Cpne6 (copine 6) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Cpne6 (copine 6) Rattus norvegicus
Analyze
Symbol: Cpne6
Name: copine 6
RGD ID: 1583895
Description: Predicted to enable calcium-dependent phospholipid binding activity and phosphatidylserine binding activity. Predicted to be involved in cellular response to calcium ion; positive regulation of dendrite extension; and postsynaptic actin cytoskeleton organization. Predicted to be located in several cellular components, including axon; clathrin-coated endocytic vesicle; and dendrite. Predicted to be active in plasma membrane. Orthologous to human CPNE6 (copine 6); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: copine VI; copine VI (neuronal); copine-6; LOC691478; similar to Copine-6 (Copine VI) (Neuronal-copine) (N-copine)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81532,968,047 - 32,975,008 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1532,968,046 - 32,975,007 (+)EnsemblGRCr8
mRatBN7.21528,998,293 - 29,005,044 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1528,998,293 - 29,005,044 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1530,843,996 - 30,850,745 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01531,991,204 - 31,997,955 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,233,550 - 30,240,303 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd1531,667,528 - 31,674,277 (+)NCBIDahl_SR_JrHsd
Lyon_Normotensive1531,372,277 - 31,379,026 (+)NCBILyon_Normotensive
Lyon_Hypertensive1531,478,761 - 31,485,510 (+)NCBILyon_Hypertensive
F344_StmMcwi1530,665,335 - 30,672,084 (+)NCBIF344_StmMcwi
Rnor_6.01534,187,229 - 34,194,107 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,187,223 - 34,194,118 (+)Ensemblrn6Rnor6.0
Rnor_5.01538,077,636 - 38,084,718 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41533,641,687 - 33,648,439 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1528,574,328 - 28,581,077 (+)NCBICelera
Cytogenetic Map15p13NCBI
JBrowse:




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

Biological Process

Cellular Component
axon  (IEA,ISO)
clathrin-coated endocytic vesicle  (IEA,ISO)
clathrin-coated vesicle  (IEA)
cytoplasm  (IEA,ISO)
cytoplasmic vesicle  (IEA)
dendrite  (IEA,ISO)
endosome  (IEA)
membrane  (IEA,ISO)
perikaryon  (IEA)
plasma membrane  (IBA,IEA,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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9886090   PMID:21087455   PMID:23533145   PMID:23999003   PMID:26723968   PMID:28131823   PMID:28158493   PMID:28211103   PMID:29802203  


Genomics

Comparative Map Data
Cpne6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81532,968,047 - 32,975,008 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1532,968,046 - 32,975,007 (+)EnsemblGRCr8
mRatBN7.21528,998,293 - 29,005,044 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1528,998,293 - 29,005,044 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1530,843,996 - 30,850,745 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01531,991,204 - 31,997,955 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,233,550 - 30,240,303 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd1531,667,528 - 31,674,277 (+)NCBIDahl_SR_JrHsd
Lyon_Normotensive1531,372,277 - 31,379,026 (+)NCBILyon_Normotensive
Lyon_Hypertensive1531,478,761 - 31,485,510 (+)NCBILyon_Hypertensive
F344_StmMcwi1530,665,335 - 30,672,084 (+)NCBIF344_StmMcwi
Rnor_6.01534,187,229 - 34,194,107 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,187,223 - 34,194,118 (+)Ensemblrn6Rnor6.0
Rnor_5.01538,077,636 - 38,084,718 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41533,641,687 - 33,648,439 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1528,574,328 - 28,581,077 (+)NCBICelera
Cytogenetic Map15p13NCBI
CPNE6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381424,070,949 - 24,078,087 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1424,070,837 - 24,078,100 (+)Ensemblhg38GRCh38
GRCh371424,540,158 - 24,547,296 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361423,610,596 - 23,617,136 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341423,610,595 - 23,617,135NCBI
Celera144,405,233 - 4,411,773 (+)NCBICelera
Cytogenetic Map14q11.2NCBI
HuRef144,654,979 - 4,662,242 (+)NCBIHuRef
CHM1_11424,538,721 - 24,545,984 (+)NCBICHM1_1
T2T-CHM13v2.01418,269,265 - 18,276,403 (+)NCBIT2T-CHM13v2.0
Cpne6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391455,747,902 - 55,754,892 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1455,747,902 - 55,754,888 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381455,510,445 - 55,517,435 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1455,510,445 - 55,517,431 (+)Ensemblmm10GRCm38
MGSCv371456,129,285 - 56,136,268 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361454,465,431 - 54,471,501 (+)NCBIMGSCv36mm8
Celera1453,299,381 - 53,322,268 (+)NCBICelera
Cytogenetic Map14C3NCBI
cM Map1428.19NCBI
Cpne6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540936,315,353 - 36,322,646 (-)Ensembl
ChiLan1.0NW_00495540936,315,353 - 36,322,646 (-)NCBIChiLan1.0ChiLan1.0
CPNE6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21525,427,055 - 25,434,189 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11424,643,547 - 24,650,681 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0144,848,845 - 4,856,085 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11422,973,157 - 22,980,341 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1422,973,157 - 22,980,341 (+)EnsemblpanPan2panpan1.1
CPNE6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.184,078,240 - 4,084,744 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl84,046,544 - 4,084,744 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha84,000,102 - 4,006,582 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.084,188,941 - 4,195,467 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.183,879,648 - 3,886,128 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.083,941,388 - 3,947,868 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.084,203,499 - 4,209,979 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cpne6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864035,926,748 - 35,934,174 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936722454,775 - 462,990 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936722454,818 - 462,324 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CPNE6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl775,213,644 - 75,219,031 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1775,213,643 - 75,219,031 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2780,484,577 - 80,491,174 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CPNE6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1241,053,980 - 1,061,544 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl241,054,488 - 1,061,578 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603612,735,993 - 12,743,598 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cpne6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248208,448,469 - 8,458,884 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248208,451,588 - 8,458,871 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Cpne6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11269,490,998 - 69,497,828 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cpne6
105 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:196
Count of miRNA genes:132
Interacting mature miRNAs:141
Transcripts:ENSRNOT00000024978
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15231575947315759Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15139411584Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15144836456Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152272835342072050Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat

Markers in Region
RH132000  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81532,974,822 - 32,974,987 (+)Marker Load Pipeline
mRatBN7.21529,004,858 - 29,005,023 (+)MAPPERmRatBN7.2
Rnor_6.01534,193,922 - 34,194,086NCBIRnor6.0
Rnor_5.01538,084,533 - 38,084,697UniSTSRnor5.0
RGSC_v3.41533,648,254 - 33,648,418UniSTSRGSC3.4
Celera1528,580,892 - 28,581,056UniSTS
RH 3.4 Map15213.3UniSTS
Cytogenetic Map15p13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
8 5 67 141 46 40 17 21 17 6 175 115 5 117 32 55 23 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000024978   ⟹   ENSRNOP00000024978
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1532,968,046 - 32,975,007 (+)Ensembl
mRatBN7.2 Ensembl1528,998,293 - 29,005,044 (+)Ensembl
Rnor_6.0 Ensembl1534,187,223 - 34,194,118 (+)Ensembl
RefSeq Acc Id: NM_001191113   ⟹   NP_001178042
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81532,968,259 - 32,975,008 (+)NCBI
mRatBN7.21528,998,293 - 29,005,044 (+)NCBI
Dahl_SR_JrHsd1531,667,528 - 31,674,277 (+)NCBI
Lyon_Normotensive1531,372,277 - 31,379,026 (+)NCBI
Lyon_Hypertensive1531,478,761 - 31,485,510 (+)NCBI
F344_StmMcwi1530,665,335 - 30,672,084 (+)NCBI
Rnor_6.01534,187,229 - 34,194,107 (+)NCBI
Rnor_5.01538,077,636 - 38,084,718 (+)NCBI
Celera1528,574,328 - 28,581,077 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063274663   ⟹   XP_063130733
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81532,968,047 - 32,975,008 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001178042 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130733 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAN89609 (Get FASTA)   NCBI Sequence Viewer  
  EDM14233 (Get FASTA)   NCBI Sequence Viewer  
  EDM14234 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000024978
  ENSRNOP00000024978.5
RefSeq Acc Id: NP_001178042   ⟸   NM_001191113
- UniProtKB: D4ACG7 (UniProtKB/TrEMBL),   A6KH05 (UniProtKB/TrEMBL),   H1UBM5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000024978   ⟸   ENSRNOT00000024978
RefSeq Acc Id: XP_063130733   ⟸   XM_063274663
- Peptide Label: isoform X1
- UniProtKB: A6KH05 (UniProtKB/TrEMBL),   D4ACG7 (UniProtKB/TrEMBL),   H1UBM5 (UniProtKB/TrEMBL)
Protein Domains
C2   VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACG7-F1-model_v2 AlphaFold D4ACG7 1-557 view protein structure

Transcriptome

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

Promoters
RGD ID:13699669
Promoter ID:EPDNEW_R10191
Type:single initiation site
Name:Cpne6_1
Description:copine 6
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_6.01534,187,238 - 34,187,298EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1583895 AgrOrtholog
BioCyc Gene G2FUF-13721 BioCyc
Ensembl Genes ENSRNOG00000018399 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024978 ENTREZGENE
  ENSRNOT00000024978.8 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
NCBI Gene 691478 ENTREZGENE
PANTHER COPINE-6 UniProtKB/TrEMBL
  PTHR10857 UniProtKB/TrEMBL
Pfam Copine UniProtKB/TrEMBL
  PF00168 UniProtKB/TrEMBL
PhenoGen Cpne6 PhenoGen
PROSITE PS50004 UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018399 RatGTEx
SMART SM00239 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF49562 UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
UniProt A6KH05 ENTREZGENE, UniProtKB/TrEMBL
  D4ACG7 ENTREZGENE, UniProtKB/TrEMBL
  H1UBM5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 Cpne6  copine 6  Cpne6  copine VI (neuronal)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-10 Cpne6  copine VI (neuronal)  Cpne6  copine VI  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Cpne6  copine VI  LOC691478  similar to Copine-6 (Copine VI) (Neuronal-copine) (N-copine)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691478  similar to Copine-6 (Copine VI) (Neuronal-copine) (N-copine)  LOC305894  similar to N-copine  Data merged from RGD:1594538 1643240 APPROVED
2006-11-20 LOC305894  similar to N-copine      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC691478  similar to Copine-6 (Copine VI) (Neuronal-copine) (N-copine)      Symbol and Name status set to provisional 70820 PROVISIONAL