Cln5 (ceroid-lipofuscinosis, neuronal 5) - Rat Genome Database

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Gene: Cln5 (ceroid-lipofuscinosis, neuronal 5) Mus musculus
Analyze
Symbol: Cln5
Name: ceroid-lipofuscinosis, neuronal 5
RGD ID: 1315880
MGI Page MGI
Description: Predicted to enable bis(monoacylglycero)phosphate synthase activity; hydrolase activity, acting on glycosyl bonds; and mannose binding activity. Acts upstream of or within lysosome organization and visual perception. Located in lysosome and vacuolar lumen. Is expressed in several structures, including central nervous system; genitourinary system; liver; sensory organ; and spleen. Used to study neuronal ceroid lipofuscinosis 5. Human ortholog(s) of this gene implicated in neuronal ceroid lipofuscinosis 5. Orthologous to human CLN5 (CLN5 intracellular trafficking protein).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: A730075N08Rik; ceroid-lipofuscinosis neuronal protein 5 homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914103,307,679 - 103,315,064 (+)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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. MGDs mouse GO annotations MGD data from the GO Consortium
2. MGD IEA MGD IEA
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. Mouse MP Annotation Import Pipeline RGD automated import 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
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12160731   PMID:12466851   PMID:12477932   PMID:15207259   PMID:15459177   PMID:15647513  
PMID:15782199   PMID:16141072   PMID:16141073   PMID:16602821   PMID:18371231   PMID:19174516   PMID:19345705   PMID:19385065   PMID:19941651   PMID:21267068   PMID:21873635   PMID:21969016  
PMID:22182690   PMID:23065637   PMID:25303899   PMID:27224923   PMID:27508227   PMID:28487519   PMID:28733362   PMID:29514215   PMID:31294445   PMID:32290105   PMID:35427157   PMID:35681535  


Genomics

Comparative Map Data
Cln5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914103,307,679 - 103,315,064 (+)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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381376,992,081 - 77,005,117 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81586,308,286 - 86,321,679 (+)NCBIGRCr8
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_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01584,995,156 - 85,004,873 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01581,922,785 - 81,932,498 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 Map15q21NCBI
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
NHGRI_mPanPan1-v21478,557,935 - 78,572,799 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11377,154,083 - 77,166,649 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01358,207,542 - 58,220,697 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11377,253,203 - 77,263,759 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1377,253,203 - 77,263,759 (+)Ensemblpanpan1.1panPan2
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 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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
160 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:350
Count of miRNA genes:280
Interacting mature miRNAs:298
Transcripts:ENSMUST00000022721
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301844Pgia29_mproteoglycan induced arthritis 29 (mouse)Not determined1474352296108352384Mouse
1558819Ossc2_mosteosarcoma susceptibility 2 (mouse)Not determined1474394976108395093Mouse
1558823Tbbmd6_mtotal body bone mineral density 6 (mouse)Not determined1477073696111073787Mouse
1357589Kdnw2_mkidney weight 2 (mouse)Not determined1420887473121269804Mouse
1300551Lprm3_mlymphoproliferation modifier 3 (mouse)Not determined1471221224105221344Mouse
10054475Ossc3_mosteosarcoma susceptibility 3 (mouse)Not determined1470863768104863926Mouse
4142508Tgq25_mtriglyceride QTL 25 (mouse)Not determined85134068119134068Mouse
14928314Manh77_mmandible shape 77 (mouse)1476767790110767790Mouse
12792981Fbmd5_mfemoral bone mineral density 5, females only (mouse)1499838217125033054Mouse
14747006Mancz12_mmandible centroid size 12 (mouse)1470071977104071977Mouse

Markers in Region
UniSTS:237240  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3814103,076,290 - 103,076,600UniSTSGRCm38
MGSCv3714103,475,507 - 103,475,817UniSTSGRCm37
Celera14101,704,163 - 101,704,473UniSTS
Cytogenetic Map14E2.3UniSTS


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001033242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC102815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AEKQ02065227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK030852 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK032293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK043247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK085741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK144635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK178065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK186511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK188119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK206757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK207183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK207214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK207345 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK207852 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK208284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK208647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK208795 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK209323 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK211228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK212110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK214368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK215986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK216111 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK216934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK217255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK217292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK218710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK218788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK218901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC025487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC141314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC141315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BY493904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSMUST00000022721   ⟹   ENSMUSP00000022721
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl14103,307,652 - 103,315,064 (+)Ensembl
GRCm38.p6 Ensembl14103,070,216 - 103,077,628 (+)Ensembl
RefSeq Acc Id: ENSMUST00000227117   ⟹   ENSMUSP00000154528
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl14103,309,166 - 103,310,732 (+)Ensembl
GRCm38.p6 Ensembl14103,071,730 - 103,073,296 (+)Ensembl
RefSeq Acc Id: NM_001033242   ⟹   NP_001028414
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914103,307,679 - 103,315,064 (+)NCBI
GRCm3814103,070,216 - 103,077,630 (+)ENTREZGENE
MGSCv3714103,469,433 - 103,476,847 (+)RGD
Celera14101,698,089 - 101,705,503 (+)RGD
cM Map14 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_001028414   ⟸   NM_001033242
- Peptide Label: precursor
- UniProtKB: Q8C054 (UniProtKB/Swiss-Prot),   Q8R152 (UniProtKB/Swiss-Prot),   Q3UMW8 (UniProtKB/Swiss-Prot),   B2RUP8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000154528   ⟸   ENSMUST00000227117
RefSeq Acc Id: ENSMUSP00000022721   ⟸   ENSMUST00000022721

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3UMW8-F1-model_v2 AlphaFold Q3UMW8 1-341 view protein structure

Promoters
RGD ID:8683138
Promoter ID:EPDNEW_M19600
Type:initiation region
Name:Cln5_1
Description:Mus musculus ceroid-lipofuscinosis, neuronal 5 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3814103,070,243 - 103,070,303EPDNEW
RGD ID:6824778
Promoter ID:MM_KWN:17666
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_001033242
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3614103,469,246 - 103,469,847 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2442253 AgrOrtholog
Ensembl Genes ENSMUSG00000022125 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000022721 ENTREZGENE
  ENSMUST00000022721.8 UniProtKB/Swiss-Prot
  ENSMUST00000227117.2 UniProtKB/TrEMBL
InterPro CLN5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:211286 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:2442253 ENTREZGENE
NCBI Gene 211286 ENTREZGENE
PANTHER CEROID-LIPOFUSCINOSIS NEURONAL PROTEIN 5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR15380 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CLN5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cln5 PhenoGen
UniProt A0A2I3BRB6_MOUSE UniProtKB/TrEMBL
  B2RUP8 ENTREZGENE, UniProtKB/TrEMBL
  CLN5_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q8C054 ENTREZGENE
  Q8R152 ENTREZGENE
UniProt Secondary Q8C054 UniProtKB/Swiss-Prot
  Q8R152 UniProtKB/Swiss-Prot