Slc28a2 (solute carrier family 28 member 2)

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Gene: Slc28a2 (solute carrier family 28 member 2) Rattus norvegicus

Analyze

Symbol:

Slc28a2

Name:

solute carrier family 28 member 2

RGD ID:

61840

Description:

Exhibits nucleoside:sodium symporter activity. Involved in protein localization to cell surface and retina homeostasis. Localizes to coated vesicle; plasma membrane; and vesicle membrane. Orthologous to human SLC28A2 (solute carrier family 28 member 2); PARTICIPATES IN azathioprine pharmacodynamics pathway; mercaptopurine pharmacodynamics pathway; mercaptopurine pharmacokinetics pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,4-dinitrotoluene; 3,3',4,4',5-pentachlorobiphenyl.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

CNT 2; concentrative nucleoside transporter 2; Na(+)/nucleoside cotransporter 2; rCNT2; sodium-coupled nucleoside transporter 2; sodium/nucleoside cotransporter 2; sodium/purine nucleoside cotransporter; solute carrier family 28 (concentrative nucleoside transporter), member 2; solute carrier family 28 (sodium-coupled nucleoside transporter) member 2; solute carrier family 28 (sodium-coupled nucleoside transporter), member 2; solute carrier family 28, member 2; SPNT

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

NCBI Annotation Information:

Annotation category: partial on reference assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	3	114,355,003 - 114,647,382 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	114,355,798 - 114,647,382 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	120,897,082 - 120,921,371 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	109,350,531 - 109,372,027 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	109,256,103 - 109,277,600 (-)	NCBI
Celera	3	108,262,866 - 108,284,103 (+)	NCBI		Celera
Cytogenetic Map	3	q35	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

AGAT deficiency (ISO)

Experimental Diabetes Mellitus (IDA)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP)

2,4-dinitrotoluene (EXP)

3,3',4,4',5-pentachlorobiphenyl (EXP)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

adenosine (ISO)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

buspirone (EXP)

buta-1,3-diene (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

clofibrate (EXP)

clofibric acid (EXP)

cobalt dichloride (EXP)

coumarin (EXP)

D-penicillamine (EXP)

decabromodiphenyl ether (EXP)

dexamethasone (EXP)

endosulfan (EXP)

flutamide (EXP)

genistein (EXP)

gentamycin (EXP)

indole-3-methanol (EXP)

leflunomide (EXP)

methimazole (EXP)

N-nitrosodiethylamine (EXP)

nefazodone (EXP)

nimesulide (EXP)

oxaliplatin (EXP)

paclitaxel (EXP)

paracetamol (ISO)

paraquat (EXP)

phenobarbital (EXP)

pirinixic acid (EXP,ISO)

pregnenolone 16alpha-carbonitrile (EXP)

rotenone (EXP)

sevoflurane (EXP)

silicon dioxide (ISO)

sodium atom (ISO)

sodium dichromate (EXP,ISO)

succimer (ISO)

testosterone (EXP)

tetrachloromethane (EXP)

thioacetamide (EXP)

toluene (EXP)

topotecan (EXP)

tributylstannane (ISO)

tunicamycin (ISO)

uridine (ISO)

ursodeoxycholic acid (EXP)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adenosine transport (IEA,ISO)

inosine transport (IEA,ISO)

neurotransmitter transport (IEA,ISO)

nucleoside transmembrane transport (IBA,IEA,ISO)

protein localization to cell surface (IDA)

purine nucleobase transmembrane transport (IEA,ISO)

purine nucleoside transmembrane transport (IEA,ISO)

pyrimidine nucleobase transport (IEA)

pyrimidine-containing compound transmembrane transport (IEA,ISO)

retina homeostasis (IBA,IDA)

uridine transport (IEA,ISO)

Cellular Component

brush border membrane (ISO)

coated vesicle (IDA)

integral component of plasma membrane (IBA,IEA)

plasma membrane (IDA)

vesicle membrane (IDA)

Molecular Function

neurotransmitter transmembrane transporter activity (IEA,ISO)

nucleoside transmembrane transporter activity (IBA,IDA)

nucleoside:sodium symporter activity (IBA,IDA,IEA,ISO)

purine nucleobase transmembrane transporter activity (ISO)

purine nucleoside transmembrane transporter activity (IBA,IEA,ISO)

pyrimidine- and adenine-specific:sodium symporter activity (IEA,ISO)

symporter activity (IBA)

uridine transmembrane transporter activity (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

azathioprine pharmacodynamics pathway (ISO)

mercaptopurine pharmacodynamics pathway (ISO)

mercaptopurine pharmacokinetics pathway (ISO)

tioguanine pharmacodynamics pathway (ISO)

References

References - curated


1.	Anderson CM, etal., Brain Res Mol Brain Res 1996 Dec;42(2):358-61.
2.	Che M, etal., J Biol Chem 1995 Jun 9;270(23):13596-9.
3.	Fernandez-Veledo S, etal., Biochem J. 2006 Apr 15;395(2):337-44.
4.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5.	GOA data from the GO Consortium
6.	Larrayoz IM, etal., Am J Physiol Cell Physiol. 2006 Dec;291(6):C1395-404. Epub 2006 Jul 12.
7.	Li JY, etal., J Cereb Blood Flow Metab 2001 Aug;21(8):929-36.
8.	Melani A, etal., Exp Neurol. 2012 Jan;233(1):193-204. doi: 10.1016/j.expneurol.2011.09.036. Epub 2011 Oct 6.
9.	MGD data from the GO Consortium
10.	Mori N, etal., Eur J Pharmacol. 2010 Feb 25;628(1-3):214-9. Epub 2009 Dec 2.
11.	Nagase K, etal., Biochim Biophys Acta. 2006 Jan;1758(1):13-9. Epub 2006 Feb 2.
12.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
13.	Pipeline to import SMPDB annotations from SMPDB into RGD
14.	RGD automated data pipeline
15.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16.	RGD automated import pipeline for gene-chemical interactions
17.	Rodriguez-Mulero S, etal., Kidney Int. 2005 Aug;68(2):665-72.
18.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
19.	Yao SY, etal., Mol Pharmacol 1996 Dec;50(6):1529-35.

Additional References at PubMed

PMID:1315767	PMID:10721696	PMID:15024061	PMID:15287894	PMID:16840788	PMID:17013559	PMID:20421393	PMID:22136384	PMID:22354287	PMID:23819782	PMID:25315414	PMID:28322028

Genomics

Comparative Map Data

Slc28a2
(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	3	114,355,003 - 114,647,382 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	114,355,798 - 114,647,382 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	120,897,082 - 120,921,371 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	109,350,531 - 109,372,027 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	109,256,103 - 109,277,600 (-)	NCBI
Celera	3	108,262,866 - 108,284,103 (+)	NCBI		Celera
Cytogenetic Map	3	q35	NCBI

SLC28A2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	45,252,234 - 45,277,846 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	45,252,234 - 45,277,846 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	45,544,428 - 45,568,132 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	43,331,726 - 43,355,425 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	15	43,331,725 - 43,355,425	NCBI
Celera	15	22,435,715 - 22,459,420 (+)	NCBI
Cytogenetic Map	15	q21.1	NCBI
HuRef	15	22,368,444 - 22,392,157 (+)	NCBI		HuRef
CHM1_1	15	45,662,894 - 45,686,614 (+)	NCBI		CHM1_1

Slc28a2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	122,256,836 - 122,291,633 (+)	NCBI	GRCm39		mm39
GRCm38	2	122,426,357 - 122,461,152 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	122,426,477 - 122,461,137 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	122,252,213 - 122,286,866 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	122,117,918 - 122,152,571 (+)	NCBI			mm8
Celera	2	123,576,831 - 123,613,534 (+)	NCBI		Celera
Cytogenetic Map	2	E5	NCBI

Slc28a2
(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_004955409	8,144,304 - 8,175,360 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955409	8,145,723 - 8,175,256 (-)	NCBI	ChiLan1.0	ChiLan1.0

SLC28A2
(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	15	42,554,204 - 42,577,891 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	42,554,142 - 42,578,096 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	15	24,199,846 - 24,223,378 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

Slc28a2
(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_004936471	7,937,490 - 7,967,568 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLC28A2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	126,472,525 - 126,511,365 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	126,472,500 - 126,511,207 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	141,072,725 - 141,110,169 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SLC28A2
(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	26	37,927,200 - 37,956,729 (-)	NCBI

Slc28a2
(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_004624731	13,999,029 - 14,051,964 (-)	NCBI

Position Markers

RH127610

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	114,379,146 - 114,379,328	NCBI	Rnor6.0
Rnor_5.0	3	120,920,944 - 120,921,126	UniSTS	Rnor5.0
RGSC_v3.4	3	109,199,517 - 109,199,698	UniSTS	RGSC3.4
Cytogenetic Map	3	q35	UniSTS
RH 3.4 Map	3	954.4	UniSTS

RH131217

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	114,647,053 - 114,647,244	NCBI	Rnor6.0
Rnor_5.0	3	121,185,952 - 121,186,143	UniSTS	Rnor5.0
RGSC_v3.4	3	109,350,669 - 109,350,860	UniSTS	RGSC3.4
Celera	3	108,476,193 - 108,476,389	UniSTS
Celera	3	108,283,774 - 108,283,965	UniSTS
Cytogenetic Map	3	q35	UniSTS
RH 3.4 Map	3	953.5	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
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	30114912	123700444	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	30846101	172879276	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	39248391	140271184	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	43295930	163640485	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	43295930	163640485	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	45406058	127023997	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	45406058	177699992	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	48561928	155263151	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	51821836	124513579	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	51822008	120917851	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	54630948	119830094	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	58204463	170534769	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	61241033	165369047	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	62922868	127023997	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	66711607	119830094	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	66711607	119830094	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	72672290	127023997	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	72973445	127023997	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	78700444	123700444	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	81136227	154416635	Rat
2302273	Gluco35	Glucose level QTL 35	5.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	83817637	119509260	Rat
7387306	Bw124	Body weight QTL 124	3.2	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	3	88910015	133910015	Rat
631649	Bp123	Blood pressure QTL 123	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	94788365	139788365	Rat
8694437	Bw167	Body weight QTL 167	22.46	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	3	97009185	142009185	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	99465522	168732722	Rat
1582219	Bw63	Body weight QTL 63	3.8	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	3	100730984	119830094	Rat
724532	Cm17	Cardiac mass QTL 17	2		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	3	101058963	146058963	Rat
2293087	Iddm27	Insulin dependent diabetes mellitus QTL 27	2.68		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	102152812	155263151	Rat
1354611	Despr2	Despair related QTL 2	3.03	0.0028	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	3	102466149	147466149	Rat
2312659	Slep7	Serum leptin concentration QTL 7		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	3	103141814	176418101	Rat
2312670	Bw94	Body weight QTL 94		0.01	inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	3	103141814	176418101	Rat
2312673	Scl63	Serum cholesterol level QTL 63		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	103141814	176418101	Rat
2302373	Gluco39	Glucose level QTL 39	5.01		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	3	103141944	170934860	Rat
1582216	Bw65	Body weight QTL 65	6.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	106900427	119830094	Rat
619618	Rf3	Renal disease susceptibility QTL 3	6.5	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate to body weight ratio (CMO:0001270)	3	114376250	159376250	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	96
Count of miRNA genes:	87
Interacting mature miRNAs:	91
Transcripts:	ENSRNOT00000036435
Prediction methods:	Microtar, Miranda, Rnahybrid
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	10	25	15	18	15			27		3	4
Low	1	33	32	26	1	26	8	11	47	35	36	7	8
Below cutoff											2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031664	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07053553	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053554	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053555	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053556	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053557	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053558	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053559	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053560	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053561	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053562	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053563	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053564	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053565	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053566	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053567	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053568	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053569	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053570	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053571	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053572	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053573	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053574	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053575	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07053576	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07072919	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01024730	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01024731	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01024732	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB485922	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY029302	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	EU032627	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U25055	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U66723	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U67084	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000024658 ⟹ ENSRNOP00000024658

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	114,355,798 - 114,647,382 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000036435 ⟹ ENSRNOP00000034564

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	114,355,814 - 114,378,941 (+)	Ensembl

RefSeq Acc Id:

NM_031664 ⟹ NP_113852

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	114,355,003 - 114,647,382 (+)	NCBI
Rnor_5.0	3	120,897,082 - 120,921,371 (+)	NCBI
RGSC_v3.4	3	109,350,531 - 109,372,027 (-)	RGD
Celera	3	108,262,866 - 108,284,103 (+)	RGD

Sequence:

show sequence

CCACGCGTCCGGTCTTGCTGAAGGGAAACCTCCACTTCCTGCTTGTGAGAGTATTAATCCCTGC
TGCAGCTGTCCATCCCCACTGACATCAGACTCCAGTTTCTCCAGGATCCAGTGTGTTCTGAAGA
TCAGCAGCTCTCCCGGAGTCTTCAAGGCGCCAGATTTGGAAGTCTGAGGCATCTGGCTTTGTAA
CCTGAGCAGCTGCCAGGTTCCAGCCATTATCTGACTGGGCTGTGCGGACCCACCCAGCACATTC
AGAGGATAACAGGAGATGGCGAAGTCAGAGGGAAGAAAGTCTGCTTCCCAGGACACATCGGAGA
ATGGCATGGAGAACCCAGGCCTGGAGCTCATGGAAGTCGGAAACCTTGAGCAAGGCAAAACACT
GGAGGAAGTGACACAGGGACATAGCCTGAAGGATGGCTTGGGGCATTCCTCTCTCTGGAGGAGG
ATTCTTCAGCCCTTCACCAAGGCGAGAAGTTTCTATCAAAGACATGCTGGTTTATTCAAAAAGA
TCCTGCTTGGTCTCTTGTGTTTAGCGTATGCTGCCTACCTCCTGGCAGCTTGCATCCTGAACTT
CCGGAGGGCACTGGCCTTGTTTGTCATCACCTGCCTTGTCATCTTCATCCTGGCTTGCCACTTT
CTGAAAAAATTCTTTGCTAAAAAGTCAATAAGATGCTTGAAGCCCTTGAAAAACACCCGCCTGA
GACTTTGGCTTAAGAGGGTGTTCATGGGAGCCGCTGTTGTCGGCCTTATTCTCTGGCTGGCTCT
GGACACAGCTCAAAGGCCAGAGCAGCTGATCTCCTTTGCGGGAATCTGCATGTTCATCCTCATC
CTCTTTGCCTGCTCCAAACACCACAGTGCGGTGAGCTGGAGGACAGTGTTTTGGGGCCTGGGCC
TTCAGTTCGTCTTTGGGATTTTGGTCATCAGAACTGAACCTGGATTTAATGCATTTCAATGGCT
GGGAGATCAGATCCAGATTTTCCTGGCATATACTGTAGAAGGATCCAGTTTTGTTTTTGGTGAC
ACACTGGTCCAAAGTGTTTTTGCTTTTCAGTCTCTCCCAATCATTATTTTCTTCGGATGTGTGA
TGTCTATTCTCTACTACCTGGGCCTTGTGCAGTGGGTGATCCAGAAGATTGCCTGGTTCCTGCA
AATCACCATGGGTACCACAGCTGCAGAGACCCTGGCCGTGGCAGGAAACATCTTTGTGGGAATG
ACAGAGGCACCTCTGCTCATCCGTCCCTACCTTGCAGACATGACCCTCTCTGAAATCCATGCAG
TGATGACTGGAGGCTTTGCTACTATAGCAGGCACAGTGTTGGGAGCCTTCATATCCTTTGGGAT
TGATGCATCATCCTTGATTTCTGCCTCAGTGATGGCTGCCCCTTGTGCACTTGCCTTGTCCAAA
CTGGTATATCCAGAAGTAGAAGAGTCCAAGTTCAAGAGCAAGGAGGGAGTGAAGCTGCCTCGAG
GGGAAGAGAGGAATATTCTGGAAGCCGCGAGCAACGGAGCCACAGATGCCATAGCGCTTGTTGC
TAATGTTGCAGCCAACCTGATTGCCTTTCTGGCTGTATTGGCCTTCATCAATTCTACCCTTTCC
TGGCTGGGGGAAATGGTGGATATCCATGGACTCACTTTCCAGGTCATCTGCTCCTATGTCCTAA
GGCCAATGGTTTTCATGATGGGTGTACAGTGGGCAGACTGCCCATTGGTGGCTGAGATAGTGGG
AGTCAAATTCTTCATAAATGAATTTGTGGCCTATCAACAACTGTCTCAGTACAAGAACAAACGT
CTCTCTGGAGTCGAAGAGTGGATCAATGGCGAGAAACAGTGGATTTCTGTGAAGGCTGAAATCA
TTGCAACATTTTCTCTCTGTGGATTTGCCAATCTTACTTCCATAGGGATCACACTGGGAGGCTT
GACATCCATGGTTCCCCAACGGAAGAGTGACTTGTGCAAGCTTGTGGTCAGGGCCCTCTTCACA
GGTGCCTGTGTTTCCTTCATCAGTGCCTGTATGGCAGGAATCCTCTATGTTCCCAGAGGCGCTG
AAACTGACTGTGTCTCATTCTTAAACACAAATTTCACCAACAGAACCTATGAGACATATGTGTG
CTGCAGAGAGCTCTTCCAGAGTACTTTGCTGAATGGCACCAACATGCCTTCTTTCTCAGGCCCC
TGGCAAGACAAGGAGTCCAGCCTCAGGAATCTTGCTAAATGCTGTGACCTCTATACCAGCACTG
TGTGTGCCTGAGGCTGGTGGGGCCATTCCGTGACAGTTCTTATAGAACAGATTCATATTACCAA
ATACATGTTCATGTACTTAGGCTTATTCTCTGAGAACTGCACTAAACTCCACAAAATGAAAGTC
CTGATCTCACTGTGGCTCTGTATAAAAACCAGCATCCACCTTTCCACTGGCATGCCACATAGTA
GATGTGAAATTCATTATAGACCCTCTTGAGCCAAAGTATGGTGGGAATGTAGCTAAGGGGGAAA
TATGTGTGTGGTAAGTGCTAAGATGGAGATTCAACCCCTGGCCAGGGCCAGAGTGGGGAGAGTG
GGGAAATCCAAGTAGATGCTTAGATTTAACTTGGTGGTACACCCTGTGGTCACTTACCTGTAAG
CTCAGAGCTAAGGGGATTGCCTCAGATCCAAGGCAAGCCTGGCCCGAACCCTGAAGTCTTTCAC
AGAAGTGATAGAGTAGAGGCCATGTCCTTGGGCAGGGATGGAGGTGAGGGAATATATTTCTAAA
GTTATATGGGAAACACTTGTGAATACTTAATGATAACATATTTTTTATTGCCAAAGGTTGTATA
CTTAAAAACTCTTTTCATTTTCATACATTACTAAAAAGCTTTCTGTAATAAAGTGTTTTTATGT
A

hide sequence

Protein Sequences


Protein RefSeqs	NP_113852	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA80640	(Get FASTA)	NCBI Sequence Viewer
	AAD00159	(Get FASTA)	NCBI Sequence Viewer
	AAD00160	(Get FASTA)	NCBI Sequence Viewer
	AAK38150	(Get FASTA)	NCBI Sequence Viewer
	BAH58083	(Get FASTA)	NCBI Sequence Viewer
	Q62773	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_113852 ⟸ NM_031664

- Sequence:

show sequence

MAKSEGRKSASQDTSENGMENPGLELMEVGNLEQGKTLEEVTQGHSLKDGLGHSSLWRRILQPF
TKARSFYQRHAGLFKKILLGLLCLAYAAYLLAACILNFRRALALFVITCLVIFILACHFLKKFF
AKKSIRCLKPLKNTRLRLWLKRVFMGAAVVGLILWLALDTAQRPEQLISFAGICMFILILFACS
KHHSAVSWRTVFWGLGLQFVFGILVIRTEPGFNAFQWLGDQIQIFLAYTVEGSSFVFGDTLVQS
VFAFQSLPIIIFFGCVMSILYYLGLVQWVIQKIAWFLQITMGTTAAETLAVAGNIFVGMTEAPL
LIRPYLADMTLSEIHAVMTGGFATIAGTVLGAFISFGIDASSLISASVMAAPCALALSKLVYPE
VEESKFKSKEGVKLPRGEERNILEAASNGATDAIALVANVAANLIAFLAVLAFINSTLSWLGEM
VDIHGLTFQVICSYVLRPMVFMMGVQWADCPLVAEIVGVKFFINEFVAYQQLSQYKNKRLSGVE
EWINGEKQWISVKAEIIATFSLCGFANLTSIGITLGGLTSMVPQRKSDLCKLVVRALFTGACVS
FISACMAGILYVPRGAETDCVSFLNTNFTNRTYETYVCCRELFQSTLLNGTNMPSFSGPWQDKE
SSLRNLAKCCDLYTSTVCA

hide sequence

RefSeq Acc Id:

ENSRNOP00000024658 ⟸ ENSRNOT00000024658

RefSeq Acc Id:

ENSRNOP00000034564 ⟸ ENSRNOT00000036435

Protein Domains

Gate Nucleos_tra2_C Nucleos_tra2_N

Transcriptome

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

Promoters

RGD ID:

13692368

Promoter ID:

EPDNEW_R2893

Type:

single initiation site

Name:

Slc28a2_1

Description:

solute carrier family 28 member 2

SO ACC ID:

SO:0000170

Source:

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

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	114,355,796 - 114,355,856	EPDNEW

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:61840	AgrOrtholog
Ensembl Genes	ENSRNOG00000028668	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000024658	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000034564	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000024658	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000036435	UniProtKB/TrEMBL
InterPro	C_nuclsd_transpt	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	C_nuclsd_transpt_met_bac	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CNT1/CNT2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CNT_C_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CNT_N_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Gate_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:60423	UniProtKB/Swiss-Prot
NCBI Gene	60423	ENTREZGENE
PANTHER	PTHR10590	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR10590:SF11	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Gate	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Nucleos_tra2_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Nucleos_tra2_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB	SLC28A2	RGD
PhenoGen	Slc28a2	PhenoGen
TIGR	TC230283
TIGRFAMs	nupC	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene	Rn.10140	ENTREZGENE
UniProt	C1PHX8_RAT	UniProtKB/TrEMBL
	F1LN73_RAT	UniProtKB/TrEMBL
	F1LXN6_RAT	UniProtKB/TrEMBL
	Q62773	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q9QWI3	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-02-24	Slc28a2	solute carrier family 28 member 2	Slc28a2	solute carrier family 28 (concentrative nucleoside transporter), member 2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2014-07-25	Slc28a2	solute carrier family 28 (concentrative nucleoside transporter), member 2	Slc28a2	solute carrier family 28 (sodium-coupled nucleoside transporter), member 2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Slc28a2	solute carrier family 28 (sodium-coupled nucleoside transporter), member 2		solute carrier family 28, member 2	Name updated	1299863	APPROVED
2002-06-10	Slc28a2	solute carrier family 28, member 2			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference

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 Annotations - SMPDB