Cln5 (CLN5, intracellular trafficking protein) - Rat Genome Database

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Gene: Cln5 (CLN5, intracellular trafficking protein) Rattus norvegicus
Analyze
Symbol: Cln5
Name: CLN5, intracellular trafficking protein
RGD ID: 1306965
Description: Predicted to enable mannose binding activity. Predicted to be involved in several processes, including lysosomal lumen acidification; nervous system development; and signal peptide processing. Predicted to act upstream of or within lysosome organization and visual perception. Predicted to be located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and vacuole. Human ortholog(s) of this gene implicated in neuronal ceroid lipofuscinosis 5. Orthologous to human CLN5 (CLN5 intracellular trafficking protein); INTERACTS WITH 2,4-dinitrotoluene; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ceroid-lipofuscinosis neuronal protein 5; ceroid-lipofuscinosis, neuronal 5; LOC306128
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21579,893,573 - 79,903,438 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1579,893,548 - 79,903,438 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1583,872,121 - 83,881,834 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01584,995,156 - 85,004,873 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01581,922,785 - 81,932,498 (+)NCBIRnor_WKY
Rnor_6.01593,634,815 - 93,644,146 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01597,122,608 - 97,131,939 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41587,080,071 - 87,089,784 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11587,095,850 - 87,104,041 (+)NCBI
Celera1579,034,732 - 79,043,598 (+)NCBICelera
Cytogenetic Map15q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:10992246   PMID:11722572   PMID:11971870   PMID:12134079   PMID:15207259   PMID:15459177   PMID:16399764   PMID:19941651   PMID:20052765   PMID:22431521   PMID:23533145   PMID:29514215  


Genomics

Comparative Map Data
Cln5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21579,893,573 - 79,903,438 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1579,893,548 - 79,903,438 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1583,872,121 - 83,881,834 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01584,995,156 - 85,004,873 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01581,922,785 - 81,932,498 (+)NCBIRnor_WKY
Rnor_6.01593,634,815 - 93,644,146 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01597,122,608 - 97,131,939 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41587,080,071 - 87,089,784 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11587,095,850 - 87,104,041 (+)NCBI
Celera1579,034,732 - 79,043,598 (+)NCBICelera
Cytogenetic Map15q23NCBI
CLN5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381376,992,081 - 77,005,117 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1376,990,660 - 77,019,143 (+)EnsemblGRCh38hg38GRCh38
GRCh371377,566,216 - 77,579,252 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361376,462,796 - 76,474,653 (+)NCBINCBI36Build 36hg18NCBI36
Build 341376,462,795 - 76,474,652NCBI
Celera1358,464,047 - 58,474,640 (+)NCBICelera
Cytogenetic Map13q22.3NCBI
HuRef1358,263,758 - 58,274,351 (+)NCBIHuRef
CHM1_11377,533,965 - 77,544,558 (+)NCBICHM1_1
T2T-CHM13v2.01376,215,721 - 76,228,757 (+)NCBIT2T-CHM13v2.0
Cln5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914103,307,652 - 103,315,066 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14103,307,652 - 103,315,064 (+)EnsemblGRCm39 Ensembl
GRCm3814103,070,216 - 103,077,630 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14103,070,216 - 103,077,628 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714103,469,433 - 103,476,847 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614101,956,722 - 101,964,130 (+)NCBIMGSCv36mm8
Celera14101,698,089 - 101,705,503 (+)NCBICelera
Cytogenetic Map14E2.3NCBI
cM Map1451.71NCBI
Cln5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540430,229,632 - 30,235,679 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540430,229,632 - 30,235,677 (-)NCBIChiLan1.0ChiLan1.0
CLN5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11377,253,203 - 77,263,759 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1377,253,203 - 77,263,759 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01358,207,542 - 58,220,697 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CLN5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12230,568,572 - 30,575,890 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2230,568,572 - 30,575,890 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2230,429,669 - 30,436,988 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02230,880,658 - 30,887,978 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2230,880,658 - 30,889,771 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12230,548,135 - 30,555,449 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02230,586,449 - 30,593,758 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02230,655,942 - 30,663,260 (+)NCBIUU_Cfam_GSD_1.0
Cln5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945128,865,789 - 128,874,778 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365114,283,009 - 4,292,376 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365114,283,016 - 4,291,968 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLN5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1149,105,878 - 49,129,886 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11149,105,822 - 49,128,425 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21153,744,011 - 53,766,580 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLN5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1356,074,701 - 56,086,433 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl356,076,226 - 56,086,963 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604612,283,338 - 12,295,116 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cln5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475123,396,789 - 23,404,906 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475123,395,284 - 23,404,798 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cln5
55 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:93
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000012928
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
61477Aia4Adjuvant induced arthritis QTL 43joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)155559608991365858Rat
631516Gluco31Glucose level QTL 317blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)155559608995018120Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
1331724Bp223Blood pressure QTL 2233.53715arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157369051895018228Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)157369051899794247Rat
70182BpQTLcluster12Blood pressure QTL cluster 123.53arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)157369065795018120Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
1581555Eae19Experimental allergic encephalomyelitis QTL 194.7nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)157630609990088744Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat

Markers in Region
BI276836  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21579,902,768 - 79,902,997 (+)MAPPERmRatBN7.2
Rnor_6.01593,643,477 - 93,643,705NCBIRnor6.0
Rnor_5.01597,131,270 - 97,131,498UniSTSRnor5.0
RGSC_v3.41587,089,115 - 87,089,343UniSTSRGSC3.4
Celera1579,042,929 - 79,043,157UniSTS
Cytogenetic Map15q22UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000093318   ⟹   ENSRNOP00000076164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1579,893,548 - 79,903,438 (+)Ensembl
RefSeq Acc Id: NM_001191689   ⟹   NP_001178618
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21579,893,723 - 79,903,438 (+)NCBI
Rnor_6.01593,634,815 - 93,644,146 (+)NCBI
Rnor_5.01597,122,608 - 97,131,939 (+)NCBI
Celera1579,034,732 - 79,043,598 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039093400   ⟹   XP_038949328
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21579,893,573 - 79,903,175 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001178618 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949328 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001178618   ⟸   NM_001191689
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_038949328   ⟸   XM_039093400
- Peptide Label: isoform X1
- UniProtKB: A0A1W2Q672 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000076164   ⟸   ENSRNOT00000093318

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306965 AgrOrtholog
BioCyc Gene G2FUF-12694 BioCyc
Ensembl Genes ENSRNOG00000062279 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000076164 ENTREZGENE
  ENSRNOP00000076164.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000093318 ENTREZGENE
  ENSRNOT00000093318.2 UniProtKB/TrEMBL
InterPro CLN5 UniProtKB/TrEMBL
NCBI Gene 306128 ENTREZGENE
PANTHER CEROID-LIPOFUSCINOSIS NEURONAL PROTEIN 5 UniProtKB/TrEMBL
  PTHR15380 UniProtKB/TrEMBL
Pfam CLN5 UniProtKB/TrEMBL
PhenoGen Cln5 PhenoGen
UniProt A0A1W2Q672 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-07-05 Cln5  CLN5, intracellular trafficking protein  Cln5  ceroid-lipofuscinosis, neuronal 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Cln5  ceroid-lipofuscinosis, neuronal 5   Cln5_predicted  ceroid-lipofuscinosis, neuronal 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cln5_predicted  ceroid-lipofuscinosis, neuronal 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED