sabaeus
Analyze
Symbol: CLN3
Name: CLN3 lysosomal/endosomal transmembrane protein, battenin
RGD ID: 18360764
Description: ENCODES a protein that exhibits calcium-dependent protein binding (inferred); glycolipid binding (inferred); sulfatide binding (inferred); INVOLVED IN actin cytoskeleton organization (ortholog); action potential (ortholog); amino acid transport (ortholog); ASSOCIATED WITH Brody myopathy (ortholog); cone-rod dystrophy (ortholog); Disease Progression (ortholog); FOUND IN endosome (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: battenin; CLN3, battenin
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1526,320,132 - 26,343,009 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl526,320,061 - 26,337,402 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660683,236,192 - 3,251,867 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
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  (IEA,ISO)
amyloid precursor protein catabolic process  (IEA)
associative learning  (IEA,ISO)
autophagosome maturation  (IEA,ISO)
autophagosome-lysosome fusion  (IEA)
blood vessel endothelial cell migration  (IEA,ISO)
endocytosis  (IEA,ISO)
establishment of localization in cell  (IEA,ISO)
glycerophospholipid biosynthetic process  (IEA)
glycolipid transport  (IEA)
Golgi to lysosome transport  (IEA)
intracellular water homeostasis  (IEA)
ionotropic glutamate receptor signaling pathway  (IEA,ISO)
L-arginine transmembrane transport  (IEA)
learning or memory  (IEA)
lysosomal lumen acidification  (IEA)
lysosomal lumen pH elevation  (IEA)
lysosomal protein catabolic process  (IEA)
lysosome organization  (IEA,ISO)
macroautophagy  (IEA,ISO)
membrane organization  (IEA,ISO)
negative regulation of apoptotic process  (IEA)
negative regulation of catalytic activity  (ISO)
negative regulation of neuron apoptotic process  (IEA,ISO)
negative regulation of proteolysis  (IEA,ISO)
neuromuscular process controlling balance  (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  (ISO)
protein localization to membrane  (IEA,ISO)
protein localization to plasma membrane  (IEA,ISO)
protein phosphorylation  (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  (IEA)
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 gene expression  (ISO)
regulation of modification of synaptic structure  (IEA)
regulation of phagosome maturation  (IEA)
regulation of protein localization to plasma membrane  (IEA)
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:22301074   PMID:30032202  


Genomics

Comparative Map Data
CLN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1526,320,132 - 26,343,009 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl526,320,061 - 26,337,402 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660683,236,192 - 3,251,867 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
CLN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381628,466,653 - 28,492,082 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1628,474,111 - 28,495,575 (-)EnsemblGRCh38hg38GRCh38
GRCh371628,477,974 - 28,503,403 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361628,396,101 - 28,411,124 (-)NCBINCBI36Build 36hg18NCBI36
Build 341628,396,101 - 28,410,717NCBI
Celera1627,700,143 - 27,715,170 (+)NCBICelera
Cytogenetic Map16p12.1NCBI
HuRef1626,514,259 - 26,529,549 (-)NCBIHuRef
CHM1_11629,500,208 - 29,515,233 (-)NCBICHM1_1
T2T-CHM13v2.01628,903,667 - 28,920,379 (+)NCBIT2T-CHM13v2.0
T2T-CHM13v2.01628,747,320 - 28,747,572 (-)NCBIT2T-CHM13v2.0
Cln3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397126,170,571 - 126,184,991 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7126,170,379 - 126,184,989 (-)EnsemblGRCm39 Ensembl
GRCm387126,571,207 - 126,585,817 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7126,571,207 - 126,585,817 (-)EnsemblGRCm38mm10GRCm38
MGSCv377133,714,914 - 133,727,794 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv367126,362,548 - 126,374,368 (-)NCBIMGSCv36mm8
Celera7126,395,665 - 126,433,408 (-)NCBICelera
Cytogenetic Map7F3NCBI
cM Map769.16NCBI
Cln3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81190,586,649 - 190,600,034 (-)NCBIGRCr8
mRatBN7.21181,156,071 - 181,169,458 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1181,156,073 - 181,167,434 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1189,507,073 - 189,518,479 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01196,693,161 - 196,704,568 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01189,360,633 - 189,371,909 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01197,986,384 - 197,999,726 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1197,986,385 - 197,997,664 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01204,965,144 - 204,978,485 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,713,096 - 185,724,375 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
LOC117978823
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21831,065,290 - 31,097,172 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11634,996,679 - 35,011,769 (+)NCBINHGRI_mPanPan1
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0618,390,161 - 18,402,054 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl618,390,161 - 18,402,054 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1618,189,180 - 18,201,073 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0618,104,266 - 18,116,159 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0618,420,341 - 18,432,234 (+)NCBIUU_Cfam_GSD_1.0
Cln3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344123,857,474 - 123,870,439 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650111,955,184 - 11,967,436 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493650111,955,334 - 11,967,338 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl318,433,836 - 18,450,290 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1318,433,564 - 18,450,296 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Cln3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478212,995,277 - 13,005,087 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478212,995,277 - 13,004,980 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CLN3
431 total Variants

