Nucb2 (nucleobindin 2) - Rat Genome Database

Name: Nucb2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Nucb2 (nucleobindin 2) Rattus norvegicus

Analyze

Symbol:

Nucb2

Name:

nucleobindin 2

RGD ID:

620888

Description:

Exhibits G-protein alpha-subunit binding activity; guanyl-nucleotide exchange factor activity; and tumor necrosis factor receptor binding activity. Involved in several processes, including negative regulation of cell communication; positive regulation of testosterone secretion; and response to melanocyte-stimulating hormone. Localizes to Golgi medial cisterna and extracellular space. Biomarker of obesity and type 2 diabetes mellitus. Orthologous to human NUCB2 (nucleobindin 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

DNA-binding protein NEFA; Nefa; NEFA precursor; nesfatin-1; nucleobindin-2; p54; prepronefastin; prepronesfatin

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

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):	NUCB2 (nucleobindin 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Nucb2 (nucleobindin 2)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Nucb2 (nucleobindin 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NUCB2 (nucleobindin 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NUCB2 (nucleobindin 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nucb2 (nucleobindin 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NUCB2 (nucleobindin 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	NUCB2 (nucleobindin 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nucb2 (nucleobindin 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NUCB2 (nucleobindin 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Nucb2 (nucleobindin 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	nucb2b (nucleobindin 2b)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	nucb-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	NUCB1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	SSP120	Alliance	DIOPT (Ensembl Compara\|PANTHER)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	170,750,830 - 170,787,356 (+)	NCBI
Rnor_6.0 Ensembl	1	185,104,656 - 185,143,272 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	185,106,773 - 185,143,278 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	192,078,545 - 192,115,045 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	174,605,677 - 174,642,111 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	174,744,922 - 174,781,355 (+)	NCBI
Celera	1	168,570,763 - 168,607,089 (+)	NCBI		Celera
Cytogenetic Map	1	q35	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

intellectual disability (ISO)

obesity (IEP)

Prostatic Neoplasms (ISO)

type 2 diabetes mellitus (IEP,ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

17beta-hydroxy-17-methylestra-4,9,11-trien-3-one (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2,3-dimethoxynaphthalene-1,4-dione (ISO)

2,4,6-trinitrobenzenesulfonic acid (ISO)

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-amino-2-deoxy-D-glucopyranose (ISO)

3-chloropropane-1,2-diol (EXP)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

acrolein (ISO)

acrylamide (EXP,ISO)

aflatoxin M1 (ISO)

aldehydo-D-glucosamine (ISO)

aldehydo-D-glucose (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

ammonium chloride (EXP)

amphetamine (EXP)

arsenous acid (ISO)

belinostat (ISO)

benzo[a]pyrene (ISO)

Benzo[ghi]perylene (ISO)

beta-D-glucosamine (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

bleomycin A2 (EXP)

buspirone (EXP)

cadmium atom (ISO)

cadmium dichloride (EXP,ISO)

calcitriol (ISO)

calcium atom (EXP)

calcium(0) (EXP)

captan (ISO)

choline (ISO)

chromium atom (ISO)

ciguatoxin CTX1B (ISO)

copper atom (EXP)

copper(0) (EXP)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

D-glucose (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

dichloroacetic acid (ISO)

dicrotophos (ISO)

dioxygen (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

entinostat (ISO)

ethyl methanesulfonate (ISO)

fipronil (EXP)

flavonoids (EXP)

flutamide (EXP)

folic acid (ISO)

folpet (ISO)

glafenine (EXP)

glucose (ISO)

isoprenaline (ISO)

KT 5720 (EXP)

L-methionine (ISO)

lipopolysaccharide (ISO)

methoxychlor (EXP)

methyl methanesulfonate (ISO)

N-nitrosodiethylamine (ISO)

N-nitrosodimethylamine (ISO)

nefazodone (EXP)

nickel dichloride (EXP,ISO)

ozone (ISO)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenobarbital (ISO)

pioglitazone (ISO)

pirinixic acid (ISO)

potassium dichromate (ISO)

quercetin (EXP)

rotenone (EXP)

SB 431542 (ISO)

sodium arsenite (EXP,ISO)

sodium fluoride (ISO)

sunitinib (ISO)

T-2 toxin (ISO)

tamoxifen (ISO)

testosterone (ISO)

tetrachloromethane (ISO)

thapsigargin (ISO)

titanium dioxide (ISO)

trichloroethene (ISO)

trichostatin A (ISO)

troglitazone (ISO)

tunicamycin (ISO)

ursodeoxycholic acid (EXP)

valproic acid (ISO)

vancomycin (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

insulin metabolic process (IDA)

negative regulation of appetite (IEA,IMP)

negative regulation of cAMP-mediated signaling (IDA)

negative regulation of fat cell differentiation (IDA)

negative regulation of glucagon secretion (IDA)

negative regulation of insulin receptor signaling pathway (IDA)

positive regulation of fatty acid oxidation (IDA)

positive regulation of testosterone secretion (IDA)

regulation of catalytic activity (IEA)

response to glucose (IEP)

response to human chorionic gonadotropin (IEP)

response to melanocyte-stimulating hormone (IEP)

response to starvation (IEP)

small GTPase mediated signal transduction (IDA)

Cellular Component

cytoplasm (IDA,ISO)

endoplasmic reticulum (ISO)

endoplasmic reticulum-Golgi intermediate compartment (IBA,IEA,ISO)

extracellular space (IDA)

Golgi medial cisterna (IDA)

nuclear outer membrane (ISO)

nucleus (ISO)

Molecular Function

calcium ion binding (IBA,IEA,ISO)

DNA binding (IEA)

G-protein alpha-subunit binding (IDA)

guanyl-nucleotide exchange factor activity (IDA)

protein binding (ISO)

tumor necrosis factor receptor binding (IPI)

References

References - curated


1.	Foo KS, etal., J Endocrinol. 2010 Mar;204(3):255-63. doi: 10.1677/JOE-09-0254. Epub 2009 Dec 23.
2.	Garcia-Galiano D, etal., Endocrinology. 2012 Apr;153(4):1959-71. doi: 10.1210/en.2011-2032. Epub 2012 Feb 14.
3.	Garcia-Marcos M, etal., J Biol Chem. 2011 Aug 12;286(32):28138-49. doi: 10.1074/jbc.M110.204099. Epub 2011 Jun 8.
4.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5.	GOA data from the GO Consortium
6.	Gonzalez R, etal., Endocrinology. 2011 Oct;152(10):3628-37. doi: 10.1210/en.2010-1471. Epub 2011 Aug 9.
7.	MGD data from the GO Consortium
8.	Morel-Huaux VM, etal., Eur J Cell Biol 2002 Feb;81(2):87-100.
9.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
10.	Oh-I S, etal., Nature. 2006 Oct 12;443(7112):709-12. Epub 2006 Oct 1.
11.	Osaki A, etal., Neurosci Lett. 2012 Jul 11;521(1):46-51. doi: 10.1016/j.neulet.2012.05.056. Epub 2012 May 26.
12.	RGD automated data pipeline
13.	RGD automated import pipeline for gene-chemical interactions
14.	Riva M, etal., Cell Tissue Res. 2011 Dec;346(3):393-405. doi: 10.1007/s00441-011-1268-5. Epub 2011 Nov 23.
15.	Roy DN, etal., Br J Pharmacol. 2010 Aug;160(7):1823-43.
16.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
17.	Tagaya Y, etal., Protein Pept Lett. 2012 Sep;19(9):997-1004.

Additional References at PubMed

PMID:10915798	PMID:15308636	PMID:15489334	PMID:16502470	PMID:17627999	PMID:18048495	PMID:19199708	PMID:19248766	PMID:19348732	PMID:19426783	PMID:19461159	PMID:19474390
PMID:19497050	PMID:19540880	PMID:19733157	PMID:19778412	PMID:19797401	PMID:19883614	PMID:19944727	PMID:19961888	PMID:20380005	PMID:20435076	PMID:20534827	PMID:20966530
PMID:21418984	PMID:21451359	PMID:21782869	PMID:22293188	PMID:22375892	PMID:22514047	PMID:22688332	PMID:22955491	PMID:22958274	PMID:23300698	PMID:23560056	PMID:23801843
PMID:24048879	PMID:24120633	PMID:24304576	PMID:24598461	PMID:24829503	PMID:24905431	PMID:24944480	PMID:25089000	PMID:25344190	PMID:25665476	PMID:25916958	PMID:25997563
PMID:26144374	PMID:26297350	PMID:26522144	PMID:26639940	PMID:26778702	PMID:26801557	PMID:27203571	PMID:27590244	PMID:27599613	PMID:27982684	PMID:28211103	PMID:28277136
PMID:28838338	PMID:28851749	PMID:28951234	PMID:29604590	PMID:30111257	PMID:31085594	PMID:31141415	PMID:31260713	PMID:31637758	PMID:32200401	PMID:33301513

Genomics

Comparative Map Data

Nucb2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	170,750,830 - 170,787,356 (+)	NCBI
Rnor_6.0 Ensembl	1	185,104,656 - 185,143,272 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	185,106,773 - 185,143,278 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	192,078,545 - 192,115,045 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	174,605,677 - 174,642,111 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	174,744,922 - 174,781,355 (+)	NCBI
Celera	1	168,570,763 - 168,607,089 (+)	NCBI		Celera
Cytogenetic Map	1	q35	NCBI

NUCB2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	11	17,208,153 - 17,349,980 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	11	17,260,337 - 17,349,980 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	17,298,286 - 17,353,758 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	17,254,862 - 17,309,646 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	11	17,254,887 - 17,309,646	NCBI
Celera	11	17,428,095 - 17,482,908 (+)	NCBI
Cytogenetic Map	11	p15.1	NCBI
HuRef	11	16,982,188 - 17,036,934 (+)	NCBI		HuRef
CHM1_1	11	17,297,833 - 17,352,630 (+)	NCBI		CHM1_1

Nucb2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	116,103,579 - 116,139,823 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	7	116,103,604 - 116,139,819 (+)	Ensembl
GRCm38	7	116,504,352 - 116,540,588 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	116,504,369 - 116,540,584 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	123,647,888 - 123,684,102 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	7	116,295,518 - 116,331,703 (+)	NCBI			mm8
Celera	7	116,437,745 - 116,475,120 (+)	NCBI		Celera
Cytogenetic Map	7	F1	NCBI

Nucb2
(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_004955414	32,062,835 - 32,105,975 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955414	32,062,870 - 32,104,117 (+)	NCBI	ChiLan1.0	ChiLan1.0

NUCB2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	11	17,002,296 - 17,072,447 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	17,036,038 - 17,072,447 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	11	17,331,742 - 17,404,682 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

NUCB2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	21	39,868,756 - 39,918,724 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	21	39,874,781 - 39,918,689 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	21	39,368,984 - 39,424,531 (+)	NCBI
ROS_Cfam_1.0	21	40,974,304 - 41,029,984 (+)	NCBI
UMICH_Zoey_3.1	21	39,987,014 - 40,041,813 (+)	NCBI
UNSW_CanFamBas_1.0	21	40,193,641 - 40,249,282 (+)	NCBI
UU_Cfam_GSD_1.0	21	40,532,928 - 40,588,133 (+)	NCBI

Nucb2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	45,684,001 - 45,729,516 (-)	NCBI
SpeTri2.0	NW_004936528	1,726,879 - 1,763,483 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NUCB2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	2	41,782,594 - 41,829,829 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	44,840,114 - 44,888,611 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NUCB2
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	1	47,634,425 - 47,690,723 (-)	NCBI
ChlSab1.1 Ensembl	1	47,634,531 - 47,689,011 (-)	Ensembl

Nucb2
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624766	8,907,475 - 8,943,838 (+)	NCBI

Position Markers

D1Rat187

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	185,129,380 - 185,129,597	NCBI	Rnor6.0
Rnor_5.0	1	192,101,152 - 192,101,369	UniSTS	Rnor5.0
RGSC_v3.4	1	174,619,286 - 174,619,504	RGD	RGSC3.4
RGSC_v3.4	1	174,619,287 - 174,619,504	UniSTS	RGSC3.4
RGSC_v3.1	1	174,758,476 - 174,758,780	RGD
Celera	1	168,584,373 - 168,584,590	UniSTS
SHRSP x BN Map	1	85.7999	UniSTS
SHRSP x BN Map	1	85.7999	RGD
Cytogenetic Map	1	q35	UniSTS

BI275463

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	185,110,730 - 185,110,882	NCBI	Rnor6.0
Rnor_5.0	1	192,082,502 - 192,082,654	UniSTS	Rnor5.0
RGSC_v3.4	1	174,638,002 - 174,638,154	UniSTS	RGSC3.4
Celera	1	168,602,977 - 168,603,129	UniSTS
RH 3.4 Map	1	1589.31	UniSTS
Cytogenetic Map	1	q35	UniSTS

GDB:177399

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	185,109,262 - 185,109,287	NCBI	Rnor6.0
Rnor_5.0	1	192,081,034 - 192,081,059	UniSTS	Rnor5.0
Cytogenetic Map	1	q35	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
737828	Hcas3	Hepatocarcinoma susceptibility QTL 3	4.9		liver integrity trait (VT:0010547)	liver tumorous lesion volume to total liver volume ratio (CMO:0001082)	1	156446196	243311614	Rat
737974	Bp161	Blood pressure QTL 161		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	175447162	197963658	Rat
4889428	Stresp24	Stress response QTL 24		0.05	heart pumping trait (VT:2000009)	absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)	1	166577232	211577232	Rat
6893347	Bw98	Body weight QTL 98	0.2	0.53	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
6893361	Bw104	Body weight QTL 104	0.59	0.27	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	100131562	236763528	Rat
738006	Anxrr14	Anxiety related response QTL 14	4	0.00035	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	141296374	186296374	Rat
8655649	Arrd1	Age-related retinal degeneration QTL 1	4.89		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	106002252	202571904	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	122614824	262664716	Rat
738028	Anxrr12	Anxiety related response QTL 12	4.9	0.00001	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	141296374	186296374	Rat
631519	Pia11	Pristane induced arthritis QTL 11	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	153656062	198656062	Rat
631544	Bp84	Blood pressure QTL 84	5.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	130779148	198585664	Rat
634315	Niddm45	Non-insulin dependent diabetes mellitus QTL 45	7.16		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	156446783	188289244	Rat
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	144634295	241482368	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	125875758	262433692	Rat
1300158	Bp173	Blood pressure QTL 173	3.48		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	1	122614824	201146953	Rat
1331751	Bp199	Blood pressure QTL 199	3.60022		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	99983293	198656062	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat
1331793	Bp200	Blood pressure QTL 200	3.71601		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	99983293	188289386	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
1354591	Cm36	Cardiac mass QTL 36	4.1		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	108986301	219232156	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	108986301	238830534	Rat
1354615	Cm32	Cardiac mass QTL 32	5.2		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	108986301	219232156	Rat
1354618	Kidm15	Kidney mass QTL 15	5		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	1	167394665	219232156	Rat
1354620	Kidm19	Kidney mass QTL 19	4		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	219232156	Rat
1354634	Kidm12	Kidney mass QTL 12	3.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	1	161784169	219232156	Rat
1354636	Lmblg1	Limb length QTL 1	6.4		tibia length (VT:0004357)	tibia length (CMO:0000450)	1	161784169	219232156	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1558645	Bw55	Body weight QTL 55	3.2	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1358189	Cstrr1	Cold stress response QTL 1		0.0001	catecholamine amount (VT:0010543)	urine norepinephrine level (CMO:0001629)	1	130779148	199254774	Rat
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	161784422	246226103	Rat
1641895	Bp298	Blood pressure QTL 298			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	130779148	199254774	Rat
1598853	Memor3	Memory QTL 3	4.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	1	153834077	232297227	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	161321256	273791893	Rat
1578770	Stresp23	Stress response QTL 23			kidney sympathetic nerve activity (VT:0004050)	stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)	1	130779148	199254774	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	161321256	273791893	Rat
61343	Bp28	Blood pressure QTL 28			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	167027868	212027868	Rat
61347	Bp197	Blood pressure QTL 197	4.2		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	1	175462885	220462885	Rat
61348	Bp30	Blood pressure QTL 30	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	154337847	215828102	Rat
70209	Niddm23	Non-insulin dependent diabetes mellitus QTL 23	2.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	99983293	216325819	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	174905700	264802994	Rat
2292222	Bp307	Blood pressure QTL 307	3.06	0.0014	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	174905700	233490237	Rat
71118	Thym1	Thymus enlargement QTL 1	10.17	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	153655976	198655976	Rat
631199	Cm23	Cardiac mass QTL 23	4.6	0.0004	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	124603592	188289386	Rat
631205	Bp196	Blood pressure QTL 196	4	0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	126240667	217054291	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
724550	Thym3	Thymus enlargement QTL 3	7.82	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	153655976	198655976	Rat
724562	Rends1	Renal damage susceptibility QTL 1		0.05	kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	1	137787261	236763528	Rat
2312420	Pur17	Proteinuria QTL 17	7.1	0.0001	urine protein amount (VT:0005160)	urine total protein excretion rate (CMO:0000756)	1	167394665	238830534	Rat
2312558	Glom17	Glomerulus QTL 17	3.9	0.001	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	1	177235071	208786962	Rat
2303622	Vencon6	Ventilatory control QTL 6		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	1	169971964	214971964	Rat
1582204	Livw1	Liver weight QTL 1	3.6	0.0003	liver mass (VT:0003402)	liver weight as percentage of body weight (CMO:0000141)	1	166100317	188289386	Rat
61341	Bp26	Blood pressure QTL 26			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	137787261	236763528	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
619614	Bp78	Blood pressure QTL 78		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	184419946	215097919	Rat
619614	Bp78	Blood pressure QTL 78		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	184419946	215097919	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
1358902	Bw47	Body weight QTL 47	1.67		body mass (VT:0001259)	body weight (CMO:0000012)	1	94201400	197187904	Rat
631548	Bp88	Blood pressure QTL 88	5	0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	167394665	191883991	Rat
61379	Bp44	Blood pressure QTL 44	19.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	156446783	189514504	Rat
1354602	Bw35	Body weight QTL 35	12.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	219232156	Rat
70160	Bw18	Body weight QTL 18	5.7		body mass (VT:0001259)	body weight (CMO:0000012)	1	156446196	214277437	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	82788437	239853971	Rat
631549	Bp89	Blood pressure QTL 89	5.7		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	130779320	219238476	Rat
619613	Bp77	Blood pressure QTL 77		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	175447029	220447029	Rat
619613	Bp77	Blood pressure QTL 77		0.01	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	175447029	220447029	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1331749	Hrtrt11	Heart rate QTL 11	2.973		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	99983293	216213510	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	88
Count of miRNA genes:	74
Interacting mature miRNAs:	77
Transcripts:	ENSRNOT00000027752
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.

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	31	43	27	19	27	1	1	71	25	39	11	1
Low		12	14	14		14	7	10	3	10	2		7
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_021663	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006230095	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF238223	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF250142	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC061778	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473956	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000043	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000027752 ⟹ ENSRNOP00000027753

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	185,104,656 - 185,143,272 (-)	Ensembl

RefSeq Acc Id:

NM_021663 ⟹ NP_067695

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	170,750,920 - 170,787,356 (+)	NCBI
Rnor_6.0	1	185,106,773 - 185,143,207 (-)	NCBI
Rnor_5.0	1	192,078,545 - 192,115,045 (-)	NCBI
RGSC_v3.4	1	174,605,677 - 174,642,111 (+)	RGD
Celera	1	168,570,763 - 168,607,089 (+)	RGD

Sequence:

show sequence

CGCGGCGGGCATCAGTCGGCTTAGCCTCGCGCACGGGGACTCTGCAGAGAAGAACGCACCAGTC
AGTTTTTCAAGGGAAAAATCTGGGCCGGGAGCCAAGGCCTGATCGCCACAAACTTAATATTGTG
TAGATTATTTTACCACCTGATCTCAGTGGCCTCATCTGTGACAAAAAGAGAGAGAAAAAGAGAT
AAAACTTTGGCCTCTCTGAAGATGAGGTGGAGGACCATCCAAGCACGGTACTGTTTTCTCTTGG
TTCCGTGCGTGCTCACTGCGCTGGAAGCTGTTCCTATTGATGTGGACAAGACCAAAGTGCACAA
CGTCGAGCCGGTGGAAAGTGCAAGGATAGAACCGCCAGACACGGGACTTTATTATGATGAATAC
CTCAAGCAAGTGATTGAAGTCTTGGAAACAGATCCGCATTTCAGAGAAAAGCTCCAGAAAGCAG
ACATAGAGGAGATAAGGAGCGGGAGGCTGAGTCAAGAGCTGGACTTAGTAAGTCACAAAGTGAG
GACGAGACTGGATGAACTGAAGAGGCAAGAAGTAGGAAGACTGAGAATGCTCATCAAAGCCAAG
CTGGATGCCCTTCAAGACACTGGCATGAATCACCACCTTCTTCTTAAGCAGTTTGAACACCTGA
ACCACCAGAATCCTGACACATTTGAATCCAAAGACTTGGATATGCTAATCAAGGCGGCCACCGC
GGATCTGGAGCAGTATGACCGGACTCGGCATGAGGAGTTTAAGAAGTATGAGATGATGAAGGAA
CATGAACGCAGAGAATATTTAAAAACGCTGAGTGAGGAGAAGAGGAAAGAGGAAGAAGCCAAGT
TTGCAGAGATGAAGAGGAAGCATGAAGACCACCCCAAAGTTAATCACCCCGGAAGCAAAGATCA
ACTAAAAGAGGTTTGGGAAGAGACTGATGGATTGGACCCTAATGACTTTGACCCCAAGACATTT
TTCAAATTACATGATGTTAACAACGATGGATTCCTGGATGAACAAGAATTGGAAGCACTGTTCA
CAAAAGAGTTGGACAAAGTGTATAACCCGCAGAATGCAGAGGATGATATGATAGAAATGGAAGA
GGAGAGGCTCAGGATGAGAGAGCACGTCATGAATGAGATTGATAACAACAAAGACCGATTGGTG
ACTCTGGAGGAATTCTTGAGAGCCACAGAGAAGAAAGAATTCTTGGAGCCCGATAGCTGGGAGA
CACTGGACCAGCAGCAGTTATTCACCGAGGAAGAGCTCAAAGAGTATGAAAGTATCATTGCTAT
CCAAGAGAGTGAACTTAAGAAGAAGGCAGATGAACTGCAGAAGCAGAAGGAGGAGCTGCAGCGC
CAGCACGACCACCTTGAGGCCCAGAAGCAGGAGTATCAGCAGGCTGTACAGCAGCTGGAACAGA
AGAAATTCCAACAAGGGATTGCTCCATCAGGGCCGGCAGGAGAGCTGAAGTTTGAGCCACACAC
ATAAAAGTCCTGATGTCTGCCAGAACTTGGAAGAAAACCGTTGACTCAACATCTGTTTCATCTT
TCAACATCCCTTCTTTTCTCTTCACTCAATAAATACTTTAAAAGCACATTTGGAATAAAGGAAG
AGACTTTTAAGTGAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006230095 ⟹ XP_006230157

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	170,750,830 - 170,787,356 (+)	NCBI
Rnor_6.0	1	185,106,773 - 185,143,278 (-)	NCBI
Rnor_5.0	1	192,078,545 - 192,115,045 (-)	NCBI

Sequence:

show sequence

GAGGCGGGCACGCATTAGGCAGTGGATCAGAGCAAGGCGGAGGGCCGTGGGCAGGGAAAAACTG
GTGTGCTCGCGGCGGGCATCAGTCGGCTTAGCCTCGCGCACGGGGACTCTGCAGAGAAGATGAG
GTGGAGGACCATCCAAGCACGGTACTGTTTTCTCTTGGTTCCGTGCGTGCTCACTGCGCTGGAA
GCTGTTCCTATTGATGTGGACAAGACCAAAGTGCACAACGTCGAGCCGGTGGAAAGTGCAAGGA
TAGAACCGCCAGACACGGGACTTTATTATGATGAATACCTCAAGCAAGTGATTGAAGTCTTGGA
AACAGATCCGCATTTCAGAGAAAAGCTCCAGAAAGCAGACATAGAGGAGATAAGGAGCGGGAGG
CTGAGTCAAGAGCTGGACTTAGTAAGTCACAAAGTGAGGACGAGACTGGATGAACTGAAGAGGC
AAGAAGTAGGAAGACTGAGAATGCTCATCAAAGCCAAGCTGGATGCCCTTCAAGACACTGGCAT
GAATCACCACCTTCTTCTTAAGCAGTTTGAACACCTGAACCACCAGAATCCTGACACATTTGAA
TCCAAAGACTTGGATATGCTAATCAAGGCGGCCACCGCGGATCTGGAGCAGTATGACCGGACTC
GGCATGAGGAGTTTAAGAAGTATGAGATGATGAAGGAACATGAACGCAGAGAATATTTAAAAAC
GCTGAGTGAGGAGAAGAGGAAAGAGGAAGAAGCCAAGTTTGCAGAGATGAAGAGGAAGCATGAA
GACCACCCCAAAGTTAATCACCCCGGAAGCAAAGATCAACTAAAAGAGGTTTGGGAAGAGACTG
ATGGATTGGACCCTAATGACTTTGACCCCAAGACATTTTTCAAATTACATGATGTTAACAACGA
TGGATTCCTGGATGAACAAGAATTGGAAGCACTGTTCACAAAAGAGTTGGACAAAGTGTATAAC
CCGCAGAATGCAGAGGATGATATGATAGAAATGGAAGAGGAGAGGCTCAGGATGAGAGAGCACG
TCATGAATGAGATTGATAACAACAAAGACCGATTGGTGACTCTGGAGGAATTCTTGAGAGCCAC
AGAGAAGAAAGAATTCTTGGAGCCCGATAGCTGGGAGACACTGGACCAGCAGCAGTTATTCACC
GAGGAAGAGCTCAAAGAGTATGAAAGTATCATTGCTATCCAAGAGAATGAACTTAAGAAGAAGG
CAGATGAACTGCAGAAGCAGAAGGAGGAGCTGCAGCGCCAGCACGACCACCTTGAGGCCCAGAA
GCAGGAGTATCAGCAGGCCGTACAGCAGCTGGAACAGAAGAAATTCCAACAAGGGATTGCTCCA
TCAGGGCCGGCAGGAGAGCTGAAGTTTGAGCCACACACATAAAAGTCCTGATGTCTGCCAGAAC
TTGGAAGAAAACCGTTGACTCAACATCTGTTTCATCTTTCAACATCCCTTCTTTTCTCTTCACT
CAATAAATACTTTAAAAGCACATTTGGAATAAAGGAAGAGACTTTTAAGTGAGAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_067695	(Get FASTA)	NCBI Sequence Viewer
	XP_006230157	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF75993	(Get FASTA)	NCBI Sequence Viewer
	AAH61778	(Get FASTA)	NCBI Sequence Viewer
	AAK66864	(Get FASTA)	NCBI Sequence Viewer
	EDM17726	(Get FASTA)	NCBI Sequence Viewer
	EDM17727	(Get FASTA)	NCBI Sequence Viewer
	EDM17728	(Get FASTA)	NCBI Sequence Viewer
	EDM17729	(Get FASTA)	NCBI Sequence Viewer
	EDM17730	(Get FASTA)	NCBI Sequence Viewer
	Q9JI85	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_067695 ⟸ NM_021663
- Peptide Label:	precursor
- UniProtKB:	Q9JI85 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MRWRTIQARYCFLLVPCVLTALEAVPIDVDKTKVHNVEPVESARIEPPDTGLYYDEYLKQVIEV LETDPHFREKLQKADIEEIRSGRLSQELDLVSHKVRTRLDELKRQEVGRLRMLIKAKLDALQDT GMNHHLLLKQFEHLNHQNPDTFESKDLDMLIKAATADLEQYDRTRHEEFKKYEMMKEHERREYL KTLSEEKRKEEEAKFAEMKRKHEDHPKVNHPGSKDQLKEVWEETDGLDPNDFDPKTFFKLHDVN NDGFLDEQELEALFTKELDKVYNPQNAEDDMIEMEEERLRMREHVMNEIDNNKDRLVTLEEFLR ATEKKEFLEPDSWETLDQQQLFTEEELKEYESIIAIQESELKKKADELQKQKEELQRQHDHLEA QKQEYQQAVQQLEQKKFQQGIAPSGPAGELKFEPHT hide sequence

RefSeq Acc Id:	XP_006230157 ⟸ XM_006230095
- Peptide Label:	isoform X1
- UniProtKB:	G3V8R1 (UniProtKB/TrEMBL)
- Sequence:	show sequence MRWRTIQARYCFLLVPCVLTALEAVPIDVDKTKVHNVEPVESARIEPPDTGLYYDEYLKQVIEV LETDPHFREKLQKADIEEIRSGRLSQELDLVSHKVRTRLDELKRQEVGRLRMLIKAKLDALQDT GMNHHLLLKQFEHLNHQNPDTFESKDLDMLIKAATADLEQYDRTRHEEFKKYEMMKEHERREYL KTLSEEKRKEEEAKFAEMKRKHEDHPKVNHPGSKDQLKEVWEETDGLDPNDFDPKTFFKLHDVN NDGFLDEQELEALFTKELDKVYNPQNAEDDMIEMEEERLRMREHVMNEIDNNKDRLVTLEEFLR ATEKKEFLEPDSWETLDQQQLFTEEELKEYESIIAIQENELKKKADELQKQKEELQRQHDHLEA QKQEYQQAVQQLEQKKFQQGIAPSGPAGELKFEPHT hide sequence

RefSeq Acc Id:

ENSRNOP00000027753 ⟸ ENSRNOT00000027752

Protein Domains

EF-hand

Transcriptome

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

Promoters

RGD ID:

13690334

Promoter ID:

EPDNEW_R859

Type:

initiation region

Name:

Nucb2_1

Description:

nucleobindin 2

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	185,143,194 - 185,143,254	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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CSV

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

Visual

CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Damaging Variants

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
1	185107418	185107419	C	T	snv	WN/N (MCW), MR/N (MCW)
1	185110827	185110828	A	G	snv	MR/N (MCW), ACI/N (MCW), Buf/N (MCW), WN/N (MCW), F344/NRrrc (MCW), WKY/N (MCW), M520/N (MCW)
1	185122299	185122300	G	A	snv	Buf/N (MCW), F344/NRrrc (MCW), ACI/N (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620888	AgrOrtholog
Ensembl Genes	ENSRNOG00000020456	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000027753	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000027752	ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:5621784	IMAGE-MGC_LOAD
InterPro	EF-hand-dom_pair	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_Hand_1_Ca_BS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_hand_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	NUCB2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Nucleobindin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:59295	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72469	IMAGE-MGC_LOAD
NCBI Gene	59295	ENTREZGENE
PANTHER	PTHR19237	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR19237:SF22	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	EF-hand_7	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Nucb2	PhenoGen
PROSITE	EF_HAND_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_HAND_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	EFh	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF47473	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	G3V8R1	ENTREZGENE, UniProtKB/TrEMBL
	NUCB2_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-09-10	Nucb2	nucleobindin 2		NEFA precursor	Name updated	1299863	APPROVED
2002-08-07	Nucb2	NEFA precursor			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_physical_interaction	binds calcium	633331
gene_protein	an extrinsic membrane protein, facing the luminal Golgi compartment	633331

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD