Cbln3 (cerebellin 3 precursor) - Rat Genome Database

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Gene: Cbln3 (cerebellin 3 precursor) Rattus norvegicus
Analyze
Symbol: Cbln3
Name: cerebellin 3 precursor
RGD ID: 1563731
Description: Predicted to be involved in maintenance of synapse structure. Predicted to be located in extracellular space. Predicted to be active in synapse. Orthologous to human CBLN3 (cerebellin 3 precursor); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cerebellin 3 precursor protein; cerebellin-3; LOC501998; RGD1563731; similar to CBLN3
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
GRCr81533,331,919 - 33,334,428 (-)NCBIGRCr8
mRatBN7.21529,362,014 - 29,364,523 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,362,302 - 29,364,612 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1531,207,673 - 31,210,182 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,354,887 - 32,357,396 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,597,244 - 30,599,753 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,548,102 - 34,550,938 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,548,295 - 34,550,860 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01538,436,404 - 38,439,238 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41534,026,962 - 34,029,272 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1528,936,004 - 28,938,314 (-)NCBICelera
Cytogenetic Map15p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17030622   PMID:17331201   PMID:25931508  


Genomics

Comparative Map Data
Cbln3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81533,331,919 - 33,334,428 (-)NCBIGRCr8
mRatBN7.21529,362,014 - 29,364,523 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,362,302 - 29,364,612 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1531,207,673 - 31,210,182 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,354,887 - 32,357,396 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,597,244 - 30,599,753 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,548,102 - 34,550,938 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,548,295 - 34,550,860 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01538,436,404 - 38,439,238 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41534,026,962 - 34,029,272 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1528,936,004 - 28,938,314 (-)NCBICelera
Cytogenetic Map15p13NCBI
CBLN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381424,426,545 - 24,429,668 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1424,426,545 - 24,430,954 (-)EnsemblGRCh38hg38GRCh38
GRCh371424,895,751 - 24,898,874 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361423,965,578 - 23,968,571 (-)NCBINCBI36Build 36hg18NCBI36
Celera144,760,374 - 4,763,367 (-)NCBICelera
Cytogenetic Map14q12NCBI
HuRef145,010,393 - 5,013,386 (-)NCBIHuRef
CHM1_11424,894,311 - 24,897,304 (-)NCBICHM1_1
T2T-CHM13v2.01418,625,275 - 18,628,398 (-)NCBIT2T-CHM13v2.0
Cbln3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391456,116,377 - 56,121,713 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1456,116,370 - 56,121,849 (-)EnsemblGRCm39 Ensembl
GRCm381455,878,920 - 55,884,256 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1455,878,913 - 55,884,392 (-)EnsemblGRCm38mm10GRCm38
MGSCv371456,497,757 - 56,503,093 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361454,832,991 - 54,838,327 (-)NCBIMGSCv36mm8
Celera1453,682,705 - 53,688,041 (-)NCBICelera
Cytogenetic Map14C3NCBI
cM Map1428.19NCBI
Cbln3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540935,881,075 - 35,882,268 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540935,880,337 - 35,882,485 (+)NCBIChiLan1.0ChiLan1.0
CBLN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21525,781,479 - 25,785,712 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11424,998,021 - 25,000,511 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0145,200,297 - 5,206,018 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11423,326,146 - 23,329,604 (-)NCBIpanpan1.1PanPan1.1panPan2
CBLN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.184,399,188 - 4,402,478 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl84,400,462 - 4,401,754 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha84,320,877 - 4,324,167 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.084,510,821 - 4,514,111 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl84,510,312 - 4,513,550 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.184,200,177 - 4,203,462 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.084,262,864 - 4,266,152 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.084,525,056 - 4,528,344 (-)NCBIUU_Cfam_GSD_1.0
Cbln3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864036,258,571 - 36,264,046 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936722125,758 - 127,063 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936722125,758 - 127,002 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CBLN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl774,864,114 - 74,868,445 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1774,865,931 - 74,868,443 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2780,136,834 - 80,139,346 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CBLN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1241,409,147 - 1,412,140 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl241,410,406 - 1,411,667 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603613,095,412 - 13,098,662 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cbln3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248208,085,705 - 8,087,053 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248208,084,910 - 8,090,580 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cbln3
11 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:419
Count of miRNA genes:217
Interacting mature miRNAs:250
Transcripts:ENSRNOT00000027794
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
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


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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 13 13 13 14 2
Low 1 2 7 6 6 6 10 33 3
Below cutoff 2 35 36 22 17 22 6 8 48 25 5 8 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027794   ⟹   ENSRNOP00000027794
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1529,362,302 - 29,364,612 (-)Ensembl
Rnor_6.0 Ensembl1534,548,540 - 34,550,850 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090228   ⟹   ENSRNOP00000073746
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1534,548,295 - 34,550,860 (-)Ensembl
RefSeq Acc Id: NM_001109330   ⟹   NP_001102800
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,331,919 - 33,334,428 (-)NCBI
mRatBN7.21529,362,014 - 29,364,523 (-)NCBI
Rnor_6.01534,548,540 - 34,550,850 (-)NCBI
Rnor_5.01538,436,404 - 38,439,238 (-)NCBI
RGSC_v3.41534,026,962 - 34,029,272 (-)RGD
Celera1528,936,004 - 28,938,314 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102800 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM14289 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027794
  ENSRNOP00000027794.2
Reference Protein Sequences
RefSeq Acc Id: NP_001102800   ⟸   NM_001109330
- Peptide Label: precursor
- UniProtKB: D3Z9H1 (UniProtKB/TrEMBL),   A6KH60 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073746   ⟸   ENSRNOT00000090228
RefSeq Acc Id: ENSRNOP00000027794   ⟸   ENSRNOT00000027794
Protein Domains
C1q

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z9H1-F1-model_v2 AlphaFold D3Z9H1 1-197 view protein structure

Transcriptome

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

Promoters
RGD ID:13699694
Promoter ID:EPDNEW_R10218
Type:initiation region
Name:Cbln3_1
Description:cerebellin 3 precursor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01534,550,764 - 34,550,824EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563731 AgrOrtholog
BioCyc Gene G2FUF-13678 BioCyc
Ensembl Genes ENSRNOG00000020503 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027794 ENTREZGENE
  ENSRNOT00000027794.4 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/TrEMBL
InterPro C1q UniProtKB/TrEMBL
  Tumour_necrosis_fac-like UniProtKB/TrEMBL
KEGG Report rno:501998 UniProtKB/TrEMBL
NCBI Gene 501998 ENTREZGENE
PANTHER CEREBELLIN-3 UniProtKB/TrEMBL
  CEREBELLIN-RELATED UniProtKB/TrEMBL
Pfam C1q UniProtKB/TrEMBL
PhenoGen Cbln3 PhenoGen
PRINTS COMPLEMNTC1Q UniProtKB/TrEMBL
PROSITE C1Q UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020503 RatGTEx
SMART C1Q UniProtKB/TrEMBL
Superfamily-SCOP TNF_like UniProtKB/TrEMBL
UniProt A6KH60 ENTREZGENE, UniProtKB/TrEMBL
  D3Z9H1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-08-29 Cbln3  cerebellin 3 precursor  Cbln3  cerebellin 3 precursor protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Cbln3  cerebellin 3 precursor protein  RGD1563731_predicted  similar to CBLN3 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563731_predicted  similar to CBLN3 (predicted)  LOC501998  similar to CBLN3  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501998  similar to CBLN3      Symbol and Name status set to provisional 70820 PROVISIONAL