Cpne9 (copine family member 9) - Rat Genome Database

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Gene: Cpne9 (copine family member 9) Rattus norvegicus
Analyze
Symbol: Cpne9
Name: copine family member 9
RGD ID: 1309212
Description: Predicted to enable calcium-dependent phospholipid binding activity. Predicted to be involved in cellular response to calcium ion and positive regulation of dendrite extension. Predicted to be active in plasma membrane. Orthologous to human CPNE9 (copine family member 9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: copine family member IX; copine IX; copine-9; LOC297516; MGC109370; RGD1309212; similar to copine family member isoform a
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
mRatBN7.24146,429,961 - 146,454,335 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4146,430,792 - 146,454,333 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4151,815,088 - 151,838,544 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04147,595,928 - 147,619,388 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04146,217,490 - 146,240,929 (+)NCBIRnor_WKY
Rnor_6.04145,238,011 - 145,262,444 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4145,238,947 - 145,262,442 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04208,536,038 - 208,559,594 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44149,165,857 - 149,189,090 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14149,410,697 - 149,433,929 (+)NCBI
Celera4134,988,163 - 135,011,651 (+)NCBICelera
Cytogenetic Map4q42NCBI
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. 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:12477932   PMID:15489334   PMID:23533145   PMID:23580065   PMID:23999003   PMID:29476059  


Genomics

Comparative Map Data
Cpne9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24146,429,961 - 146,454,335 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4146,430,792 - 146,454,333 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4151,815,088 - 151,838,544 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04147,595,928 - 147,619,388 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04146,217,490 - 146,240,929 (+)NCBIRnor_WKY
Rnor_6.04145,238,011 - 145,262,444 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4145,238,947 - 145,262,442 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04208,536,038 - 208,559,594 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44149,165,857 - 149,189,090 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14149,410,697 - 149,433,929 (+)NCBI
Celera4134,988,163 - 135,011,651 (+)NCBICelera
Cytogenetic Map4q42NCBI
CPNE9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3839,703,833 - 9,729,908 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl39,703,826 - 9,729,908 (+)EnsemblGRCh38hg38GRCh38
GRCh3739,745,517 - 9,771,592 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3639,720,510 - 9,746,592 (+)NCBINCBI36Build 36hg18NCBI36
Celera39,680,220 - 9,706,296 (+)NCBICelera
Cytogenetic Map3p25.3NCBI
HuRef39,681,870 - 9,707,942 (+)NCBIHuRef
CHM1_139,695,714 - 9,721,793 (+)NCBICHM1_1
T2T-CHM13v2.039,695,788 - 9,721,866 (+)NCBIT2T-CHM13v2.0
Cpne9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396113,259,244 - 113,282,532 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6113,259,268 - 113,282,588 (+)EnsemblGRCm39 Ensembl
GRCm386113,282,283 - 113,305,571 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6113,282,307 - 113,305,627 (+)EnsemblGRCm38mm10GRCm38
MGSCv376113,232,301 - 113,255,565 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366113,248,084 - 113,271,348 (+)NCBIMGSCv36mm8
Celera6115,109,272 - 115,132,547 (+)NCBICelera
Cytogenetic Map6E3NCBI
Cpne9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555611,238,862 - 1,258,045 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555611,238,916 - 1,258,000 (+)NCBIChiLan1.0ChiLan1.0
CPNE9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.139,893,478 - 9,920,944 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl39,893,662 - 9,920,728 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v039,655,280 - 9,682,266 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CPNE9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1208,511,267 - 8,529,630 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl208,511,350 - 8,529,473 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha208,544,337 - 8,562,825 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0208,540,563 - 8,559,022 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl208,540,564 - 8,558,946 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1208,263,025 - 8,281,488 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0208,607,545 - 8,625,890 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0208,581,186 - 8,599,646 (-)NCBIUU_Cfam_GSD_1.0
Cpne9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494215,446,795 - 15,470,540 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366023,439,172 - 3,462,951 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CPNE9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1365,995,534 - 66,019,077 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11365,994,369 - 66,019,080 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21373,128,376 - 73,156,320 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CPNE9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12245,714,168 - 45,738,368 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041120,831,004 - 120,857,147 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cpne9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247314,342,172 - 4,362,931 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247314,341,091 - 4,363,112 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Position Markers
D4Mgh8  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24146,446,565 - 146,446,691 (+)MAPPERmRatBN7.2
Rnor_6.04145,254,666 - 145,254,791NCBIRnor6.0
Rnor_5.04208,551,825 - 208,551,950UniSTSRnor5.0
RGSC_v3.44149,181,320 - 149,181,446RGDRGSC3.4
RGSC_v3.44149,181,321 - 149,181,446UniSTSRGSC3.4
RGSC_v3.14149,426,161 - 149,426,287RGD
Celera4135,003,882 - 135,004,007UniSTS
RH 3.4 Map4934.3UniSTS
RH 3.4 Map4934.3RGD
Cytogenetic Map4q42UniSTS
RH132464  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24146,454,112 - 146,454,314 (+)MAPPERmRatBN7.2
Rnor_6.04145,262,222 - 145,262,423NCBIRnor6.0
Rnor_5.04208,559,372 - 208,559,573UniSTSRnor5.0
RGSC_v3.44149,188,868 - 149,189,069UniSTSRGSC3.4
Celera4135,011,429 - 135,011,630UniSTS
RH 3.4 Map4937.0UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)485253748148090731Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)485253748150276390Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4103194656148194656Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105789505150789505Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
12798527Anxrr58Anxiety related response QTL 584.110.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4119463257147278687Rat
70201Gcr1Gastric cancer resistance QTL 12.7stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)4120260281147278687Rat
2293840Kiddil9Kidney dilation QTL 92.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)4120926564148090731Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:43
Count of miRNA genes:37
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000067396
Prediction methods: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.