Expression

RNA-SEQ Expression

ectoderm
endocrine system
hemolymphoid system
mesenchyme
mesoderm
nervous system
reproductive system
76 36 20 36 36 60 20

Sequence


Ensembl Acc Id: ENSCSAT00000004324   ⟹   ENSCSAP00000002581
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl526,320,061 - 26,337,402 (-)Ensembl
RefSeq Acc Id: XM_007989145   ⟹   XP_007987336
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1526,320,132 - 26,343,009 (-)NCBI
Vero_WHO_p1.0NW_0236660683,236,192 - 3,251,867 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007989155   ⟹   XP_007987346
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1526,320,132 - 26,337,212 (-)NCBI
Vero_WHO_p1.0NW_0236660683,236,382 - 3,251,867 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007989168   ⟹   XP_007987359
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1526,320,132 - 26,343,009 (-)NCBI
Vero_WHO_p1.0NW_0236660683,236,503 - 3,251,867 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007989178   ⟹   XP_007987369
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1526,320,132 - 26,343,009 (-)NCBI
Vero_WHO_p1.0NW_0236660683,236,192 - 3,251,867 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007989186   ⟹   XP_007987377
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1526,320,132 - 26,343,009 (-)NCBI
Vero_WHO_p1.0NW_0236660683,236,503 - 3,251,867 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007989198   ⟹   XP_007987389
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1526,320,132 - 26,343,009 (-)NCBI
Vero_WHO_p1.0NW_0236660683,236,314 - 3,251,867 (+)NCBI
Sequence:
RefSeq Acc Id: XM_037989672   ⟹   XP_037845600
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_0236660683,236,260 - 3,251,867 (+)NCBI
RefSeq Acc Id: XM_037989673   ⟹   XP_037845601
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_0236660683,236,263 - 3,251,867 (+)NCBI
RefSeq Acc Id: XM_037989674   ⟹   XP_037845602
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_0236660683,236,787 - 3,251,867 (+)NCBI
RefSeq Acc Id: XP_007987369   ⟸   XM_007989178
- Peptide Label: isoform X5
- UniProtKB: A0A0D9R1U2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007987359   ⟸   XM_007989168
- Peptide Label: isoform X4
- UniProtKB: A0A0D9R1U2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007987377   ⟸   XM_007989186
- Peptide Label: isoform X6
RefSeq Acc Id: XP_007987336   ⟸   XM_007989145
- Peptide Label: isoform X1
- UniProtKB: A0A0D9R1U2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007987389   ⟸   XM_007989198
- Peptide Label: isoform X6
RefSeq Acc Id: XP_007987346   ⟸   XM_007989155
- Peptide Label: isoform X2
- UniProtKB: A0A0D9R1U2 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCSAP00000002581   ⟸   ENSCSAT00000004324
RefSeq Acc Id: XP_037845600   ⟸   XM_037989672
- Peptide Label: isoform X1
- UniProtKB: A0A0D9R1U2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037845601   ⟸   XM_037989673
- Peptide Label: isoform X3
- UniProtKB: A0A0D9R1U2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037845602   ⟸   XM_037989674
- Peptide Label: isoform X6


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000006291 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000004324.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1250.20 UniProtKB/TrEMBL
InterPro Battenin_disease_Cln3 UniProtKB/TrEMBL
  Battenin_disease_Cln3_subgr UniProtKB/TrEMBL
  MFS_trans_sf UniProtKB/TrEMBL
KEGG Report csab:103230417 UniProtKB/TrEMBL
NCBI Gene CLN3 ENTREZGENE
PANTHER BATTENIN UniProtKB/TrEMBL
  PTHR10981 UniProtKB/TrEMBL
Pfam CLN3 UniProtKB/TrEMBL
PIRSF CLN3_BTN1 UniProtKB/TrEMBL
PRINTS BATTENIN UniProtKB/TrEMBL
Superfamily-SCOP SSF103473 UniProtKB/TrEMBL
UniProt A0A0D9R1U2 ENTREZGENE, UniProtKB/TrEMBL