Slc46a3 (solute carrier family 46, member 3)

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Gene: Slc46a3 (solute carrier family 46, member 3) Rattus norvegicus

Analyze

Symbol:

Slc46a3

Name:

solute carrier family 46, member 3

RGD ID:

1307594

Description:

Predicted to have transmembrane transporter activity. Predicted to be involved in vacuolar transmembrane transport. Predicted to localize to integral component of lysosomal membrane. Orthologous to human SLC46A3 (solute carrier family 46 member 3); INTERACTS WITH (+)-schisandrin B; acetamide; acrylamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC288454; MGC108818; RGD1307594; similar to RIKEN cDNA 1200006F02; solute carrier family 46 member 3

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):	SLC46A3 (solute carrier family 46 member 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Slc46a3 (solute carrier family 46, member 3)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Slc46a3 (solute carrier family 46 member 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SLC46A3 (solute carrier family 46 member 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SLC46A3 (solute carrier family 46 member 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Slc46a3 (solute carrier family 46 member 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SLC46A3 (solute carrier family 46 member 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	SLC46A3 (solute carrier family 46 member 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Slc46a3 (solute carrier family 46 member 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Slc46a3 (solute carrier family 46, member 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	SLC46A3 (solute carrier family 46 member 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	si:dkey-5g14.1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	slc46a3 (solute carrier family 46 member 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG15553	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Saccharomyces cerevisiae (baker's yeast):	YJL163C	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG15890	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	Y43F8A.5	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	Y4C6B.5	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG30345	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG42514	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	7,140,610 - 7,157,093 (+)	NCBI
Rnor_6.0 Ensembl	12	8,725,517 - 8,741,951 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	8,725,479 - 8,741,944 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	10,842,174 - 10,858,621 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	7,698,889 - 7,715,296 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	7,728,816 - 7,745,223 (+)	NCBI
Celera	12	8,884,584 - 8,901,010 (+)	NCBI		Celera
Cytogenetic Map	12	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

prostate cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(-)-epigallocatechin 3-gallate (ISO)

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

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

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

3-isobutyl-1-methyl-7H-xanthine (ISO)

7,12-dimethyltetraphene (ISO)

acetamide (EXP)

acrylamide (EXP)

aflatoxin B1 (ISO)

atrazine (EXP)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

Benzo[k]fluoranthene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

carbon nanotube (ISO)

cefaloridine (EXP)

chromium(6+) (ISO)

chrysene (ISO)

cisplatin (ISO)

clofibrate (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dichloroacetic acid (ISO)

dioxygen (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

entinostat (ISO)

ferric oxide (ISO)

glafenine (EXP)

indometacin (ISO)

isotretinoin (ISO)

metformin (EXP)

nickel sulfate (ISO)

oxaliplatin (EXP)

paracetamol (ISO)

perfluorononanoic acid (ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

pregnenolone 16alpha-carbonitrile (ISO)

progesterone (ISO)

rifampicin (ISO)

rotenone (EXP)

SB 431542 (ISO)

silicon dioxide (ISO)

Soman (EXP)

sunitinib (ISO)

Tesaglitazar (EXP)

tetrachloroethene (ISO)

tetrachloromethane (EXP,ISO)

tetraphene (ISO)

thioacetamide (EXP)

topotecan (EXP)

tremolite asbestos (ISO)

trichostatin A (ISO)

valproic acid (ISO)

vinclozolin (EXP)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

vacuolar transmembrane transport (IEA,ISO)

Cellular Component

integral component of lysosomal membrane (IEA,ISO)

Molecular Function

protein binding (ISO)

transmembrane transporter activity (IEA,ISO)

References

References - curated


1.	MGD data from the GO Consortium
2.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:19056867

Genomics

Comparative Map Data

Slc46a3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	7,140,610 - 7,157,093 (+)	NCBI
Rnor_6.0 Ensembl	12	8,725,517 - 8,741,951 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	8,725,479 - 8,741,944 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	10,842,174 - 10,858,621 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	7,698,889 - 7,715,296 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	7,728,816 - 7,745,223 (+)	NCBI
Celera	12	8,884,584 - 8,901,010 (+)	NCBI		Celera
Cytogenetic Map	12	p11	NCBI

SLC46A3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	13	28,700,064 - 28,718,970 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	13	28,700,080 - 28,718,970 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	13	29,274,217 - 29,293,107 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	13	28,172,217 - 28,190,962 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	13	10,349,991 - 10,368,926 (-)	NCBI
Cytogenetic Map	13	q12.3	NCBI
HuRef	13	10,095,902 - 10,114,829 (-)	NCBI		HuRef
CHM1_1	13	29,242,542 - 29,261,446 (-)	NCBI		CHM1_1

Slc46a3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	147,812,707 - 147,831,670 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	5	147,815,247 - 147,831,625 (-)	Ensembl
GRCm38	5	147,875,897 - 147,894,861 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	147,878,437 - 147,894,815 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	148,690,017 - 148,706,378 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	5	148,188,801 - 148,205,164 (-)	NCBI			mm8
Celera	5	145,873,979 - 145,890,370 (-)	NCBI		Celera
Cytogenetic Map	5	G3	NCBI

Slc46a3
(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_004955497	8,015,017 - 8,033,302 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955497	8,015,244 - 8,034,195 (-)	NCBI	ChiLan1.0	ChiLan1.0

SLC46A3
(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	13	28,327,633 - 28,347,534 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	13	28,327,633 - 28,347,534 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	13	9,987,309 - 10,007,152 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

SLC46A3
(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	25	11,032,483 - 11,049,433 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	25	11,031,696 - 11,050,265 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Slc46a3
(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_004936472	23,779,294 - 23,800,088 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLC46A3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	11	5,982,429 - 6,000,701 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	11	5,983,198 - 6,000,728 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	11	5,678,731 - 5,692,527 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SLC46A3
(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	3	7,802,170 - 7,819,608 (-)	NCBI
ChlSab1.1 Ensembl	3	7,801,728 - 7,819,584 (-)	Ensembl

Slc46a3
(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_004624776	9,783,827 - 9,802,993 (+)	NCBI

Position Markers

RH127449

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	8,741,580 - 8,741,787	NCBI	Rnor6.0
Rnor_5.0	12	10,858,257 - 10,858,464	UniSTS	Rnor5.0
RGSC_v3.4	12	7,714,933 - 7,715,140	UniSTS	RGSC3.4
Celera	12	8,900,644 - 8,900,851	UniSTS
RH 3.4 Map	12	73.5	UniSTS
Cytogenetic Map	12	p11	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
1300174	Bw15	Body weight QTL 15	2.93		body mass (VT:0001259)	body weight loss (CMO:0001399)	12	1	11765163	Rat
2312418	Kidm41	Kidney mass QTL 41	3.7	0.0001	kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	12	1	22650917	Rat
10450854	Stl34	Serum triglyceride level QTL 34	3.5	0.05	blood LDL triglyceride amount (VT:0010699)	blood lipoprotein triglyceride level (CMO:0002685)	12	1	22853017	Rat
10755457	Coatc14	Coat color QTL 14		0.01759	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	12	1	23035872	Rat
6893681	Bw109	Body weight QTL 109	2.3	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	12	1	23758197	Rat
1581516	Cm56	Cardiac mass QTL 56	4.2	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	1	30749723	Rat
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	36919844	Rat
7387292	Kidm42	Kidney mass QTL 42	3.03	0.0004	kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	12	1	38334225	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	150810	45150810	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	150810	45150810	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	492578	45492578	Rat
7243862	Mcs30	Mammary carcinoma susceptibility QTL 30	8.62		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	12	1258139	10257059	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	2475687	47475687	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	2513442	47513442	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	2513442	47513442	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	4210051	49210051	Rat
724526	Uae3	Urinary albumin excretion QTL 3	4.9	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	12	5406094	12355490	Rat
1600391	Edcs2	Endometrial carcinoma susceptibility QTL2	3.5	0.01	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	12	8249608	20590080	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	323
Count of miRNA genes:	187
Interacting mature miRNAs:	216
Transcripts:	ENSRNOT00000001243
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium			27	27	2	27				6	1	1
Low	3	43	30	14	17	14	8	11	74	29	40	10	8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001024968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006248833	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC091179	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ218873	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000224	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000001243 ⟹ ENSRNOP00000001243

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	8,725,517 - 8,741,951 (+)	Ensembl

RefSeq Acc Id:

NM_001024968 ⟹ NP_001020139

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	7,140,668 - 7,157,093 (+)	NCBI
Rnor_6.0	12	8,725,536 - 8,741,944 (+)	NCBI
Rnor_5.0	12	10,842,174 - 10,858,621 (+)	NCBI
RGSC_v3.4	12	7,698,889 - 7,715,296 (+)	RGD
Celera	12	8,884,584 - 8,901,010 (+)	RGD

Sequence:

show sequence

CGGCGACCGAGCCACCACTAGGGCCCAAAGAACCAGAGTGCAGCGAAGCGGGGAGCGGAGGAGA
CTGAGTCCAGGGCCACTAAAGCCCCGGAGGTGTGCTTATCTATCTTTGGCTTCTAACAGACCTC
CAGTGTCCCGTTCCAAGGGACGTCCCCCTCTCGCGGTCCAGTCCACCTCTCTGCCCTGTCCTTT
GGCTGTCCCCAGCTGGAAAACCGTGCTGAAAAGACGGGGGCCGCTGCGCCCCGCACTGGGTAAC
CGAGAACACAGTGCTGAGCTCGGTCCAACCTGTGCCGTGCCTAGCAGGAAGACCTTAACCGTGG
GACTCCACCAGCCCGCTTGAGCAGATATGAAGATCTCATTCATCGAGCCCGCCATTCTCCTTTA
CGCCTTTGCTATGACGCTGACCATCCCGCTGACAGCGCAGTATGTGTACCGGAGGATATGGGAA
GAAACCGGTAACTACACCTTTACCTCCAGTAGCAATGTCTCTGAATGCGAGCAAAACAAAAGCA
GTTCCACCTTTGCATTCCAGGAGGAAGTTCAGAAAAAGGCATCTCTCTTCAGCCTGCAGGTGGA
AATAAGTGGGTTAATTCCTGGTCTAGTGTCTACCTTCATGCTTTTATCGAGTAGCGACAACCAC
GGACGGAAACTTCCCATGGTCCTGTCATCTCTTGGCTCTCTGGGAACCAACCTTTGGCTGTGTG
CGATGTCCTACTTTGACCTTCCCCTCCAGCTTCTGGTAGCATCCACCTTTATTGGCGCCCTCTT
TGGGAATTACACCACGTTCTGGGGAGCTTGCTTCGCCTACATTGTGGATCAGGAGAAAGAATAC
AAGCACAGAATCATCCGCATAGCCGTCCTGGATTTTATGCTGGGAGTCGTTACTGGGCTAACAG
GCCTGTCGTCTGGCTATTTCATCCGAGAGCTGGGTTTTGCGTGGTCCTATTTCATTATTGCCGT
AGTTGTTCTAGTCAACCTGGCCTACATTCTATTTTTCCTCAGTGATCCCATAAAGGAGTCTTCA
TCTCAGATAGTCACTATGTCCTGTAGTGAAAGCCTCAAGGACCTATTTTACCGGACTTACATGC
TGTTTAAAAATGGTTCCTGTAAGCGGCGTTCTTTGCTCTGTCTGCTGATTTTTACCCTTGTCGT
CTATTTTTTTGTGGTCTTCGGCATCACCCCGGTTTTCACACTCTATGAGCTGGGTCCTCCGCTC
TGCTGGAATGAGGTCTACATAGGCTATGGCTCAGCTTTGGGCAGCCTCTCCTTCCTGAGTAGTT
TCCTGGGCATCTGGCTGTTCTCTTACTGTTTGAAGGATATTCACATCGCCTATGTCGGCATTTT
TACCACGATGGTGGGAATGATGCTCACCGCCTTCACCAGGACCACTCTGATGATGTTTTTAGTC
CGAATATCGTTCTTTTTCACCATCATGCCACTTTCCATTCTGAGGTCCATGCTGTCAAAGGTGG
TCCACTCAACGGAACAAGGTGTGCTGTTTGCTTGCATAGCTTTCTTAGAAACGCTTGGCGGCGT
CACTTCGACCTCGGCGTATAATGGGATTTATTCAGCCACTGTTGCCTGGTACCCTGGGTTCGTC
TTCCTGCTGTCCGCTGGCCTCCTGGTCCTCCCAGCCGTCAGTCTCTGCATGGTCAAATGCATTG
GCTGGGAAGAGGGAAGCTATACACTGCTCATCCATGACGAGCCCAGTGAGCACACATCAGACTC
GTGACAGCAGCAATGCACACGCCCTGTGTGCGACTCCTGAAGAACTGCGACTCCTGAAGAACTG
CTCCGCAGTCAGTATTTCACTAGCGATCCACGTGACAAAACCCTGTCTCCAACCAAGTGAGTTG
GGAGGACACACCGAGCTCTGCTGCTTCTGGGGCCACCCAGCAGCACACTGGGTTCTTCAAAGAG
CAGACCCCAGTACCGTCCTCACTTCTCCATGGACCAGAGAAACACAGTGGAGAGCAGAGGAATG
CTTGCGAAACCTTGCTAAAACTTTAAAGCAATAACTTCACTGACATGCTCCAGTCTCCCATGAG
GAGACTAAGGAGTTCTGACCTCAGTCTCTCCGTCTGCACAATGGGCTTGCTGGCCTCTCAGGGA
TTTTTTTGAAGACACAATGAGGAATTTTTATTTGCAATAATCACTGAAATGGAAATGTCTCAGG
CATTTCTAGTTCTTCCTGGACTTGACTGACGTTTCAAGAGCCTGTCAAGGCTTTACTAATGGAA
TGAAAAATGAAGCACCTTTTAAAATGTGTTTTTCATTTTTCCTAGTGTTTTATTCTGTGACAAG
CCTGATGATGTTTTTATATGTAATGAAGGGGGTGGGTAGAAAATCAGATTATAAATAAAATCGT
CCTAATGTGAAAACTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAA

hide sequence

RefSeq Acc Id:

XM_006248833 ⟹ XP_006248895

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	7,140,610 - 7,157,089 (+)	NCBI
Rnor_6.0	12	8,725,479 - 8,741,944 (+)	NCBI
Rnor_5.0	12	10,842,174 - 10,858,621 (+)	NCBI

Sequence:

show sequence

GGAGGCGGGTGGCAGCTCGGGCCGAAGATTACCACCTCCAAGCCGAGTGATGATGCTCGGCGAC
CGAGCCACCACTAGGGCCCAAAGAACCAGAGTGCAGCGAAGCGGGGAGCGGAGGAGACTGAGTC
CAGGGCCACTAAAGCCCCGGAGACTCCACCAGCCCGCTTGAGCAGATATGAAGATCTCATTCAT
CGAGCCCGCCATTCTCCTTTACGCCTTTGCTATGACGCTGACCATCCCGCTGACAGCGCAGTAT
GTGTACCGGAGGATATGGGAAGAAACCGGTAACTACACCTTTACCTCCAGTAGCAATGTCTCTG
AATGCGAGCAAAACAAAAGCAGTTCCACCTTTGCATTCCAGGAGGAAGTTCAGAAAAAGGCATC
TCTCTTCAGCCTGCAGGTGGAAATAAGTGGGTTAATTCCTGGTCTAGTGTCTACCTTCATGCTT
TTATCGAGTAGCGACAACCACGGACGGAAACTTCCCATGGTCCTGTCATCTCTTGGCTCTCTGG
GAACCAACCTTTGGCTGTGTGCGATGTCCTACTTTGACCTTCCCCTCCAGCTTCTGGTAGCATC
CACCTTTATTGGCGCCCTCTTTGGGAATTACACCACGTTCTGGGGAGCTTGCTTCGCCTACATT
GTGGATCAGGAGAAAGAATACAAGCACAGAATCATCCGCATAGCCGTCCTGGATTTTATGCTGG
GAGTCGTTACTGGGCTAACAGGCCTGTCGTCTGGCTATTTCATCCGAGAGCTGGGTTTTGCGTG
GTCCTATTTCATTATTGCCGTAGTTGTTCTAGTCAACCTGGCCTACATTCTATTTTTCCTCAGT
GATCCCATAAAGGAGTCTTCATCTCAGATAGTCACTATGTCCTGTAGTGAAAGCCTCAAGGACC
TATTTTACCGGACTTACATGCTGTTTAAAAATGGTTCCTGTAAGCGGCGTTCTTTGCTCTGTCT
GCTGATTTTTACCCTTGTCGTCTATTTTTTTGTGGTCTTCGGCATCACCCCGGTTTTCACACTC
TATGAGCTGGGTCCTCCGCTCTGCTGGAATGAGGTCTACATAGGCTATGGCTCAGCTTTGGGCA
GCCTCTCCTTCCTGAGTAGTTTCCTGGGCATCTGGCTGTTCTCTTACTGTTTGAAGGATATTCA
CATCGCCTATGTCGGCATTTTTACCACGATGGTGGGAATGATGCTCACCGCCTTCACCAGGACC
ACTCTGATGATGTTTTTAGTCCGAATATCGTTCTTTTTCACCATCATGCCACTTTCCATTCTGA
GGTCCATGCTGTCAAAGGTGGTCCACTCAACGGAACAAGGTGTGCTGTTTGCTTGCATAGCTTT
CTTAGAAACGCTTGGCGGCGTCACTTCGACCTCGGCGTATAATGGGATTTATTCAGCCACTGTT
GCCTGGTACCCTGGGTTCGTCTTCCTGCTGTCCGCTGGCCTCCTGGTCCTCCCAGCCGTCAGTC
TCTGCATGGTCAAATGCATTGGCTGGGAAGAGGGAAGCTATACACTGCTCATCCATGACGAGCC
CAGTGAGCACACATCAGACTCGTGACAGCAGCAATGCACACGCCCTGTGTGCGACTCCTGAAGA
ACTGCGACTCCTGAAGAACTGCTCCGCAGTCAGTATTTCACTAGCGATCCACGTGACAAAACCC
TGTCTCCAACCAAGTGAGTTGGGAGGACACACCGAGCTCTGCTGCTTCTGGGGCCACCCAGCAG
CACACTGGGTTCTTCAAAGAGCAGACCCCAGTACCGTCCTCACTTCTCCATGGACCAGAGAAAC
ACAGTGGAGAGCAGAGGAATGCTTGCGAAACCTTGCTAAAACTTTAAAGCAATAACTTCACTGA
CATGCTCCAGTCTCCCATGAGGAGACTAAGGAGTTCTGACCTCAGTCTCTCCGTCTGCACAATG
GGCTTGCTGGCCTCTCAGGGATTTTTTTGAAGACACAATGAGGAATTTTTATTTGCAATAATCA
CTGAAATGGAAATGTCTCAGGCATTTCTAGTTCTTCCTGGACTTGACTGACGTTTCAAGAGCCT
GTCAAGGCTTTACTAATGGAATGAAAAATGAAGCACCTTTTAAAATGTGTTTTTCATTTTTCCT
AGTGTTTTATTCTGTGACAAGCCTGATGATGTTTTTATATGTAATGAAGGGGGTGGGTAGAAAA
TCAGATTATAAATAAAATCGTCCTAATGTGAAAACTCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001020139	(Get FASTA)	NCBI Sequence Viewer
	XP_006248895	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH91179	(Get FASTA)	NCBI Sequence Viewer
	EDL89550	(Get FASTA)	NCBI Sequence Viewer
	Q5BK75	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001020139 ⟸ NM_001024968
- Peptide Label:	precursor
- UniProtKB:	Q5BK75 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MKISFIEPAILLYAFAMTLTIPLTAQYVYRRIWEETGNYTFTSSSNVSECEQNKSSSTFAFQEE VQKKASLFSLQVEISGLIPGLVSTFMLLSSSDNHGRKLPMVLSSLGSLGTNLWLCAMSYFDLPL QLLVASTFIGALFGNYTTFWGACFAYIVDQEKEYKHRIIRIAVLDFMLGVVTGLTGLSSGYFIR ELGFAWSYFIIAVVVLVNLAYILFFLSDPIKESSSQIVTMSCSESLKDLFYRTYMLFKNGSCKR RSLLCLLIFTLVVYFFVVFGITPVFTLYELGPPLCWNEVYIGYGSALGSLSFLSSFLGIWLFSY CLKDIHIAYVGIFTTMVGMMLTAFTRTTLMMFLVRISFFFTIMPLSILRSMLSKVVHSTEQGVL FACIAFLETLGGVTSTSAYNGIYSATVAWYPGFVFLLSAGLLVLPAVSLCMVKCIGWEEGSYTL LIHDEPSEHTSDS hide sequence

RefSeq Acc Id:	XP_006248895 ⟸ XM_006248833
- Peptide Label:	isoform X1
- UniProtKB:	Q5BK75 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MKISFIEPAILLYAFAMTLTIPLTAQYVYRRIWEETGNYTFTSSSNVSECEQNKSSSTFAFQEE VQKKASLFSLQVEISGLIPGLVSTFMLLSSSDNHGRKLPMVLSSLGSLGTNLWLCAMSYFDLPL QLLVASTFIGALFGNYTTFWGACFAYIVDQEKEYKHRIIRIAVLDFMLGVVTGLTGLSSGYFIR ELGFAWSYFIIAVVVLVNLAYILFFLSDPIKESSSQIVTMSCSESLKDLFYRTYMLFKNGSCKR RSLLCLLIFTLVVYFFVVFGITPVFTLYELGPPLCWNEVYIGYGSALGSLSFLSSFLGIWLFSY CLKDIHIAYVGIFTTMVGMMLTAFTRTTLMMFLVRISFFFTIMPLSILRSMLSKVVHSTEQGVL FACIAFLETLGGVTSTSAYNGIYSATVAWYPGFVFLLSAGLLVLPAVSLCMVKCIGWEEGSYTL LIHDEPSEHTSDS hide sequence

RefSeq Acc Id:

ENSRNOP00000001243 ⟸ ENSRNOT00000001243

Transcriptome

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

Promoters

RGD ID:

13698397

Promoter ID:

EPDNEW_R8922

Type:

initiation region

Name:

Slc46a3_1

Description:

solute carrier family 46, member 3

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	12	8,725,523 - 8,725,583	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:1307594	AgrOrtholog
Ensembl Genes	ENSRNOG00000000937	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000001243	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000001243	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7325773	IMAGE-MGC_LOAD
InterPro	MFS	UniProtKB/Swiss-Prot
	MFS_trans_sf	UniProtKB/Swiss-Prot
KEGG Report	rno:288454	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:108818	IMAGE-MGC_LOAD
NCBI Gene	288454	ENTREZGENE
Pfam	MFS_1	UniProtKB/Swiss-Prot
PhenoGen	Slc46a3	PhenoGen
Superfamily-SCOP	SSF103473	UniProtKB/Swiss-Prot
UniProt	Q5BK75	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-07	Slc46a3	solute carrier family 46, member 3	RGD1307594	similar to RIKEN cDNA 1200006F02	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	RGD1307594	similar to RIKEN cDNA 1200006F02	RGD1307594_predicted	similar to RIKEN cDNA 1200006F02 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1307594_predicted	similar to RIKEN cDNA 1200006F02 (predicted)	LOC288454_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC288454_predicted	similar to RIKEN cDNA 1200006F02 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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