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 29
Low 1 3 14 2 4 2 19 7 4
Below cutoff 2 16 14 10 15 10 8 9 14 17 21 7 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067396   ⟹   ENSRNOP00000059939
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4146,430,840 - 146,454,333 (+)Ensembl
Rnor_6.0 Ensembl4145,238,947 - 145,262,442 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091934   ⟹   ENSRNOP00000074693
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4146,430,840 - 146,454,333 (+)Ensembl
Rnor_6.0 Ensembl4145,239,034 - 145,262,234 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000111242   ⟹   ENSRNOP00000097811
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4146,430,792 - 146,454,333 (+)Ensembl
RefSeq Acc Id: NM_001024982   ⟹   NP_001020153
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,430,840 - 146,454,335 (+)NCBI
Rnor_6.04145,238,947 - 145,262,444 (+)NCBI
Rnor_5.04208,536,038 - 208,559,594 (+)NCBI
RGSC_v3.44149,165,857 - 149,189,090 (+)RGD
Celera4134,988,163 - 135,011,651 (+)RGD
Sequence:
RefSeq Acc Id: XM_006237022   ⟹   XP_006237084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,429,961 - 146,454,335 (+)NCBI
Rnor_6.04145,238,011 - 145,262,444 (+)NCBI
Rnor_5.04208,536,038 - 208,559,594 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592573   ⟹   XP_017448062
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,429,961 - 146,454,335 (+)NCBI
Rnor_6.04145,239,026 - 145,262,444 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039107402   ⟹   XP_038963330
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,429,961 - 146,454,335 (+)NCBI
RefSeq Acc Id: XM_039107403   ⟹   XP_038963331
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,429,961 - 146,443,830 (+)NCBI
RefSeq Acc Id: XM_039107404   ⟹   XP_038963332
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,429,961 - 146,454,335 (+)NCBI
RefSeq Acc Id: XM_039107405   ⟹   XP_038963333
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,440,805 - 146,454,335 (+)NCBI
RefSeq Acc Id: XM_039107406   ⟹   XP_038963334
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,440,223 - 146,454,335 (+)NCBI
RefSeq Acc Id: XM_039107407   ⟹   XP_038963335
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,440,271 - 146,454,335 (+)NCBI
RefSeq Acc Id: XR_005503198
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,429,961 - 146,454,335 (+)NCBI
RefSeq Acc Id: XR_005503199
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24146,429,961 - 146,442,816 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001020153   ⟸   NM_001024982
- UniProtKB: Q5BJS7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006237084   ⟸   XM_006237022
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017448062   ⟸   XM_017592573
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000059939   ⟸   ENSRNOT00000067396
RefSeq Acc Id: ENSRNOP00000074693   ⟸   ENSRNOT00000091934
RefSeq Acc Id: XP_038963332   ⟸   XM_039107404
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038963330   ⟸   XM_039107402
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963331   ⟸   XM_039107403
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038963334   ⟸   XM_039107406
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038963335   ⟸   XM_039107407
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038963333   ⟸   XM_039107405
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000097811   ⟸   ENSRNOT00000111242
Protein Domains
C2   VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BJS7-F1-model_v2 AlphaFold Q5BJS7 1-553 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309212 AgrOrtholog
BioCyc Gene G2FUF-43398 BioCyc
Ensembl Genes ENSRNOG00000023077 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059939 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOP00000074693.2 UniProtKB/TrEMBL
  ENSRNOP00000097811 ENTREZGENE
  ENSRNOP00000097811.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067396 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOT00000091934.2 UniProtKB/TrEMBL
  ENSRNOT00000111242 ENTREZGENE
  ENSRNOT00000111242.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7316601 IMAGE-MGC_LOAD
InterPro C2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2B_Copine UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Copine UniProtKB/Swiss-Prot
  Copine UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Copine UniProtKB/TrEMBL
  VWF_A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:297516 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109370 IMAGE-MGC_LOAD
NCBI Gene 297516 ENTREZGENE
PANTHER PTHR10857 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Copine UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cpne9 PhenoGen
PROSITE PS50004 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWFA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49562 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF53300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140TAJ0_RAT UniProtKB/TrEMBL
  A0A8I6GMP3_RAT UniProtKB/TrEMBL
  A0A8L2R9J4_RAT UniProtKB/TrEMBL
  CPNE9_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 Cpne9  copine family member 9  Cpne9  copine family member IX  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Cpne9  copine family member IX  RGD1309212  similar to copine family member isoform a  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1309212  similar to copine family member isoform a  RGD1309212_predicted  similar to copine family member isoform a (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1309212_predicted  similar to copine family member isoform a (predicted)  LOC297516_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC297516_predicted  similar to copine family member isoform a (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL