Slc45a2 (solute carrier family 45, member 2)

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Gene: Slc45a2 (solute carrier family 45, member 2) Rattus norvegicus

Analyze

Symbol:

Slc45a2

Name:

solute carrier family 45, member 2

RGD ID:

1306690

Description:

Predicted to have sucrose:proton symporter activity. Predicted to be involved in developmental pigmentation and sucrose transport. Predicted to localize to membrane. Human ortholog(s) of this gene implicated in oculocutaneous albinism type IV and pigmentation disease. Orthologous to human SLC45A2 (solute carrier family 45 member 2); INTERACTS WITH acrylamide; bisphenol A; copper atom.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC310152; Matp; membrane associated transporter protein; membrane-associated transporter protein

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

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	2	60,966,671 - 60,999,398 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	60,966,789 - 60,999,398 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	83,685,368 - 83,717,569 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	60,349,773 - 60,383,838 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	60,278,089 - 60,311,585 (+)	NCBI
Celera	2	58,688,367 - 58,720,772 (-)	NCBI		Celera
Cytogenetic Map	2	q16	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

alpha-methylacyl-CoA racemase deficiency (ISO)

basal cell carcinoma (ISO)

genetic disease (ISO)

hemorrhagic disease (ISO)

melanoma (ISO)

Neurodevelopmental Disorders (ISO)

Nonsyndromic Oculocutaneous Albinism (ISO)

oculocutaneous albinism (ISO,ISS)

oculocutaneous albinism type IV (ISO)

skin melanoma (ISO)

Skin/Hair/Eye Pigmentation, Variation In, 5 (ISO)

squamous cell carcinoma (ISO)

substance-related disorder (ISO)

thrombocytopenia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

3-Iodothyronamine (ISO)

4-hydroxyphenyl retinamide (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

calcitriol (ISO)

clothianidin (ISO)

colforsin daropate hydrochloride (ISO)

copper atom (EXP)

copper(0) (EXP)

cyclosporin A (ISO)

disodium selenite (ISO)

monosodium L-glutamate (ISO)

propanal (ISO)

resveratrol (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

testosterone (ISO)

xylitol (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

developmental pigmentation (ISO)

sucrose transport (ISO)

Cellular Component

cellular_component (ND)

integral component of membrane (IEA)

membrane (IBA)

Molecular Function

molecular_function (ND)

sucrose:proton symporter activity (IBA,ISO)

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.	Inagaki K, etal., Am J Hum Genet. 2004 Mar;74(3):466-71. Epub 2004 Feb 11.
3.	MGD data from the GO Consortium
4.	OMIM Disease Annotation Pipeline
5.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6.	RGD automated import pipeline for gene-chemical interactions
7.	RGD comprehensive gene curation

Additional References at PubMed

PMID:11700328	PMID:25164149

Genomics

Candidate Gene Status

Slc45a2 is a candidate Gene for QTL Gdil2

Comparative Map Data

Slc45a2
(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	2	60,966,671 - 60,999,398 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	60,966,789 - 60,999,398 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	83,685,368 - 83,717,569 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	60,349,773 - 60,383,838 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	60,278,089 - 60,311,585 (+)	NCBI
Celera	2	58,688,367 - 58,720,772 (-)	NCBI		Celera
Cytogenetic Map	2	q16	NCBI

SLC45A2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	5	33,944,623 - 33,984,693 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	33,944,623 - 33,984,693 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	33,944,721 - 33,984,780 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	33,980,478 - 34,020,537 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	33,980,486 - 34,020,506	NCBI
Celera	5	33,833,208 - 33,873,213 (-)	NCBI
Cytogenetic Map	5	p13.2	NCBI
HuRef	5	33,922,738 - 33,962,743 (-)	NCBI		HuRef
CHM1_1	5	33,946,354 - 33,986,351 (-)	NCBI		CHM1_1

Slc45a2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	11,000,807 - 11,029,319 (+)	NCBI	GRCm39		mm39
GRCm38	15	11,000,721 - 11,029,233 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	11,000,721 - 11,029,233 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	10,930,476 - 10,958,988 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	15	10,945,446 - 10,973,958 (+)	NCBI			mm8
Celera	15	10,792,914 - 10,821,506 (+)	NCBI		Celera
Cytogenetic Map	15	A1	NCBI
cM Map	15	5.4	NCBI

Slc45a2
(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_004955426	19,498,942 - 19,530,628 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955426	19,498,942 - 19,530,628 (-)	NCBI	ChiLan1.0	ChiLan1.0

SLC45A2
(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	5	81,743,254 - 81,784,565 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	81,743,254 - 81,784,565 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	76,357,549 - 76,398,571 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

SLC45A2
(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	4	73,815,291 - 73,867,437 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	4	73,838,684 - 73,868,222 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Slc45a2
(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_004936518	7,094,949 - 7,139,961 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLC45A2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	16	19,952,451 - 20,023,285 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	16	19,958,315 - 20,002,198 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	16	20,718,138 - 20,759,105 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SLC45A2
(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	4	33,178,614 - 33,219,664 (-)	NCBI
ChlSab1.1 Ensembl	4	33,179,349 - 33,219,028 (-)	Ensembl

Slc45a2
(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_004624759	20,640,407 - 20,701,790 (+)	NCBI

Position Markers

D2Got316

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	2	60,972,186 - 60,972,362	NCBI	Rnor6.0
Rnor_5.0	2	83,711,996 - 83,712,172	UniSTS	Rnor5.0
RGSC_v3.4	2	60,355,170 - 60,355,346	UniSTS	RGSC3.4
Celera	2	58,715,199 - 58,715,375	UniSTS
Cytogenetic Map	2	q16	UniSTS

D2Got380

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	2	60,966,490 - 60,966,758	NCBI	Rnor6.0
Rnor_5.0	2	83,717,600 - 83,717,868	UniSTS	Rnor5.0
RGSC_v3.4	2	60,349,474 - 60,349,742	UniSTS	RGSC3.4
Celera	2	58,720,803 - 58,721,079	UniSTS
Cytogenetic Map	2	q16	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
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
5684990	Bmd82	Bone mineral density QTL 82	2.8		tibia mineral mass (VT:1000283)	bone mineral content (CMO:0001554)	2	60325352	106432915	Rat
5684996	Bmd85	Bone mineral density QTL 85	4.7	0.024	tibia mineral mass (VT:1000283)	bone mineral density (CMO:0001226)	2	60325352	106432915	Rat
6480225	Gdil1	Gastrointestinal dilation QTL 1			enteric ganglion morphology trait (VT:0001045)	length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)	2	58344100	75687607	Rat
631500	Bp99	Blood pressure QTL 99	2.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	60325686	105059293	Rat
9590095	Sffal3	Serum free fatty acids level QTL 3	6.78	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	2	27760301	72760301	Rat
7387318	Stl32	Serum triglyceride level QTL 32	3.2	0.0003	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	2	22612952	67612952	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	56244671	217498710	Rat
10402051	Gdil2	Gastrointestinal dilation QTL 2			enteric ganglion morphology trait (VT:0001045)	length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)	2	23280647	75687607	Rat
1300155	Bp174	Blood pressure QTL 174	4.09		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	2	42776916	62238534	Rat
1302794	Stl27	Serum triglyceride level QTL 27	4.4	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	2	23837491	149614623	Rat
1354592	Rf50	Renal function QTL 50	3.5		urine output (VT:0003620)	timed urine volume (CMO:0000260)	2	54436698	75687607	Rat
1354601	Slep1	Serum leptin concentration QTL 1	5.39		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	2	43149788	198704485	Rat
1354603	Bp243	Blood pressure QTL 243	3.9		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26186097	135654963	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	26186097	83819822	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	26186097	83819822	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26186097	83819822	Rat
1558648	Smcn1	Smooth muscle cell number QTL 1		0.039	blood vessel smooth muscle cell quantity (VT:0010525)	aorta smooth muscle cell count per unit vessel length (CMO:0001646)	2	60131410	135646395	Rat
1357990	Ael1	Aortic elastin QTL 1	3.1	0.00091	aorta elastin amount (VT:0003905)	aortic elastin	2	19016465	64016465	Rat
1578671	Bmd10	Bone mineral density QTL 10	5.4		femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	2	9444679	68866454	Rat
61371	Edpm1	Estrogen-dependent pituitary mass QTL 1	4	0.05	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	2	34088175	91101903	Rat
61438	Cia7	Collagen induced arthritis QTL 7	4.6	0.0001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	2	60325352	147522851	Rat
2290453	Scl55	Serum cholesterol level QTL 55	2.83		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	2	26186097	142053534	Rat
631208	Bw1	Body weight QTL1	5.09		mesenteric fat pad mass (VT:0010427)	mesenteric fat pad weight as a percentage of body weight (CMO:0000654)	2	43149788	85642672	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46537589	217498710	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43133606	217498545	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43133606	217498545	Rat
2293835	Kiddil5	Kidney dilation QTL 5	3.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42776916	169852800	Rat
2293843	Kiddil6	Kidney dilation QTL 6	3.1		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42776916	195645082	Rat
2306903	Bp336	Blood pressure QTL 336		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	36245223	112175725	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
12879843	Am3	Aortic mass QTL 3		0.016	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	2	27161361	148295267	Rat
12879841	Cm87	Cardiac mass QTL 87		0.026	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	2	27161361	148295267	Rat
10755499	Bp389	Blood pressure QTL 389	2.61		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	16679272	245624402	Rat
1358894	Kidm24	Kidney mass QTL 24	4.03		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	23837491	169852800	Rat
1358901	Cm38	Cardiac mass QTL 38	2		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	169852800	Rat
2300168	Bmd47	Bone mineral density QTL 47	6.6	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	2	20641371	65641371	Rat
1358911	Kidm28	Kidney mass QTL 28	5.42		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	23837491	169852800	Rat
1358904	Cm39	Cardiac mass QTL 39	2.26		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	169852800	Rat
731167	Glom4	Glomerulus QTL 4	2.4	0.0082	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	2	20276981	65276981	Rat
1358908	Bw49	Body weight QTL 49	3.36		body mass (VT:0001259)	body weight (CMO:0000012)	2	23837719	169852670	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	40171834	105089682	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	40171834	105089682	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	40171834	105089682	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	40171834	105089682	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	2	40171834	105089682	Rat
1358887	Bw50	Body weight QTL 50	2.39		body mass (VT:0001259)	body weight (CMO:0000012)	2	23837719	169852670	Rat
2293682	Bmd24	Bone mineral density QTL 24	8.9	0.0001	femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	2	43141290	114164944	Rat
2293676	Bmd19	Bone mineral density QTL 19	10.7	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	2	43141290	114164944	Rat
12879844	Kidm62	Kidney mass QTL 62		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	27161361	148295267	Rat
10755434	Coatc7	Coat color QTL 7		0.04794	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	31272379	76272379	Rat
1582246	Cm60	Cardiac mass QTL 60	5.8		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	57715603	78466260	Rat
1358910	Kidm27	Kidney mass QTL 27	5.77		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	23837491	169852800	Rat
10755436	Coatc8	Coat color QTL 8		0.02431	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	35133202	80133202	Rat
61355	Bp36	Blood pressure QTL 36	2.9		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	2	3127638	105149020	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
2293671	Bss44	Bone structure and strength QTL 44	10.97	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	2	43141290	154583160	Rat
1358899	Kidm23	Kidney mass QTL 23	3.88		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	23837491	169852800	Rat
12879842	Cm88	Cardiac mass QTL 88		0.042	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	27161361	148295267	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	339
Count of miRNA genes:	205
Interacting mature miRNAs:	234
Transcripts:	ENSRNOT00000025490
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

	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium
Low									1
Below cutoff	9	3	6	3	3	3	34	6	26	1	3

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107653	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017590831	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AAHX01013808	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01013809	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01013810	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC128089	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474058	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000025490 ⟹ ENSRNOP00000025490

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	2	60,966,789 - 60,999,398 (+)	Ensembl

RefSeq Acc Id:

NM_001107653 ⟹ NP_001101123

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	2	60,966,789 - 60,999,398 (+)	NCBI
Rnor_5.0	2	83,685,368 - 83,717,569 (-)	NCBI
RGSC_v3.4	2	60,349,773 - 60,383,838 (+)	RGD
Celera	2	58,688,367 - 58,720,772 (-)	RGD

