Cpne3 (copine 3) - Rat Genome Database

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Gene: Cpne3 (copine 3) Rattus norvegicus
Analyze
Symbol: Cpne3
Name: copine 3
RGD ID: 1310178
Description: Predicted to enable several functions, including calcium-dependent phospholipid binding activity; calcium-dependent protein binding activity; and receptor tyrosine kinase binding activity. Predicted to be involved in several processes, including ERBB2 signaling pathway; cellular response to calcium ion; and positive regulation of cell migration. Predicted to be located in several cellular components, including focal adhesion; mitochondrion; and nuclear lumen. Predicted to be active in plasma membrane. Orthologous to human CPNE3 (copine 3); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: copine III; copine-3; LOC313087
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
GRCr8537,811,566 - 37,860,840 (-)NCBIGRCr8
mRatBN7.2533,014,658 - 33,063,934 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl533,016,307 - 33,063,934 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx535,132,866 - 35,163,717 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0536,725,433 - 36,756,284 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0536,664,563 - 36,695,414 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0533,525,307 - 33,574,610 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl533,528,154 - 33,574,596 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0538,179,711 - 38,229,012 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4534,154,672 - 34,203,959 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1534,157,039 - 34,189,593 (-)NCBI
Celera532,108,679 - 32,139,506 (-)NCBICelera
Cytogenetic Map5q13NCBI
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
cell junction  (ISO)
cytoplasm  (ISO)
cytosol  (IEA,ISO)
focal adhesion  (ISO)
mitochondrion  (IEA,ISO)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (ISO)
plasma membrane  (IBA,ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9430674   PMID:11041869   PMID:12949241   PMID:19056867   PMID:19199708   PMID:20010870   PMID:20458337   PMID:21087455   PMID:22658674   PMID:23376485   PMID:23533145  


Genomics

Comparative Map Data
Cpne3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8537,811,566 - 37,860,840 (-)NCBIGRCr8
mRatBN7.2533,014,658 - 33,063,934 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl533,016,307 - 33,063,934 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx535,132,866 - 35,163,717 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0536,725,433 - 36,756,284 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0536,664,563 - 36,695,414 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0533,525,307 - 33,574,610 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl533,528,154 - 33,574,596 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0538,179,711 - 38,229,012 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4534,154,672 - 34,203,959 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1534,157,039 - 34,189,593 (-)NCBI
Celera532,108,679 - 32,139,506 (-)NCBICelera
Cytogenetic Map5q13NCBI
CPNE3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38886,514,435 - 86,561,498 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl886,514,435 - 86,561,498 (+)EnsemblGRCh38hg38GRCh38
GRCh37887,526,664 - 87,573,726 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36887,595,788 - 87,642,842 (+)NCBINCBI36Build 36hg18NCBI36
Build 34887,595,787 - 87,642,842NCBI
Celera883,721,201 - 83,768,282 (+)NCBICelera
Cytogenetic Map8q21.3NCBI
HuRef882,736,053 - 82,783,152 (+)NCBIHuRef
CHM1_1887,568,152 - 87,615,225 (+)NCBICHM1_1
T2T-CHM13v2.0887,634,662 - 87,681,751 (+)NCBIT2T-CHM13v2.0
Cpne3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39419,519,252 - 19,570,108 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl419,519,254 - 19,570,108 (-)EnsemblGRCm39 Ensembl
GRCm38419,519,252 - 19,570,108 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl419,519,254 - 19,570,108 (-)EnsemblGRCm38mm10GRCm38
MGSCv37419,446,399 - 19,497,251 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36419,446,399 - 19,497,251 (-)NCBIMGSCv36mm8
Celera419,281,183 - 19,332,079 (-)NCBICelera
Cytogenetic Map4A3NCBI
cM Map47.53NCBI
Cpne3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554174,115,308 - 4,145,939 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554174,115,298 - 4,146,878 (+)NCBIChiLan1.0ChiLan1.0
CPNE3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27103,916,914 - 103,963,965 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1879,455,749 - 79,502,801 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0883,209,949 - 83,257,088 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1885,179,146 - 85,225,585 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl885,151,133 - 85,225,585 (+)Ensemblpanpan1.1panPan2
CPNE3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12932,682,019 - 32,736,871 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2932,695,714 - 32,727,950 (+)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.02932,836,903 - 32,892,322 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2932,836,919 - 32,885,994 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12932,880,698 - 32,935,491 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02932,905,282 - 32,960,515 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02933,325,872 - 33,381,277 (+)NCBIUU_Cfam_GSD_1.0
Cpne3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530346,642,423 - 46,698,457 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365441,104,791 - 1,147,320 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365441,094,257 - 1,147,964 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CPNE3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl450,276,426 - 50,345,366 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1450,276,330 - 50,345,400 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2455,192,149 - 55,251,298 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CPNE3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1881,697,014 - 81,744,851 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl881,711,571 - 81,745,019 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603959,205,525 - 59,253,357 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cpne3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247445,237,708 - 5,273,384 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247445,234,431 - 5,288,598 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cpne3
290 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:97
Interacting mature miRNAs:101
Transcripts:ENSRNOT00000008281
Prediction methods:Microtar, 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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)52483871044045280Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat

Markers in Region
RH139338  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2533,015,066 - 33,015,189 (+)MAPPERmRatBN7.2
Rnor_6.0533,525,716 - 33,525,838NCBIRnor6.0
Rnor_5.0538,180,120 - 38,180,242UniSTSRnor5.0
RGSC_v3.4534,155,079 - 34,155,201UniSTSRGSC3.4
Celera532,105,201 - 32,105,323UniSTS
RH 3.4 Map18448.5UniSTS
Cytogenetic Map5q13UniSTS


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 3 41 56 40 19 40 8 8 70 35 34 11 8
Low 2 1 1 1 3 4 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008281   ⟹   ENSRNOP00000008281
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl533,016,307 - 33,063,934 (-)Ensembl
Rnor_6.0 Ensembl533,528,154 - 33,574,596 (-)Ensembl
RefSeq Acc Id: NM_001107917   ⟹   NP_001101387
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8537,811,566 - 37,860,840 (-)NCBI
mRatBN7.2533,014,658 - 33,063,934 (-)NCBI
Rnor_6.0533,529,194 - 33,560,043 (-)NCBI
Rnor_5.0538,179,711 - 38,229,012 (-)NCBI
RGSC_v3.4534,154,672 - 34,203,959 (-)RGD
Celera532,108,679 - 32,139,506 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101387 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAN89608 (Get FASTA)   NCBI Sequence Viewer  
  EDL98495 (Get FASTA)   NCBI Sequence Viewer  
  EDL98496 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000008281
  ENSRNOP00000008281.5
Reference Protein Sequences
RefSeq Acc Id: NP_001101387   ⟸   NM_001107917
- UniProtKB: D3ZLA3 (UniProtKB/TrEMBL),   A6IIC6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008281   ⟸   ENSRNOT00000008281
Protein Domains
C2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZLA3-F1-model_v2 AlphaFold D3ZLA3 1-533 view protein structure

Transcriptome

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

Promoters
RGD ID:13693588
Promoter ID:EPDNEW_R4112
Type:initiation region
Name:Cpne3_1
Description:copine 3
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_6.0533,574,547 - 33,574,607EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310178 AgrOrtholog
BioCyc Gene G2FUF-41840 BioCyc
Ensembl Genes ENSRNOG00000006298 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008281 ENTREZGENE
  ENSRNOT00000008281.8 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/TrEMBL
InterPro C2_Ca-dep UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/TrEMBL
  C2B_Copine UniProtKB/TrEMBL
  Copine UniProtKB/TrEMBL
  Copine UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:313087 UniProtKB/TrEMBL
NCBI Gene 313087 ENTREZGENE
PANTHER COPINE-3 UniProtKB/TrEMBL
  PTHR10857 UniProtKB/TrEMBL
Pfam Copine UniProtKB/TrEMBL
  PF00168 UniProtKB/TrEMBL
PhenoGen Cpne3 PhenoGen
PROSITE PS50004 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006298 RatGTEx
SMART SM00239 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF49562 UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
UniProt A6IIC6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZLA3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 Cpne3  copine 3  Cpne3  copine III  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Cpne3  copine III   Cpne3_predicted  copine III (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cpne3_predicted  copine III (predicted)      Symbol and Name status set to approved 70820 APPROVED