Cxcr5 (C-X-C motif chemokine receptor 5)

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Gene: Cxcr5 (C-X-C motif chemokine receptor 5) Rattus norvegicus

Analyze

Symbol:

Cxcr5

Name:

C-X-C motif chemokine receptor 5

RGD ID:

62010

Description:

Predicted to have C-C chemokine binding activity and C-C chemokine receptor activity. Predicted to be involved in several processes, including leukocyte chemotaxis; lymph node development; and positive regulation of cytokinesis. Predicted to localize to external side of plasma membrane. Orthologous to human CXCR5 (C-X-C motif chemokine receptor 5); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 3H-1,2-dithiole-3-thione; ammonium chloride; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Blr1; Burkitt lymphoma receptor 1; burkitt lymphoma receptor 1 homolog; C-X-C chemokine receptor type 5; chemochine (C-X-C motif) receptor 5; chemokine (C-X-C motif) receptor 5; CXC-R5; CXCR-5; neurolymphatic receptor; NLR

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):	CXCR5 (C-X-C motif chemokine receptor 5)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Cxcr5 (chemokine (C-X-C motif) receptor 5)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Cxcr5 (C-X-C motif chemokine receptor 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CXCR5 (C-X-C motif chemokine receptor 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CXCR5 (C-X-C motif chemokine receptor 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cxcr5 (C-X-C motif chemokine receptor 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CXCR5 (C-X-C motif chemokine receptor 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	CXCR5 (C-X-C motif chemokine receptor 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cxcr5 (C-X-C motif chemokine receptor 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Cxcr5 (chemokine (C-X-C motif) receptor 5)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	CXCR5 (C-X-C motif chemokine receptor 5)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	npr-20	Alliance	DIOPT (Ensembl Compara\|InParanoid)

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
Rnor_6.0	8	48,835,688 - 48,852,032 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	48,836,957 - 48,850,671 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	47,454,074 - 47,470,348 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	47,485,125 - 47,498,509 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	47,493,890 - 47,494,999 (-)	NCBI
Celera	8	44,428,390 - 44,441,750 (-)	NCBI		Celera
Cytogenetic Map	8	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Dwarfism (ISO)

Glycogen Storage Disease IB (ISO)

immunodeficiency 19 (ISO)

long QT syndrome 10 (ISO)

primary biliary cholangitis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

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

3H-1,2-dithiole-3-thione (EXP)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

aripiprazole (ISO)

arsane (ISO)

arsenic atom (ISO)

asperentin (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bisphenol A (EXP)

buta-1,3-diene (ISO)

butanal (ISO)

calcium atom (ISO)

calcium(0) (ISO)

carbon nanotube (ISO)

ceric oxide (EXP)

chlordecone (ISO)

chloroprene (ISO)

chrysene (ISO)

copper atom (EXP)

copper(0) (EXP)

dioxygen (ISO)

endosulfan (EXP)

fumonisin B1 (ISO)

genistein (ISO)

L-ascorbic acid (ISO)

lead(0) (ISO)

lead(2+) (ISO)

mycophenolic acid (ISO)

mycotoxin (ISO)

neoechinulin A (ISO)

ozone (ISO)

pentanal (ISO)

pevonedistat (ISO)

phosgene (ISO)

scopolamine (EXP)

sterigmatocystin (ISO)

sulforaphane (ISO)

tamibarotene (ISO)

tetrachloromethane (ISO)

tetraphene (ISO)

titanium dioxide (ISO)

trimellitic anhydride (ISO)

zearalenone (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

B cell activation (IEA)

calcium-mediated signaling (IBA)

cell chemotaxis (IBA)

chemokine-mediated signaling pathway (IEA)

G protein-coupled receptor signaling pathway (IEA)

immune response (IBA,IEA)

leukocyte chemotaxis (IEA,ISO)

lymph node development (IEA,ISO)

positive regulation of cytokinesis (IEA,ISO)

positive regulation of cytosolic calcium ion concentration (IBA)

Cellular Component

external side of plasma membrane (IBA,IEA,ISO)

integral component of membrane (IEA)

Molecular Function

C-C chemokine binding (IBA)

C-C chemokine receptor activity (IBA)

C-X-C chemokine receptor activity (IEA)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

chemokine mediated signaling pathway (IEA)

cytokine mediated signaling pathway (IEA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Kouba M, etal., FEBS Lett 1993 Apr 26;321(2-3):173-8.
3.	MGD data from the GO Consortium
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	Pipeline to import KEGG annotations from KEGG into RGD
6.	RGD automated data pipeline
7.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12732660	PMID:22888021	PMID:23583643	PMID:25348153

Genomics

Comparative Map Data

Cxcr5
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	8	48,835,688 - 48,852,032 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	48,836,957 - 48,850,671 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	47,454,074 - 47,470,348 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	47,485,125 - 47,498,509 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	47,493,890 - 47,494,999 (-)	NCBI
Celera	8	44,428,390 - 44,441,750 (-)	NCBI		Celera
Cytogenetic Map	8	q22	NCBI

CXCR5
(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	118,883,892 - 118,897,787 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	11	118,883,892 - 118,897,787 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	118,754,475 - 118,766,980 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	118,259,777 - 118,272,181 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	11	118,269,310 - 118,272,180	NCBI
Celera	11	115,914,233 - 115,926,662 (+)	NCBI
Cytogenetic Map	11	q23.3	NCBI
HuRef	11	114,694,357 - 114,706,861 (+)	NCBI		HuRef
CHM1_1	11	118,640,782 - 118,653,288 (+)	NCBI		CHM1_1

Cxcr5
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	44,423,084 - 44,437,741 (-)	NCBI	GRCm39		mm39
GRCm38	9	44,511,787 - 44,526,444 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	44,511,787 - 44,561,877 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	44,319,870 - 44,334,504 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	9	44,262,782 - 44,277,416 (-)	NCBI			mm8
Celera	9	41,765,140 - 41,779,807 (-)	NCBI		Celera
Cytogenetic Map	9	A5.2	NCBI
cM Map	9	24.84	NCBI

Cxcr5
(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_004955412	20,016,587 - 20,031,629 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955412	20,016,768 - 20,031,635 (+)	NCBI	ChiLan1.0	ChiLan1.0

CXCR5
(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	117,652,368 - 117,664,852 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	117,652,368 - 117,664,852 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	11	113,722,084 - 113,735,987 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

CXCR5
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	5	14,923,089 - 14,932,762 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	5	14,921,447 - 14,932,937 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Cxcr5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936542	3,860,536 - 3,872,528 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CXCR5
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	9	46,127,488 - 46,146,637 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	9	46,134,243 - 46,146,638 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	9	51,169,120 - 51,183,302 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CXCR5
(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	110,253,792 - 110,267,251 (+)	NCBI
ChlSab1.1 Ensembl	1	110,254,723 - 110,265,597 (+)	Ensembl

Cxcr5
(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_004624784	14,285,998 - 14,298,679 (+)	NCBI

Position Markers

G45300

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	48,843,137 - 48,843,316	NCBI	Rnor6.0
Rnor_5.0	8	47,461,523 - 47,461,702	UniSTS	Rnor5.0
RGSC_v3.4	8	47,491,148 - 47,491,327	UniSTS	RGSC3.4
Celera	8	44,434,413 - 44,434,580	UniSTS
Cytogenetic Map	8	q22	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
2317032	Ginf2	Gastrointestinal inflammation QTL 2	3.21	0.005	liver integrity trait (VT:0010547)	liver granuloma severity score (CMO:0002157)	8	7368076	52368076	Rat
2317036	Livw3	Liver weight QTL 3	2.43	0.01	liver mass (VT:0003402)	liver weight to body weight ratio (CMO:0000633)	8	7368076	52368076	Rat
2317048	Ginf1	Gastrointestinal inflammation QTL 1	3.52	0.005	cecum mucosa thickness (VT:0010234)	enterocolitis severity score (CMO:0002138)	8	7368076	52368076	Rat
2301416	Bp315	Blood pressure QTL 315		0.008	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	8738677	53738677	Rat
1581557	Eae16	Experimental allergic encephalomyelitis QTL 16	3.8		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	8	9531047	119211942	Rat
1354627	Despr14	Despair related QTL 14		0.0056	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	8	10388439	55388439	Rat
1354595	Despr4	Despair related QTL 4	2.16	0.0036	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	8	10388439	55388439	Rat
631650	Stl6	Serum triglyceride level QTL 6	4	0.0019	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	10938911	120496129	Rat
1598824	Memor4	Memory QTL 4	2.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	8	11373267	57541668	Rat
2317030	Wbc5	White blood cell count QTL 5	3.21	0.005	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	8	11448251	56448251	Rat
2317051	Aia18	Adjuvant induced arthritis QTL 18	2.42		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	8	11448251	56448251	Rat
1558646	Swd5	Spike wave discharge measurement QTL 5	3.45	0.00036	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge frequency (CMO:0001742)	8	17666555	62666555	Rat
61373	Mcs4	Mammary carcinoma susceptibility QTL 4	1.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	8	20717592	65717592	Rat
631271	Lecl1	Lens clarity QTL 1		0.001	lens clarity trait (VT:0001304)	age of onset/diagnosis of cataract (CMO:0001584)	8	21464919	91140553	Rat
731182	Uae24	Urinary albumin excretion QTL 24	6.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	21813070	100873963	Rat
631842	Inf1	Infertility severity QTL 1	4.1	0.001	seminal gland mass (VT:0010524)	seminal vesicle wet weight (CMO:0001603)	8	27841496	72841496	Rat
1359021	Bp271	Blood pressure QTL 271	1.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	28168023	50708951	Rat
631648	Stl5	Serum triglyceride level QTL 5	4	0.0003	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	29867983	59908353	Rat
1358892	Kidm26	Kidney mass QTL 26	3.69		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	29867983	106526740	Rat
1358896	Bp262	Blood pressure QTL 262	2.89		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	29867983	106526740	Rat
1358907	Cm40	Cardiac mass QTL 40	1.89		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	29867983	106526740	Rat
2303564	Gluco43	Glucose level QTL 43	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	30144800	75144800	Rat
2303572	Insul13	Insulin level QTL 13	2		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	8	30144800	75144800	Rat
1331804	Cm30	Cardiac mass QTL 30	3.77443		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	8	30918112	58858224	Rat
1300146	Rf17	Renal function QTL 17	2.9		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	8	30918112	75918112	Rat
8662823	Vetf5	Vascular elastic tissue fragility QTL 5	1.9		artery integrity trait (VT:0010639)	patent ductus arteriosus score (CMO:0002566)	8	30918112	107206309	Rat
2302278	Gluco36	Glucose level QTL 36	4.2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	32201981	54065241	Rat
724514	Uae15	Urinary albumin excretion QTL 15	2.9		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	32201981	75971421	Rat
1549908	Neudeg1	Neurodegradation QTL 1	5.5	0	nervous system integrity trait (VT:0010566)	logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)	8	32888352	101374135	Rat
1331744	Bp217	Blood pressure QTL 217	3.398		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	62857995	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	33558660	65717592	Rat
1359033	Bp273	Blood pressure QTL 273			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
11556286	Cm81	Cardiac mass QTL 81		0.01	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	33558660	65717592	Rat
2313046	Bss78	Bone structure and strength QTL 78	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	8	33558660	89058369	Rat
2313057	Bss76	Bone structure and strength QTL 76	3	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	8	33558660	89058369	Rat
2313067	Bss77	Bone structure and strength QTL 77	3.1	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	8	33558660	89058369	Rat
2313088	Bss75	Bone structure and strength QTL 75	3.1	0.0001	body length (VT:0001256)	body length, nose to rump (CMO:0000079)	8	33558660	89058369	Rat
1578765	Klgr1	Kidney lesion grade QTL 1	3.3	0.0001	kidney morphology trait (VT:0002135)	organ lesion measurement (CMO:0000677)	8	33558660	109028082	Rat
1578769	Uae31	Urinary albumin excretion QTL 31	3.3	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	33558660	109028082	Rat
1578755	Pur5	Proteinuria QTL 5	3.3	0.0001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	8	33558660	109028082	Rat
2316950	Scl66	Serum cholesterol level QTL 66	4.1		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	33558764	113580387	Rat
1298065	Scl16	Serum cholesterol level QTL 16	3.8		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	35041414	80041414	Rat
1582222	Epfw2	Epididymal fat weight QTL 2	3.2	0.0005	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	8	35925594	80925594	Rat
1331838	Niddm61	Non-insulin dependent diabetes mellitus QTL 61	3.53	0.0004	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39230130	106506973	Rat
61358	Bp39	Blood pressure QTL 39	2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	39927901	84927901	Rat
61464	Niddm11	Non-insulin dependent diabetes mellitus QTL 11	3.1	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39958022	84958022	Rat
737824	Hcar10	Hepatocarcinoma resistance QTL 10	2.9		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	8	44219197	89542960	Rat
1358906	Bp253	Blood pressure QTL 253	4	0.0004	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	44219197	100873963	Rat
1554321	Bmd3	Bone mineral density QTL 3	7.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	8	44458129	118087517	Rat
1331769	Rf39	Renal function QTL 39	3.871		urine output (VT:0003620)	timed urine volume (CMO:0000260)	8	45712344	80003418	Rat
1298079	Activ2	Activity QTL 2	9.5	0.000001	voluntary movement trait (VT:0003491)	rearing measurement (CMO:0001515)	8	45712344	90712344	Rat
631216	Stl9	Serum triglyceride level QTL 9	4.71	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	8	45712475	75971259	Rat
5684993	Bmd84	Bone mineral density QTL 84	4.1		tibia mineral mass (VT:1000283)	bone mineral content (CMO:0001554)	8	46588437	54065241	Rat
70161	Bp62	Blood pressure QTL 62	2.9	0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	46588437	96998640	Rat
12879882	Am8	Aortic mass QTL 8		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	8	47200750	106394378	Rat
12879878	Bw183	Body weight QTL 183		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	8	47200750	106394378	Rat
12879879	Cm99	Cardiac mass QTL 99		0.001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	47200750	106394378	Rat
12879880	Cm100	Cardiac mass QTL 100		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	8	47200750	106394378	Rat
12879881	Cm101	Cardiac mass QTL 101		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	8	47200750	106394378	Rat
12879883	Kidm65	Kidney mass QTL 65		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	47200750	106394378	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	44
Count of miRNA genes:	41
Interacting mature miRNAs:	44
Transcripts:	ENSRNOT00000016580
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	2				11						1
Low	1		37	25	8	25		1		19	29	11
Below cutoff		43	20	16		16	8	10	67	16	11		8

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053303	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006242901	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AAHX01054361	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC105645	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473975	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X71463	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000016580 ⟹ ENSRNOP00000016580

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	8	48,836,957 - 48,850,671 (-)	Ensembl

RefSeq Acc Id:

NM_053303 ⟹ NP_445755

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	8	48,837,114 - 48,850,498 (-)	NCBI
Rnor_5.0	8	47,454,074 - 47,470,348 (-)	NCBI
RGSC_v3.4	8	47,485,125 - 47,498,509 (-)	RGD
Celera	8	44,428,390 - 44,441,750 (-)	RGD

Sequence:

show sequence

ATGAACTCCCCGATATCGCTAGACATGGGCGCCATCACCTACAACATGGACGATCTGTACAAGG
AACTGGCCATCTACAGTAACAGCACGGAGATCCCCCTACAGGACAGTATCTTCTGTTCTACAGA
GGAGGGGCCCCTACTGACTTCCTTTAAGACGATATTCATGCCTGTGGCCTACAGCCTCATCTTC
CTCCTGGGTATGATGGGAAACATCCTCGTACTGGTAATCCTGGAGAGGCACCGGCACACTCGGA
GCTCAACGGAGACCTTCCTGTTCCACCTGGCAGTAGCCGACCTTCTCTTGGTCTTCATCTTGCC
TTTTGCAGTGGCTGAGGGCTCTGTGGGTTGGGTCCTAGGGACCTTCCTCTGCAAAACTGTGATC
GCCCTGCACAAGATCAATTTCTACTGCAGCAGCCTGCTGCTGGCCTGCATAGCTGTCGACCGTT
ATCTGGCCATCGTCCATGCGGTCCACGCCTACCGCCGCCGCCGTCTCCTCTCTATCCACATCAC
CTGCTCGACTATTTGGCTAGCCGGCTTCCTATTTGCCTTGCCAGAACTCCTCTTTGCCAAGGTT
GTCCAACCTCATAACAACGAGTCCTTACCACAGTGCATCTTCTCCCAAGAAAATGAAGCCGAAA
CTAGAGCCTGGTTCGCCTCCCGGTTTCTCTACCACACTGGGGGCTTCCTGCTACCGATGCTCGT
GATGGCCTGGTGTTATGTGGGAGTGGTACACAGGCTATTGCAGGCCCAGCGGCGCCCTCAGAGG
CAGAAGGCAGTCAGGGTGGCCATCTTGGTGACAAGCATCTTCCTTCTCTGCTGGTCACCCTACC
ACATTGTCATCTTCCTCGATACACTGGAAAGGCTGAAGGCTGTGAACAGCAGTTGCGAATTGAG
TGGCTACCTCTCAGTGGCTATCACCTTATGTGAATTCCTGGGCCTGGCTCACTGCTGTCTCAAT
CCCATGCTCTACACCTTCGCTGGCGTAAAGTTCCGCAGTGACTTGTCTCGGCTTCTGACCAAGC
TGGGCTGTGCTGGCCCGGCCTCCCTTTGTCAGCTCTTTCCGGGCTGGCGCAAGAGCAGTCTCTC
TGAGTCAGAGAACGCTACTTCTCTTACCACCTTCTAGATCCCGGGGTCTCAGCCCCCGGCTCTG
TTTCTGTTTTCCT

hide sequence

RefSeq Acc Id:

XM_006242901 ⟹ XP_006242963

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	8	48,835,688 - 48,852,032 (-)	NCBI
Rnor_5.0	8	47,454,074 - 47,470,348 (-)	NCBI

Sequence:

show sequence

ACTACAATAGCCCAAAGAGAGCCTAAAAGTCTTCACACTTTAGTCCTGAGGAAGATGTGTATAT
TGAGGAAGAGGAGGGACTATAACCAAGCTTTGAAGGCAGAGAAAGGTGAGACTGGACTATGGAG
GAGATGATGGAAGAGGAATGCTGCCAGGACAGGATCCCCTCGGGAGGAAAGGGAAGGGTAATAA
CAATGGCAAAGCAGAGAACAGCACGGCCTGTGTGGGTGGTGATTTGGCTTAGAAGGGGAGGGTG
ATTGCAGAGTCGGGGCAAAGCAAAGCAAAACACACAAACAGTAGTGCCTTTAGGTACAGTCTTA
CACCATCGTGGACTAAGTCGGGAAATGCCCTTCCATGGAGGAAAACCCACCAGGACAAGACCTG
GTGGGAAATGGATCAATGCCCACCACAGTTCTTCATGAAAGAAGCAGCTTTCAGGATGGGACAG
AGCAGGCGCGGTGAGCTTGCCAATGGGAGAGGTTGACAACCATGGAGTCAGGACCCTTGGGTGC
AAGGTAGCCATCATTGGACCATTGGTGCATTATGGGATCCTGGGCGCTGGCATCGACCTTCTCA
GCATCAGACAGTGACCAGCCTGGTGACGCAGAGCTGTAGCGATGAACTACCCACTAACCTTGGA
CATAGACTCCATCACCTACAACATGGATGAGCTGTACAAGGAACTGGCCATCTACAGTAACAGC
ACGGAGATCCCCCTACAGGACAGTATCTTCTGTTCTACAGAGGAGGGGCCCCTACTGACTTCCT
TTAAGACGATATTCATGCCTGTGGCCTACAGCCTCATCTTCCTCCTGGGTATGATGGGAAACAT
CCTCGTACTGGTAATCCTGGAGAGGCACCGGCACACTCGGAGCTCAACGGAGACCTTCCTGTTC
CACCTGGCAGTAGCCGACCTTCTCTTGGTCTTCATCTTGCCTTTTGCAGTGGCTGAGGGCTCTG
TGGGTTGGGTCCTAGGGACCTTCCTCTGCAAAACTGTGATCGCCCTGCACAAGATCAATTTCTA
CTGCAGCAGCCTGCTGCTGGCCTGCATAGCTGTCGACCGTTATCTGGCCATCGTCCATGCGGTC
CACGCCTACCGCCGCCGCCGTCTCCTCTCCATCCACATCACCTGCTCGACTATTTGGCTAGCCG
GCTTCCTATTTGCCTTGCCAGAACTCCTCTTTGCCAAGGTTGTCCAACCTCATAACAACGAGTC
CTTACCACAGTGCATCTTCTCCCAAGAAAATGAAGCCGAAACTAGAGCCTGGTTCGCCTCCCGG
TTTCTCTACCACACTGGGGGCTTCCTGCTACCGATGCTCGTGATGGCCTGGTGTTATGTGGGAG
TGGTACACAGGCTATTGCAGGCCCAGCGGCGCCCTCAGAGGCAGAAGGCAGTCAGGGTGGCCAT
CTTGGTGACAAGCATCTTCCTTCTCTGCTGGTCACCCTACCACATTGTCATCTTCCTCGATACA
CTGGAAAGGCTGAAGGCTGTGAACAGCAGTTGCGAATTGAGTGGCTACCTCTCGGTGGCTATCA
CCTTATGTGAATTCCTGGGCCTGGCTCACTGCTGTCTCAATCCCATGCTCTACACCTTCGCTGG
CGTAAAGTTCCGCAGTGACTTGTCTCGGCTTCTGACCAAGCTGGGCTGTGCTGGCCCGGCCTCC
CTTTGTCAGCTCTTTCCGGGCTGGCGCAAGAGCAGTCTCTCTGAGTCAGAGAACGCTACTTCTC
TTACCACCTTCTAGATCCCGGGGTCTCAGCCCCCGGCTCTGTTTCTGTTTTCCTTGGGAGCATA
AACGTGGTGTTAGAAACCTGTCTAACATAAGCTGGGATTCTAAGAGCTATTGGGGCCAGTGTCC
CCCAGCTGGGACGGCTAGACAAACTCTTTCTAGAATGTTCCCAAAGCTCTTCTGCCAGCCCTCA
GGCTAGACTAGAGCCACAGGAGGGGAAAGCGGCCCAAAGGCAAGGCAAGCAATACCCAGACCAC
CTATATCCCCTTGGACGAAGAGGACTCCACACACCTCCCATCTTAACAAGCTAAAGTGAAGACT
CAGCTTTATTTCTTCCTGGCCATAGGGAAAAGCCACCTCTGCCTGCGGCACACAGTCTCATCTT
CCTCCCAATTATGAGCTCAGACTCTCCTCAGCTACCGACTGCTGCAGCTCCCCATTACTCCTAC
ACCACTGAGGAACAGCCACCTGGCGGCAGACTGTGGCCTTAATGTGCCTGTCTCCTAAATACAG
ACGTATGCCAGACCTTCACCCGTGCCTTTCTCCTAACCAGCAGGAACCTGAAACTGATCTGCTT
TAGGTAGCTGTCTGCTCCAACCAAACCACCACTGGATCAGCCCCATGTTACTGGATCTTGGATT
ACAGACTGAGGGCAAGTTCCAGAAGGTCCTGGAACCTTGCCAGTATCCTGAGAAGAGTAAAGGG
CAAGCAAGCCAGCAGGAAAGAGGCCCAGTGGAAAAAAATGGAAAGACACCTTTTCCAGGCTCCA
AAGAGGAACAAGTAAAAATCCAACCCAGCTGTCTTCTCCACCCATGGACCAAAGCTTCCAGATT
GGCAGGGAGATGAGATCCAGGGCCCTAGTGGATTCTGGGCACCGATGGGGAAGGAGGTCAACTG
CCTGGGGAAAGTAAGCCTCAGGAGAGGGGACATTTAGCTAAGAGAATGAAGATAGAGGTCCCTG
TCTTCATTAGGTAGAGACAAAGTGAGAAGCCGACCTGGGTGGGCAAGTCCCCAGGCCCAGGGAG
GCAGTACCTTGCACCTGGGAGGGTACTACTCAGATAGAACCAGCGGAAACTGCTCCACACCTAC
TTAGGGGAAGCCAGCAGGCAACTCTGAGCTCTGCTTCCTCCCAGCCACTGATCTAGGAGGGTGG
GGGGTGGACTGAGGGAAGCAGAGTTGCCTAGCACCACTCAAGTCAACCATACAGGCTCCCGGGG
GACCCCACTGGGGAAATCAATGCTATAGCTCCGGAGACTGTATCCTCATTGCAGAATGGTGGTG
ACACCTGGGGATCCCCTTTTCTGCTCCCAGCTTCTGACAGCCAGCTGGGCAGAGGCGAAACCAG
ACACAGAAATAAAAATGCAAGAGAAGGCATTTTTGAATTTTCTTTTTAATAAAAAGGCACCTAT
AAAACAGGGCAATACAGTACAGGCTGCACAGAGACCCCCGGAACAAGCCTAAAAAGTGTTTCAA
AATAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_445755	(Get FASTA)	NCBI Sequence Viewer
	XP_006242963	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	CAA50582	(Get FASTA)	NCBI Sequence Viewer
	EDL95327	(Get FASTA)	NCBI Sequence Viewer
	P34997	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_445755 ⟸ NM_053303

- UniProtKB:

P34997 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MNSPISLDMGAITYNMDDLYKELAIYSNSTEIPLQDSIFCSTEEGPLLTSFKTIFMPVAYSLIF
LLGMMGNILVLVILERHRHTRSSTETFLFHLAVADLLLVFILPFAVAEGSVGWVLGTFLCKTVI
ALHKINFYCSSLLLACIAVDRYLAIVHAVHAYRRRRLLSIHITCSTIWLAGFLFALPELLFAKV
VQPHNNESLPQCIFSQENEAETRAWFASRFLYHTGGFLLPMLVMAWCYVGVVHRLLQAQRRPQR
QKAVRVAILVTSIFLLCWSPYHIVIFLDTLERLKAVNSSCELSGYLSVAITLCEFLGLAHCCLN
PMLYTFAGVKFRSDLSRLLTKLGCAGPASLCQLFPGWRKSSLSESENATSLTTF

hide sequence

RefSeq Acc Id:	XP_006242963 ⟸ XM_006242901
- Peptide Label:	isoform X1
- UniProtKB:	G3V7M1 (UniProtKB/TrEMBL)
- Sequence:	show sequence MNYPLTLDIDSITYNMDELYKELAIYSNSTEIPLQDSIFCSTEEGPLLTSFKTIFMPVAYSLIF LLGMMGNILVLVILERHRHTRSSTETFLFHLAVADLLLVFILPFAVAEGSVGWVLGTFLCKTVI ALHKINFYCSSLLLACIAVDRYLAIVHAVHAYRRRRLLSIHITCSTIWLAGFLFALPELLFAKV VQPHNNESLPQCIFSQENEAETRAWFASRFLYHTGGFLLPMLVMAWCYVGVVHRLLQAQRRPQR QKAVRVAILVTSIFLLCWSPYHIVIFLDTLERLKAVNSSCELSGYLSVAITLCEFLGLAHCCLN PMLYTFAGVKFRSDLSRLLTKLGCAGPASLCQLFPGWRKSSLSESENATSLTTF hide sequence

RefSeq Acc Id:

ENSRNOP00000016580 ⟸ ENSRNOT00000016580

Protein Domains

G_PROTEIN_RECEP_F1_2

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/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)

ACI/EurMcwi (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

ACI/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

BBDP/Wor (RGD)

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CSV

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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

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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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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

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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)

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CSV

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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

F344/NRrrc (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

FHH/EurMcwi (MCW)

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CSV

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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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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

FHL/EurMcwi (MCW)

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CSV

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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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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

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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CSV

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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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CSV

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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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CSV

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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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CSV

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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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CSV

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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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CSV

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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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CSV

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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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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

SBN/Ygl (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:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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CSV

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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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:62010	AgrOrtholog
Ensembl Genes	ENSRNOG00000012430	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000016580	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016580	ENTREZGENE, UniProtKB/TrEMBL
InterPro	Chemokine_CXCR5	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	GPCR_Rhodpsn	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	GPCR_Rhodpsn_7TM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:29363	UniProtKB/Swiss-Prot
NCBI Gene	29363	ENTREZGENE
Pfam	7tm_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Cxcr5	PhenoGen
PRINTS	CXCCHMKINER5	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	GPCRRHODOPSN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	G_PROTEIN_RECEP_F1_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	G_PROTEIN_RECEP_F1_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene	Rn.127121	ENTREZGENE
UniProt	CXCR5_RAT	UniProtKB/Swiss-Prot
	G3V7M1	ENTREZGENE, UniProtKB/TrEMBL
	P34997	ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-03-22	Cxcr5	C-X-C motif chemokine receptor 5	Cxcr5	chemokine (C-X-C motif) receptor 5	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-26	Cxcr5	chemokine (C-X-C motif) receptor 5	Cxcr5	chemochine (C-X-C motif) receptor 5	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-05-15	Cxcr5	chemochine (C-X-C motif) receptor 5	Blr1	Burkitt lymphoma receptor 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Blr1	Burkitt lymphoma receptor 1			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in the brain and spleen	61543

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

Imported Annotations - KEGG (archival)