Cpne1 (copine 1) - Rat Genome Database

Name: Cpne1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Cpne1 (copine 1) Rattus norvegicus

Analyze

Symbol:

Cpne1 (Ensembl: Rbm12)

Name:

copine 1 (Ensembl:RNA binding motif protein 12)

RGD ID:

1311148

Description:

Predicted to enable several functions, including NF-kappaB binding activity; identical protein binding activity; and phospholipid binding activity. Predicted to be involved in several processes, including cellular response to calcium ion; neuron projection extension; and regulation of signal transduction. Predicted to be located in cytosol; nuclear membrane; and nucleoplasm. Predicted to be active in plasma membrane. Orthologous to human CPNE1 (copine 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; aconitine; bisphenol A.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

copine I; copine-1; copine-1-like; LOC100910990; LOC362249

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CPNE1 (copine 1)	HGNC	Ensembl, HomoloGene, OrthoDB, OrthoMCL
Mus musculus (house mouse):	Cpne1 (copine I)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Cpne1 (copine 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CPNE1 (copine 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CPNE1 (copine 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cpne1 (copine 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	RBM12 (RNA binding motif protein 12)	HGNC	HomoloGene
Alliance orthologs ³
Homo sapiens (human):	CPNE1 (copine 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Cpne1 (copine I)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Rbm12 (RNA binding motif protein 12)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	cpne1 (copine I)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	rbm12 (RNA binding motif protein 12)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	rbm-12	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	CG7879	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	cpne1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	165,047,615 - 165,089,994 (-)	NCBI		GRCr8
mRatBN7.2	3	144,587,531 - 144,629,911 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	144,588,995 - 144,598,636 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	148,454,985 - 148,462,709 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	157,072,257 - 157,079,981 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	154,811,783 - 154,819,507 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	151,617,733 - 151,625,448 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	151,616,037 - 151,625,644 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0 Ensembl	3	152,150,152 - 152,159,749 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	157,980,656 - 157,994,839 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.1	3	146,386,321 - 146,433,463 (-)	NCBI
Celera	3	143,310,994 - 143,318,709 (-)	NCBI		Celera
Cytogenetic Map	3	q42	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

schizophrenia 19 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2-amino-14,16-dimethyloctadecan-3-ol (ISO)

5-aza-2'-deoxycytidine (ISO)

acetylsalicylic acid (ISO)

aconitine (EXP)

aflatoxin B1 (ISO)

aristolochic acid A (ISO)

arsenous acid (ISO)

atrazine (ISO)

beauvericin (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

bromobenzene (EXP)

CGP 52608 (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (ISO)

clozapine (ISO)

cobalt dichloride (ISO)

diarsenic trioxide (ISO)

Dibutyl phosphate (ISO)

dibutyl phthalate (ISO)

doxorubicin (ISO)

endosulfan (EXP)

enzyme inhibitor (ISO)

ethanol (ISO)

folic acid (ISO)

ivermectin (ISO)

lead diacetate (ISO)

leflunomide (ISO)

paracetamol (EXP)

PCB138 (ISO)

rotenone (ISO)

SB 431542 (ISO)

sulindac (ISO)

temozolomide (ISO)

tert-butyl hydroperoxide (ISO)

thapsigargin (ISO)

theophylline (ISO)

trichloroethene (EXP)

triphenyl phosphate (ISO)

triptonide (ISO)

valproic acid (ISO)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to calcium ion (IBA,IEA,ISO)

negative regulation of gene expression (IEA,ISO)

negative regulation of non-canonical NF-kappaB signal transduction (IEA,ISO)

neuron projection extension (IEA,ISO)

positive regulation of neuron differentiation (IEA,ISO)

positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (IEA,ISO)

positive regulation of tumor necrosis factor-mediated signaling pathway (IBA,IEA,ISO)

proteolysis (IEA,ISO)

regulation of canonical NF-kappaB signal transduction (IBA,IEA,ISO)

regulation of RNA splicing (IBA)

Cellular Component

cytoplasm (ISO)

cytosol (IEA,ISO)

membrane (ISO)

nuclear membrane (IEA,ISO)

nucleoplasm (IBA,ISO)

nucleus (ISO)

plasma membrane (IBA)

ribonucleoprotein complex (IBA)

Molecular Function

calcium ion binding (IEA,ISO)

calcium-dependent phospholipid binding (IBA,IEA)

endopeptidase activity (IEA,ISO)

identical protein binding (IEA,ISO)

NF-kappaB binding (IEA,ISO)

phosphatidylserine binding (IEA,ISO)

protein binding (ISO)

RNA binding (IBA)

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.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:9430674	PMID:12949241	PMID:14674885	PMID:15632090	PMID:18212740	PMID:20458337	PMID:21087455	PMID:23263657	PMID:23533145	PMID:25450385	PMID:32958249	PMID:37132099

Genomics

Comparative Map Data

Cpne1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	165,047,615 - 165,089,994 (-)	NCBI		GRCr8
mRatBN7.2	3	144,587,531 - 144,629,911 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	144,588,995 - 144,598,636 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	148,454,985 - 148,462,709 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	157,072,257 - 157,079,981 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	154,811,783 - 154,819,507 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	151,617,733 - 151,625,448 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	151,616,037 - 151,625,644 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0 Ensembl	3	152,150,152 - 152,159,749 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	157,980,656 - 157,994,839 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.1	3	146,386,321 - 146,433,463 (-)	NCBI
Celera	3	143,310,994 - 143,318,709 (-)	NCBI		Celera
Cytogenetic Map	3	q42	NCBI

CPNE1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	20	35,626,044 - 35,664,900 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	20	35,626,031 - 35,664,956 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	20	34,213,966 - 34,252,822 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	20	33,677,380 - 33,716,262 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	20	33,677,381 - 33,716,262	NCBI
Celera	20	30,962,261 - 31,001,142 (-)	NCBI		Celera
Cytogenetic Map	20	q11.22	NCBI
HuRef	20	30,991,367 - 31,030,291 (-)	NCBI		HuRef
CHM1_1	20	34,115,593 - 34,154,510 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	20	37,347,020 - 37,385,875 (-)	NCBI		T2T-CHM13v2.0

Cpne1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	155,913,765 - 155,953,847 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	155,913,762 - 155,953,885 (-)	Ensembl		GRCm39 Ensembl
GRCm38	2	156,071,841 - 156,111,965 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	156,071,842 - 156,111,965 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	155,897,577 - 155,937,701 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	155,763,286 - 155,803,405 (-)	NCBI		MGSCv36	mm8
Celera	2	162,007,248 - 162,047,562 (-)	NCBI		Celera
Cytogenetic Map	2	H1	NCBI
cM Map	2	77.34	NCBI

Cpne1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955422	25,793,819 - 25,837,564 (+)	Ensembl	ChiLan1.0
ChiLan1.0 Ensembl	NW_004955422	25,793,841 - 25,806,956 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955422	25,793,841 - 25,837,680 (+)	NCBI	ChiLan1.0	ChiLan1.0

CPNE1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	24	24,554,636 - 24,589,748 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	24	24,554,636 - 24,589,731 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	24	24,199,753 - 24,234,861 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	24	25,247,213 - 25,282,324 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	24	25,246,568 - 25,282,307 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	24	24,533,545 - 24,568,660 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	24	24,628,580 - 24,663,692 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	24	25,067,994 - 25,103,125 (-)	NCBI		UU_Cfam_GSD_1.0

CPNE1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	17	38,956,673 - 38,964,890 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	17	38,956,489 - 38,997,189 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	17	44,285,465 - 44,326,165 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

Cpne1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624842	3,808,069 - 3,822,734 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624842	3,787,275 - 3,823,635 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Cpne1
82 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	119
Count of miRNA genes:	72
Interacting mature miRNAs:	80
Transcripts:	ENSRNOT00000026657, ENSRNOT00000067490
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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
619618	Rf3	Renal disease susceptibility QTL 3	6.5	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate to body weight ratio (CMO:0001270)	3	107693393	152693393	Rat
1578656	Vnigr2	Vascular neointimal growth QTL 2	4.2		artery morphology trait (VT:0002191)	lesioned artery residual lumen area (CMO:0001417)	3	130656562	169034231	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	43827364	169034231	Rat
2302373	Gluco39	Glucose level QTL 39	5.01		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	3	98535386	161695835	Rat
1331726	Bp208	Blood pressure QTL 208	3.129		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	141339013	162184794	Rat
1298068	Bp167	Blood pressure QTL 167		0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	141074471	169034231	Rat
631673	Iddm13	Insulin dependent diabetes mellitus QTL 13	1.3	0.663	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	3	130193298	161695983	Rat
2312659	Slep7	Serum leptin concentration QTL 7		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	3	98535255	168026850	Rat
2312670	Bw94	Body weight QTL 94		0.01	inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	3	98535255	168026850	Rat
2312673	Scl63	Serum cholesterol level QTL 63		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	98535255	168026850	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	urine total protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	78196190	146592722	Rat
1578653	Vnigr3	Vascular neointimal growth QTL 3	3.1		artery morphology trait (VT:0002191)	artery neointimal hyperplastic lesion area (CMO:0001414)	3	130656562	169034231	Rat
631541	Bp81	Blood pressure QTL 81	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	124122556	169034231	Rat
1581568	Rf53	Renal function QTL 53			urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	56395968	161299569	Rat
1598877	Bp285	Blood pressure QTL 285	1.5	0.03	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	120538241	165538241	Rat
2298477	Eau4	Experimental allergic uveoretinitis QTL 4		0.0011	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	3	137398739	169034231	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	94856903	159898684	Rat
1576306	Schws3	Schwannoma susceptibility QTL 3		0.001	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	3	118839124	163839124	Rat
1578754	Stresp16	Stress response QTL 16	4	0.001	blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	3	112681431	157681431	Rat
1300159	Kidm4	Kidney mass QTL 4	3.83		kidney mass (VT:0002707)	right kidney wet weight to body weight ratio (CMO:0001953)	3	121056165	157309487	Rat
1300173	Rf11	Renal function QTL 11	3.38		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	121056165	145956249	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	41874578	155617519	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
2303620	Vencon4	Ventilatory control QTL 4	3.9		respiration trait (VT:0001943)	tidal volume (CMO:0000222)	3	127162703	168026850	Rat
2293087	Iddm27	Insulin dependent diabetes mellitus QTL 27	2.68		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	97551417	147415807	Rat
61335	Bp20	Blood pressure QTL 20	3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	141339236	155617360	Rat
5686842	Rf59	Renal function QTL 59			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	3	140069424	146976080	Rat
9589106	Insul23	Insulin level QTL 23	13.86	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	3	131635904	169034231	Rat
8552952	Pigfal13	Plasma insulin-like growth factor 1 level QTL 13			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	3	138799500	169034231	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	59242096	157323038	Rat
10755461	Coatc16	Coat color QTL 16			coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	3	122438700	167438700	Rat

Markers in Region

REN58508

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	144,595,209 - 144,595,461 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	152,157,821 - 152,158,072	NCBI	Rnor6.0
Rnor_6.0	3	151,623,716 - 151,623,967	NCBI	Rnor6.0
Rnor_5.0	3	157,988,334 - 157,988,585	UniSTS	Rnor5.0
Rnor_5.0	3	159,532,709 - 159,532,960	UniSTS	Rnor5.0
RGSC_v3.4	3	146,486,723 - 146,486,974	UniSTS	RGSC3.4
Celera	3	143,316,977 - 143,317,228	UniSTS
Cytogenetic Map	3	q42	UniSTS

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			8	2	6	2			18	8	14
Low	3	43	49	39	13	39	8	11	56	27	27	11	8
Below cutoff	1		4	2	3	2			15	2	13	2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001256465	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003749608	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006235453	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006235456	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006235457	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008762412	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008762413	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008762414	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017592258	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017592259	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017602647	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017602648	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_342555	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC118414	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AM747279	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474050	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000026657 ⟹ ENSRNOP00000026657

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	144,588,995 - 144,598,636 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000067490 ⟹ ENSRNOP00000059795

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	144,588,995 - 144,598,636 (-)	Ensembl

RefSeq Acc Id:

NM_001256465 ⟹ NP_001243394

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	165,047,615 - 165,089,994 (-)	NCBI
mRatBN7.2	3	144,587,531 - 144,629,911 (-)	NCBI
Rnor_6.0	3	151,617,733 - 151,625,448 (-)	NCBI
Rnor_5.0	3	157,980,656 - 157,994,839 (-)	NCBI
Celera	3	143,310,994 - 143,318,709 (-)	NCBI

Sequence:

show sequence

ATGGCCCATTGTGTGACCTTGGTTCAGCTGTCCGTTTCCTGTGACCACCTCATTGACAAGGACA
TCGGCTCCAAGTCTGACCCACTCTGCGTCCTTTTACAGGATGTGGGAGGTGCCTGGGCTGAGCT
TTGTCGGACTGAACGTGTTCGCAACTGCTCGAGCCCTGCATTCTCTAAGACTCTGCAGATAGAA
TACCACTTTGAGACTGTCCAGAAGTTACGCTTTGGAATCTATGACATAGACAACAAGACACCTG
AGCTGGGGGATGATGACTTTCTAGGGGGAGCTGAATGCTCCCTAGGCCAGATTGTGTCCAGCCA
GACGCTGACTCTACCCTTGATGTTGAAGCCTGGGAAACCTGCTGGACGGGGAACCATTACAGTT
TCAGCTCAGGAGTTAAAGGACAGCCGTGTAGTAACCATGGAGGTGGAAGCTAGAAACCTAGATA
AGAAGGACTTTCTAGGAAAATCTGATCCATTCTTGGAGTTCTTCCGGCAAGGTGATGGGAAGTG
GCACCTGGCATATAGAACTGAGGTAGTCAAGAACAACCTGAACCCTACGTGGAAACGCTTCTCA
GTCTCTCTCCAGCATTTCTGTGGCGGGGACCTCAACACACCCATCCAGGTGCGCTGCTCAGACT
ATGACAGTGATGGGTCACATGATCTCATCGGTACCTTTCACACTACCTTGGCCCAACTGCAAGC
AGTCCCGGCTGAGTTTGAATGTATCCACCCTGAGAAGCAGCAGAGAAAGAAAAGCTACAAGAAC
TCTGGAACTGTCTGTGTCAAGACTTGCCGGGTAGAGACAGAGTATTCCTTCCTGGACTATGTGA
TGGGAGGCTGCCAAATTAACTTTACCGTGGGTGTGGACTTCACTGGCTCCAACGGTGACCCATC
CTCACCTGACTCCCTGCACTATCTGAGCCCTACAGGAGTCAATGAGTATCTGACAGCCCTGTGG
AGTGTGGGCAGCGTGGTTCAAGACTATGACTCAGACAAGCTGTTTCCAGCATTTGGATTTGGAG
CCCAAGTACCCCCTGATTGGCAGGTCTCACATGAGTTTGCCTTGAACTTCAACCCCAGTAACCC
ATACTGTGCAGGCATCCAGGGTATCGTAGACGCCTACCGTCAAGCACTTCCCCAAGTTCGTCTC
TATGGCCCCACCAACTTTGCACCCATCATCAACCACGTGGCCAGGTTTGCAGCTCAGGCTGCAC
AACAGAGGACTGCCTCGCAATACTTCGTACTGCTGCTCTTGACTGACGGCGCTGTGACCGATGT
GGAGGCCACGTGTAAGGCTGTGGTGGAAGCCTCAAAGCTGCCCATGTCGGTGATCATCGTGGGT
GTGGGTGGTGCTGACTTTGAGGTCATGGAACAGCTGGATGCTGATGGCGGCCCACTTCGTACAC
GCTCTGGAGAAGCAGCTGCCCGAGACATAGTGCAGTTTGTGCCTTATCGACGATTTCAGAATGC
TCCACGGGAGACACTTGCAATGACTGTGCTTGCAGAAGTGCCCACTCAGATGGTTTCCTACTTC
AAAGCCCAAGGTTGGGCCCCATTAAAGACACTCCCAGCCCCAGCCAAGGGCCCTGCACAGGCCC
CACAGGTGTAG

hide sequence

Protein Sequences


Protein RefSeqs	NP_001243394	(Get FASTA)	NCBI Sequence Viewer
	XP_342556	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	CAO00504	(Get FASTA)	NCBI Sequence Viewer
	EDL85869	(Get FASTA)	NCBI Sequence Viewer
	EDL85870	(Get FASTA)	NCBI Sequence Viewer
	EDL85872	(Get FASTA)	NCBI Sequence Viewer
	EDL85873	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000026657.6
	ENSRNOP00000059795
	ENSRNOP00000059795.2

RefSeq Acc Id:

NP_001243394 ⟸ NM_001256465

- UniProtKB:

D4A1R8 (UniProtKB/Swiss-Prot), D3ZSJ8 (UniProtKB/Swiss-Prot), H1UBM6 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MAHCVTLVQLSVSCDHLIDKDIGSKSDPLCVLLQDVGGAWAELCRTERVRNCSSPAFSKTLQIE
YHFETVQKLRFGIYDIDNKTPELGDDDFLGGAECSLGQIVSSQTLTLPLMLKPGKPAGRGTITV
SAQELKDSRVVTMEVEARNLDKKDFLGKSDPFLEFFRQGDGKWHLAYRTEVVKNNLNPTWKRFS
VSLQHFCGGDLNTPIQVRCSDYDSDGSHDLIGTFHTTLAQLQAVPAEFECIHPEKQQRKKSYKN
SGTVCVKTCRVETEYSFLDYVMGGCQINFTVGVDFTGSNGDPSSPDSLHYLSPTGVNEYLTALW
SVGSVVQDYDSDKLFPAFGFGAQVPPDWQVSHEFALNFNPSNPYCAGIQGIVDAYRQALPQVRL
YGPTNFAPIINHVARFAAQAAQQRTASQYFVLLLLTDGAVTDVEATCKAVVEASKLPMSVIIVG
VGGADFEVMEQLDADGGPLRTRSGEAAARDIVQFVPYRRFQNAPRETLAMTVLAEVPTQMVSYF
KAQGWAPLKTLPAPAKGPAQAPQV

hide sequence

RefSeq Acc Id:

ENSRNOP00000059795 ⟸ ENSRNOT00000067490

RefSeq Acc Id:

ENSRNOP00000026657 ⟸ ENSRNOT00000026657

Protein Domains

C2 VWFA

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A1R8-F1-model_v2	AlphaFold	D4A1R8	1-536	view protein structure
AF-Q6XLI7-F1-model_v2	AlphaFold	Q6XLI7	1-1032	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311148	AgrOrtholog
BioCyc Gene	G2FUF-47106	BioCyc
Ensembl Genes	ENSRNOG00000046990	Ensembl
	ENSRNOG00000050864	Ensembl
	ENSRNOG00000069087	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000026657.8	UniProtKB/TrEMBL
	ENSRNOT00000067490	ENTREZGENE
	ENSRNOT00000067490.4	UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.40.150	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	3.40.50.410	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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_C	UniProtKB/TrEMBL
	VWF_A	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	vWFA_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:362249	UniProtKB/Swiss-Prot
NCBI Gene	Cpne1	ENTREZGENE
PANTHER	COPINE-1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR10857	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Copine	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PF00168	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Cpne1	PhenoGen
PROSITE	PS50004	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000046990	RatGTEx
	ENSRNOG00000050864	RatGTEx
	ENSRNOG00000069087	RatGTEx
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	A0A8L2QF48_RAT	UniProtKB/TrEMBL
	CPNE1_RAT	UniProtKB/Swiss-Prot
	D3ZSJ8	ENTREZGENE
	D4A1R8	ENTREZGENE
	H1UBM6	ENTREZGENE
UniProt Secondary	D3ZSJ8	UniProtKB/Swiss-Prot
	H1UBM6	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-12-20	Cpne1	copine 1	LOC100910990	copine-1-like	Data merged from RGD:6495669	737654	PROVISIONAL
2016-02-03	Cpne1	copine 1	Cpne1	copine I	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-07-05	LOC100910990	copine-1-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2008-04-30	Cpne1	copine I	Cpne1_predicted	copine I (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Cpne1_predicted	copine I (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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