Sequence:

show sequence

CCTCCTCCAGCCTCCCCATCTCCGTTGGCTGCTCAGACAGGCTTCATGTCAGACCCGGTTTGGA
GCACAAATCTGAGGACCGCGCTGGAAAGTTACCCTCTCCGTGGTCATGAGTGGAAGCAATGGGC
CAACTGACACCCGTGCCTATCAATCCTTAGCTGAGGATTGCCCCTTTGGGTCTGCGGAACAACC
CAAGAGATCCACGGGGAGACTCGTCATGCACAGCATGGCCATGTTCGGCCGAGAGTTTTGCTAT
GCGGTGGAGGCAGCTTACGTGACTCCAGTTCTGCTCAGCGTGGGCCTGCCTAAGAGTCTGTACA
GCATGGTGTGGCTCCTTAGTCCCATCCTGGGATTCCTGCTCCAGCCTGTGGTAGGGTCAGCTAG
TGATCACTGCAGAGCCAGGTGGGGTCGCCGGAGACCCTACATCCTGACTCTGGGTGTCATGATG
CTCTTGGGAATGGCTCTGTACCTCAATGGAGATGCTGCTGTATCAGCTTTGGTTGCTAACCCGA
GGCAGAAACTGGTCTGGGCCATAAGCATCACCATGATAGGTGTGGTTCTCTTCGATTTTTCTGC
TGACTTCATCGATGGGCCCATCAAAGCCTACTTATTTGATGTCTGCTCCCACCAGGACAAGGAG
AAGGGCCTCCACTACCATGCCCTCTTCACAGGTTTTGGAGGTGCTCTTGGTTACCTTTTGGGTG
CCATAGACTGGATGCATCTAGAGCTGGGAAAACTGCTGGGCACTGAATTCCAGGTCATGTTCTT
CTTCTCTGCCCTGGTTCTCACCTTGTGCTTCATCACGCACCTGTGCAGTATCCCTGAAGACCCA
CTCAGAGATGATGCAACAGACCCTCCCTTACAGCCAGACCCTCAGGGCTCGTCACTGTCAGCAG
ATGGGATGCCCCGATATGGTTCCATTGAGAAGGTTAAAAATGGAGATGCAGACACAGGACTGCC
AGTGCAGGGAGGGAAAAACAAGAAGCCTTCTGGACAGAGTCAGAGGACAATGTCGATGAAGTCA
CTTCTTCGGGCACTAGTGAACATGCCTTCCCATTATCGCTGCCTTTGCATCAGCCACCTCATTG
GATGGACTGCCTTCCTGTCAAACATGCTCTTCTTCACAGATTTCATGGGGCAGATCGTATACCA
TGGGGATCCCTACGGTGCACACAACTCCACAGAGTTTCTCATCTATGAAAGAGGAGTTGAGGTC
GGATGTTGGGGCTTGTGCATCAACTCGGTGTTTTCTTCAGTTTATTCTTACTTTCAGAAAGTTA
TGGTTTCCTATATTGGATTAAAAGGCCTTTATTTCATGGGATACTTGCTCTTTGGCCTGGGAAC
AGGATTCATAGGACTCTTTCCAAATGTGTACTCTACCCTGGTCCTCTGTTCTATGTTTGGGGTC
ATGTCCAGCACATTATACACCGTGCCTTTTAACCTCATTGCTGAGTACCACCGTGAGGAGGAGA
AAGAGAAGCAGCAGGAAGTCCCAGGAGGCCCTGACAACCACGGGCGAGGCAAAGGTGTGGACTG
CGCTGCTCTCACCTGCATGGTGCAGCTGGCTCAGATATTGGTTGGAGGTGGCCTGGGTTTCCTG
GTCAACATGGCTGGGAGTGTCGTCGTCGTGGTGATCACAGCCTCTGCAGTGGCACTGATAGGCT
GTTGCTTTGTGGCTCTCTTTGTAAGATATGTAGATTAGATTCATAAACATCACCTCAAACCTCA
GACAAAAGAAGCCCACAGCAAGAAATCGCTCTTTTCTCGGACTCTTCGGCAATGGGGACTGTAT
GCCCATGCTGGCACTGCAGCTTGCATGTGTGGTGGGATTGCCTGCCCCCTGCATCACATCCTTA
CTGTCCCTCAATGGGAGAGTCAAGTTCGGCTTCTCAAGAGGATTTCAAGCCTTCATAGCCTCTG
AGGAACAAATGCATCCTACCTGCGATGCTTCTAATGTAATTATAAAAGAACAATTTATACACCA
TAGGGAAATCACGTATTTCACCAAATTCAGAAGTACTTAAAATATTGCTGAGTTTTTTTTATCG
TGCTGATTTATACAAAGTTAATTGGCTCATAATTAATTCCCATTAATGTATGACATTCTCGACA
AACCTGAGTTGGATGTCTCATTCTGCAAGCTCTGCGATTCAAACATGTTCATCCATTTCATTGA
TGCAGTAAGCACATTTTTCTT

hide sequence

RefSeq Acc Id:

XM_017590831 ⟹ XP_017446320

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	2	60,966,671 - 60,992,583 (+)	NCBI

Sequence:

show sequence

AGCATTCTAAGGACCCAGAGGGCTCACAACAGCTAATCTCTGTCATGCTTCTGAGTGCCAACGC
CCCCTTTGCTTCTCATCGTAACTTGTGATCTTGGAGCATGAAAGAATTTCAGCCCCTCCTCCAG
CCTCCCCATCTCCGTTGGCTGCTCAGACAGGCTTCATGTCAGACCCGGTTTGGAGCACAAATCT
GAGGACCGCGCTGGAAAGTTACCCTCTCCGTGGTCATGAGTGGAAGCAATGGGCCAACTGACAC
CCGTGCCTATCAATCCTTAGCTGAGGATTGCCCCTTTGGGTCTGCGGAACAACCCAAGAGATCC
ACGGGGAGACTCGTCATGCACAGCATGGCCATGTTCGGCCGAGAGTTTTGCTATGCGGTGGAGG
CAGCTTACGTGACTCCAGTTCTGCTCAGCGTGGGCCTGCCTAAGAGTCTGTACAGCATGGTGTG
GCTCCTTAGTCCCATCCTGGGATTCCTGCTCCAGCCTGTGGTAGGGTCAGCTAGTGATCACTGC
AGAGCCAGGTGGGGTCGCCGGAGACCCTACATCCTGACTCTGGGTGTCATGATGCTCTTGGGAA
TGGCTCTGTACCTCAATGGAGATGCTGCTGTATCAGCTTTGGTTGCTAACCCGAGGCAGAAACT
GGTCTGGGCCATAAGCATCACCATGATAGGTGTGGTTCTCTTCGATTTTTCTGCTGACTTCATC
GATGGGCCCATCAAAGCCTACTTATTTGATGTCTGCTCCCACCAGGACAAGGAGAAGGGCCTCC
ACTACCATGCCCTCTTCACAGGTTTTGGAGGTGCTCTTGGTTACCTTTTGGGTGCCATAGACTG
GATGCATCTAGAGCTGGGAAAACTGCTGGGCACTGAATTCCAGGTCATGTTCTTCTTCTCTGCC
CTGGTTCTCACCTTGTGCTTCATCACGCACCTGTGCAGTATCCCTGAAGACCCACTCAGAGATG
ATGCAACAGACCCTCCCTTACAGCCAGACCCTCAGGGCTCGTCACTGTCAGCAGATGGGATGCC
CCGATATGGTTCCATTGAGAAGGTTAAAAATGGAGATGCAGACACAGGACTGCCAGTGCAGGGA
GGGAAAAACAAGAAGCCTTCTGGACAGTCAGAGGACAATGTCGATGAAGTCACTTCTTCGGGCA
CTAGTGAACATGCCTTCCCATTATCGCTGCCTTTGCATCAGCCACCTCATTGGATGGACTGCCT
TCCTGTCAAACATGCTCTTCTTCACAGATTTCATGGGGCAGATCGTATACCATGGGGATCCCTA
CGGTGCACACAACTCCACAGAGTTTCTCATCTATGAAAGAGGAGTTGAGGTCGGATGTTGGGGC
TTGTGCATCAAC

hide sequence

Protein Sequences


Protein RefSeqs	NP_001101123	(Get FASTA)	NCBI Sequence Viewer
	XP_017446320	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL82981	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001101123 ⟸ NM_001107653

- UniProtKB:

D3ZR99 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSGSNGPTDTRAYQSLAEDCPFGSAEQPKRSTGRLVMHSMAMFGREFCYAVEAAYVTPVLLSVG
LPKSLYSMVWLLSPILGFLLQPVVGSASDHCRARWGRRRPYILTLGVMMLLGMALYLNGDAAVS
ALVANPRQKLVWAISITMIGVVLFDFSADFIDGPIKAYLFDVCSHQDKEKGLHYHALFTGFGGA
LGYLLGAIDWMHLELGKLLGTEFQVMFFFSALVLTLCFITHLCSIPEDPLRDDATDPPLQPDPQ
GSSLSADGMPRYGSIEKVKNGDADTGLPVQGGKNKKPSGQSQRTMSMKSLLRALVNMPSHYRCL
CISHLIGWTAFLSNMLFFTDFMGQIVYHGDPYGAHNSTEFLIYERGVEVGCWGLCINSVFSSVY
SYFQKVMVSYIGLKGLYFMGYLLFGLGTGFIGLFPNVYSTLVLCSMFGVMSSTLYTVPFNLIAE
YHREEEKEKQQEVPGGPDNHGRGKGVDCAALTCMVQLAQILVGGGLGFLVNMAGSVVVVVITAS
AVALIGCCFVALFVRYVD

hide sequence

RefSeq Acc Id:

XP_017446320 ⟸ XM_017590831

- Peptide Label:

isoform X1

- Sequence:

show sequence

MSGSNGPTDTRAYQSLAEDCPFGSAEQPKRSTGRLVMHSMAMFGREFCYAVEAAYVTPVLLSVG
LPKSLYSMVWLLSPILGFLLQPVVGSASDHCRARWGRRRPYILTLGVMMLLGMALYLNGDAAVS
ALVANPRQKLVWAISITMIGVVLFDFSADFIDGPIKAYLFDVCSHQDKEKGLHYHALFTGFGGA
LGYLLGAIDWMHLELGKLLGTEFQVMFFFSALVLTLCFITHLCSIPEDPLRDDATDPPLQPDPQ
GSSLSADGMPRYGSIEKVKNGDADTGLPVQGGKNKKPSGQSEDNVDEVTSSGTSEHAFPLSLPL
HQPPHWMDCLPVKHALLHRFHGADRIPWGSLRCTQLHRVSHL

hide sequence

RefSeq Acc Id:

ENSRNOP00000025490 ⟸ ENSRNOT00000025490

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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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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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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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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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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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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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_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
2	83692197	83692198	C	A	snv	NIG-III/Hok (KyushuU)
2	83717367	83717368	T	A	snv	GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), LL/MavRrrc (KNAW), WAG/Rij (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), BUF/N (KNAW), F344/NCrl (KNAW), F344/DuCrlCrlj (KyushuU), ACI/N (KNAW), SHR/OlaIpcvPrin (KNAW), WKY/N (KNAW), LE/Stm (SOLiD) (KNAW), MNS/Gib (KNAW), WN/N (KNAW), BUF/MNa (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Jcl (KyushuU), SBN/Ygl (KNAW), SHR/OlaIpcv (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/Stm (KyushuU), ZF (KyushuU), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), SS/JrHsdMcwi (KNAW), F344/NRrrc (Illumina) (KNAW), FHH/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), Crl:SD (UDEL), LE/Stm (KyushuU), KFRS3B/Kyo (KyushuU), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBN/Ygl (MCW), SR/JrHsd (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), SHR/NHsd (KNAW), WKY/NHsd (KNAW), F344/NSlc (KyushuU), LEC/Tj (KyushuU), FHL/EurMcwi (MCW), LH/MavRrrc (KNAW), MHS/Gib (KNAW), MR/N (KNAW), SHR/NCrlPrin (KNAW), DA/BklArbNsi (KNAW), F344/NHsd (KNAW), LEW/Crl (KNAW), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), LN/MavRrrc (KNAW), FHL/EurMcwi (KNAW), LE/OrlBarth (UDEL), HTX/Kyo (KyushuU), HWY/Slc (KyushuU), ZFDM (KyushuU), SS/Jr (KNAW), WKY/NCrl (KNAW), GK/Ox (KNAW), LEW/NCrl (KNAW), M520/N (KNAW), IS/Kyo (KyushuU), RCS/Kyo (KyushuU)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
2	60966991	60966992	A	T	snv	COP/CrCrl (MCW & UW), WKY/NHsd (RGD), WN/N (MCW), FHL/EurMcwi (RGD), FHH/EurMcwi (RGD), SHR/NHsd (RGD), GH/OmrMcwi (MCW), F344/NRrrc (MCW), M520/N (MCW), LEW/Crl (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBN/Ygl (RGD), SBN/Ygl (MCW), MR/N (MCW), BBDP/Wor (RGD), WKY/Gcrc (RGD), FHL/EurMcwi (MCW), CDS, GK/Ox (RGD), LE/Stm (RGD), ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW), LEW/NCrlBR (RGD), SS/JrHsdMcwi (RGD), Buf/N (MCW), WKY/N (MCW), F344/NCrl (RGD), LN/MavRrrc (RGD), SR/JrHsd (RGD), WKY/NCrl (RGD), ACI/N (MCW), ACI/EurMcwi (RGD), LH/MavRrrc (RGD), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/Jr (RGD), WAG/Rij (RGD), CDR

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
2	60349975	60349976	A	T	snv	ACI/N (KNAW), F344/NHsd (ICAHN), LEW/Crl (ICL), LEW/NCrl (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SHR/OlaIpcv (KNAW), GH/OmrMcwi (MCW), LL/MavRrrc (ICL), LN/MavRrrc (ICL), LCR/1Mco (UMich), FHH/EurMcwi (MDC), SR/JrHsd (MCW), BBDP/WorN (ICL), F344/NCrl (ICL), FHL/EurMcwi (ICL), WKY/Gcrc (ICL), DA/BklArbNsi (ICAHN), SHR/OlaIpcv (ICL), BUF/N (KNAW), F344/NRrrc (KNAW), FHL/EurMcwi (MCW), MNS/Gib (ICL), SHR/OlaIpcv (ICL), SS/JrHsdMcwi (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), LCR/2Mco (UMich), MR/N (KNAW), ACI/EurMcwi (MCW), SHR/NHsd (ICL), LH/MavRrrc (ICL), HCR/2Mco (UMich), SS/JrHsdMcwi (MDC), M520/N (KNAW), WKY/N (KNAW), WN/N (KNAW), MHS/Gib (ICL), SBN/Ygl (ICL), LE/Stm (KNAW), FHH/EurMcwi (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), LE/Stm (ICL), FHH/EurMcwi (ICL), GK/Ox (ICL), WAG/Rij (ICL), HCR/1Mco (UMich), ACI/EurMcwi (ICL)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1306690	AgrOrtholog
Ensembl Genes	ENSRNOG00000018759	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000025490	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000025490	ENTREZGENE, UniProtKB/TrEMBL
InterPro	MFS_trans_sf	UniProtKB/TrEMBL
KEGG Report	rno:310152	UniProtKB/TrEMBL
NCBI Gene	310152	ENTREZGENE
PhenoGen	Slc45a2	PhenoGen
Superfamily-SCOP	MFS_gen_substrate_transporter	UniProtKB/TrEMBL
UniGene	Rn.218545	ENTREZGENE
UniProt	D3ZR99	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Slc45a2	solute carrier family 45, member 2	Slc45a2_predicted	solute carrier family 45, member 2 (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-30	Slc45a2_predicted	solute carrier family 45, member 2 (predicted)	Matp_predicted	membrane associated transporter protein (predicted)	Symbol and Name updated	1299863	APPROVED
2005-01-12	Matp_predicted	membrane associated transporter protein (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM