Slc46a1 (solute carrier family 46 member 1)

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Gene: Slc46a1 (solute carrier family 46 member 1) Rattus norvegicus

Analyze

Symbol:

Slc46a1

Name:

solute carrier family 46 member 1

RGD ID:

1309472

Description:

Exhibits folic acid transmembrane transporter activity and methotrexate transmembrane transporter activity. Involved in folic acid transport and methotrexate transport. Localizes to brush border membrane. Biomarker of chronic kidney disease. Human ortholog(s) of this gene implicated in hereditary folate malabsorption. Orthologous to human SLC46A1 (solute carrier family 46 member 1); PARTICIPATES IN altered folate cycle metabolic pathway; folate cycle metabolic pathway; folate metabolic pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

heme carrier protein 1; LOC303333; MGC108986; PCFT/HCP1; proton-coupled folate transporter; RGD1309472; similar to DNA segment, Chr 11, ERATO Doi 18, expressed; solute carrier family 46 (folate transporter), member 1; solute carrier family 46, member 1

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):	SLC46A1 (solute carrier family 46 member 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB
Mus musculus (house mouse):	Slc46a1 (solute carrier family 46, member 1)	HGNC	NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Slc46a1 (solute carrier family 46 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SLC46A1 (solute carrier family 46 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SLC46A1 (solute carrier family 46 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Slc46a1 (solute carrier family 46 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SLC46A1 (solute carrier family 46 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	SLC46A1 (solute carrier family 46 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Slc46a1 (solute carrier family 46 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Slc46a1 (solute carrier family 46, member 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	SLC46A1 (solute carrier family 46 member 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	slc46a1 (solute carrier family 46 member 1)	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)
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):	CG30344	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):	CG31321	Alliance	DIOPT (Ensembl Compara\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG42514	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG8046	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG8008	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|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	10	63,361,504 - 63,367,940 (+)	NCBI
Rnor_6.0 Ensembl	10	65,733,991 - 65,740,828 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	65,728,508 - 65,741,708 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	65,902,790 - 65,915,107 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	64,576,068 - 64,582,504 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	64,589,690 - 64,596,123 (+)	NCBI
Celera	10	62,338,075 - 62,344,511 (+)	NCBI		Celera
Cytogenetic Map	10	q25	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

anemia (ISO)

chronic kidney disease (IEP)

Experimental Liver Cirrhosis (ISO)

hereditary folate malabsorption (ISO)

hyperhomocysteinemia (ISO)

intellectual disability (ISO)

Malabsorption Syndromes (ISO)

pancytopenia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (EXP,ISO)

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

3,3',5,5'-tetrabromobisphenol A (EXP)

3-Iodothyronamine (ISO)

4,4'-diaminodiphenylmethane (EXP)

4,4'-diisothiocyano-trans-stilbene-2,2'-disulfonic acid (ISO)

5-aza-2'-deoxycytidine (ISO)

5-formyltetrahydrofolic acid (ISO)

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (EXP)

5-methyltetrahydrofolic acid (ISO)

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

AM-251 (ISO)

amiodarone (EXP)

antirheumatic drug (ISO)

ATP (ISO)

benzbromarone (EXP)

benzo[a]pyrene (ISO)

Benzo[k]fluoranthene (ISO)

bisphenol A (EXP)

bromosulfophthalein (EXP,ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

calciol (ISO)

calcitriol (ISO)

carbon nanotube (ISO)

chromium(6+) (EXP,ISO)

cisplatin (ISO)

clofibrate (EXP)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dextran sulfate (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

ethyl methanesulfonate (ISO)

ferroheme b (ISO)

folic acid (EXP,ISO)

formaldehyde (ISO)

fructose (EXP)

heme b (ISO)

homocysteine (ISO)

hydrogen peroxide (ISO)

ICI D1694 (ISO)

L-ethionine (EXP)

lipopolysaccharide (ISO)

methotrexate (EXP,ISO)

methyl methanesulfonate (ISO)

miconazole (ISO)

N-nitrosodiethylamine (EXP)

N-nitrosodimethylamine (EXP)

nefazodone (EXP)

omeprazole (EXP)

paracetamol (ISO)

pemetrexed (ISO)

phenylmercury acetate (ISO)

pirinixic acid (EXP)

potassium chromate (ISO)

pyrimethamine (ISO)

rotenone (EXP)

SB 431542 (ISO)

sodium arsenite (ISO)

sodium dichromate (EXP)

Soman (EXP)

sulfasalazine (EXP,ISO)

sunitinib (ISO)

tert-butyl hydroperoxide (ISO)

testosterone (EXP)

tetrachloromethane (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trovafloxacin (EXP)

tunicamycin (ISO)

urethane (ISO)

valdecoxib (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

folate import across plasma membrane (ISO)

folic acid transport (IDA,ISO,ISS)

heme transport (ISO,ISS)

methotrexate transport (IDA,ISO)

proton transmembrane transport (ISO)

Cellular Component

apical plasma membrane (ISO,ISS)

basolateral plasma membrane (ISO)

brush border membrane (IDA)

cytoplasm (ISO,ISS)

integral component of membrane (IEA)

plasma membrane (ISO)

Molecular Function

folic acid binding (IEA)

folic acid transmembrane transporter activity (IDA,ISO,ISS)

heme transmembrane transporter activity (ISO,ISS)

methotrexate transmembrane transporter activity (IDA)

proton transmembrane transporter activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

altered folate cycle metabolic pathway (ISO)

folate cycle metabolic pathway (ISO)

folate metabolic pathway (ISO)

hereditary folate malabsorption pathway (ISO)

methotrexate pharmacodynamics pathway (ISO)

References

References - curated


1.	Blom HJ and Smulders Y, J Inherit Metab Dis. 2011 Feb;34(1):75-81. doi: 10.1007/s10545-010-9177-4. Epub 2010 Sep 4.
2.	Bukhari FJ, etal., Nephrol Dial Transplant. 2011 Jul;26(7):2137-44. doi: 10.1093/ndt/gfq675. Epub 2010 Dec 13.
3.	Inoue K, etal., Am J Physiol Gastrointest Liver Physiol. 2008 Mar;294(3):G660-8. doi: 10.1152/ajpgi.00309.2007. Epub 2008 Jan 3.
4.	MGD data from the GO Consortium
5.	OMIM Disease Annotation Pipeline
6.	Pipeline to import SMPDB annotations from SMPDB into RGD
7.	RGD automated data pipeline
8.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	RGD automated import pipeline for gene-chemical interactions
10.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
11.	Wani NA, etal., Indian J Med Res. 2012 Nov;136(5):758-65.
12.	Watkins D and Rosenblatt DS, J Inherit Metab Dis. 2012 Jul;35(4):665-70. doi: 10.1007/s10545-011-9418-1. Epub 2011 Nov 23.

Additional References at PubMed

PMID:15489334	PMID:16143108	PMID:17129779	PMID:17475902	PMID:17898134	PMID:19581412	PMID:19762432	PMID:21069807	PMID:21861943	PMID:22163044	PMID:28720846

Genomics

Comparative Map Data

Slc46a1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	63,361,504 - 63,367,940 (+)	NCBI
Rnor_6.0 Ensembl	10	65,733,991 - 65,740,828 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	65,728,508 - 65,741,708 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	65,902,790 - 65,915,107 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	64,576,068 - 64,582,504 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	64,589,690 - 64,596,123 (+)	NCBI
Celera	10	62,338,075 - 62,344,511 (+)	NCBI		Celera
Cytogenetic Map	10	q25	NCBI

SLC46A1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	17	28,394,642 - 28,407,197 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	17	28,394,642 - 28,406,630 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	17	26,721,661 - 26,733,230 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	23,745,788 - 23,757,355 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	17	23,583,422 - 23,594,992 (-)	NCBI
Cytogenetic Map	17	q11.2	NCBI
HuRef	17	22,930,003 - 22,941,574 (-)	NCBI		HuRef
CHM1_1	17	26,784,574 - 26,796,145 (-)	NCBI		CHM1_1

Slc46a1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	78,356,527 - 78,362,771 (+)	NCBI	GRCm39		mm39
GRCm38	11	78,465,701 - 78,471,945 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	78,465,697 - 78,472,059 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	78,279,203 - 78,285,447 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	78,281,913 - 78,288,125 (+)	NCBI			mm8
Celera	11	88,097,777 - 88,104,021 (+)	NCBI		Celera
Cytogenetic Map	11	B5	NCBI
cM Map	11	46.74	NCBI

Slc46a1
(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_004955481	4,734,967 - 4,745,586 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955481	4,735,325 - 4,741,810 (+)	NCBI	ChiLan1.0	ChiLan1.0

SLC46A1
(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	17	28,870,678 - 28,877,632 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	28,870,678 - 28,877,632 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	28,367,674 - 28,379,618 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

SLC46A1
(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	9	42,643,328 - 42,650,188 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	9	42,638,670 - 42,650,241 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Slc46a1
(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_004936538	4,549,032 - 4,642,870 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLC46A1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	44,677,502 - 44,686,250 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	44,677,499 - 44,686,277 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	18	33,258 - 42,053 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SLC46A1
(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	16	22,164,661 - 22,173,376 (-)	NCBI
ChlSab1.1 Ensembl	16	22,166,318 - 22,173,240 (-)	Ensembl

Slc46a1
(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_004624786	1,000,444 - 1,006,984 (-)	NCBI

Position Markers

D11Seg28

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	65,732,529 - 65,732,659	NCBI	Rnor6.0
Rnor_5.0	10	65,910,961 - 65,911,091	UniSTS	Rnor5.0
RGSC_v3.4	10	64,574,206 - 64,574,336	UniSTS	RGSC3.4
Celera	10	62,336,213 - 62,336,343	UniSTS
Cytogenetic Map	10	q25	UniSTS

RH132585

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	65,739,515 - 65,739,725	NCBI	Rnor6.0
Rnor_5.0	10	65,903,895 - 65,904,105	UniSTS	Rnor5.0
RGSC_v3.4	10	64,581,192 - 64,581,402	UniSTS	RGSC3.4
Celera	10	62,343,199 - 62,343,409	UniSTS
Cytogenetic Map	10	q25	UniSTS

RH133220

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	65,740,336 - 65,740,553	NCBI	Rnor6.0
Rnor_5.0	10	65,903,067 - 65,903,284	UniSTS	Rnor5.0
RGSC_v3.4	10	64,582,013 - 64,582,230	UniSTS	RGSC3.4
Celera	10	62,344,020 - 62,344,237	UniSTS
Cytogenetic Map	10	q25	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
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	764421	66221621	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6229095	75983805	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6429075	99492409	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9841807	108540162	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14827894	92423564	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14827894	107857673	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	20170031	102897474	Rat
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	21523906	83549467	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	21523906	90312401	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	21523906	90312401	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22901497	93886300	Rat
1331762	Rf40	Renal function QTL 40	3.873		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	10	23861015	66539843	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	27237530	101482600	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	27237530	102427718	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	28789280	73789280	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30983805	75983805	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31919397	78343192	Rat
1578779	Tcas10	Tongue tumor susceptibility QTL 10	3.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	10	33179030	78179030	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	33343192	78343192	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	35139424	80139424	Rat
6893342	Cm78	Cardiac mass QTL 78	0.1	0.88	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	36185929	82675365	Rat
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	36185929	95845311	Rat
1358897	Stresp6	Stress response QTL 6	4.17	0.022	blood norepinephrine amount (VT:0005663)	plasma norepinephrine level (CMO:0001010)	10	36584373	66539843	Rat
61441	Btemp1	Thermal response to stress QTL 1	4		body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	10	36584560	66015527	Rat
2317042	Aia20	Adjuvant induced arthritis QTL 20	3.38		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	40514044	85514044	Rat
2317043	Aia7	Adjuvant induced arthritis QTL 7	3.82		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	40514044	85514044	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	41260363	106105607	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
8552805	Bw145	Body weight QTL 145	2.2		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	10	43188659	81042642	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	43289657	108540162	Rat
61463	Bp12	Blood pressure QTL 12	6.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	43704955	88704955	Rat
2300218	Hpcl2	Hepatic cholesterol level QTL 2			liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	46593021	98939209	Rat
9589030	Epfw9	Epididymal fat weight QTL 9	19.24	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	10	46848346	91848346	Rat
7411614	Foco18	Food consumption QTL 18		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	46848346	91848346	Rat
8694173	Bw149	Body weight QTL 149	4.38	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	10	46848346	91848346	Rat
631547	Bp87	Blood pressure QTL 87	4.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	50638337	95638337	Rat
2293652	Bmd22	Bone mineral density QTL 22	4.9	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	51289203	84596393	Rat
2293669	Bmd33	Bone mineral density QTL 33	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	10	51289203	84596393	Rat
2293679	Bmd30	Bone mineral density QTL 30	3.5	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	51289203	84596393	Rat
2293705	Bmd25	Bone mineral density QTL 25	7.1	0.0001	femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	10	51289203	84596393	Rat
7207811	Bmd90	Bone mineral density QTL 90	5.2		femur size trait (VT:1000369)	femoral neck cross-sectional area (CMO:0001697)	10	51289203	84596393	Rat
1549846	Scl47	Serum cholesterol level QTL 47	3.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	53104718	98104718	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	53621375	112626471	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	53621375	112626471	Rat
631530	Tls3	T-lymphoma susceptibility QTL 3	0	0.0001	thymus integrity trait (VT:0010555)	percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)	10	53625815	98939209	Rat
631535	Cm51	Cardiac mass QTL 51	3		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	53637485	94807701	Rat
1359017	Hrtrt21	Heart rate QTL 21	2.4		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	10	55224855	100224855	Rat
2306787	Ean3	Experimental allergic neuritis QTL 3	3.1		nervous system integrity trait (VT:0010566)	body weight loss (CMO:0001399)	10	55678976	69385767	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	55678976	112626471	Rat
70164	Bw21	Body weight QTL 21	4.36	0.00005	body mass (VT:0001259)	body weight (CMO:0000012)	10	55679084	102427604	Rat
1354608	Cm33	Cardiac mass QTL 33	2.8		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	10	56698730	101698730	Rat
1549831	Bss6	Bone structure and strength QTL 6	4		lumbar vertebra strength trait (VT:0010574)	vertebra ultimate force (CMO:0001678)	10	60450007	105450007	Rat
2312662	Slep8	Serum leptin concentration QTL 8		0.05	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	10	60875260	105875260	Rat
2312668	Scl65	Serum cholesterol level QTL 65		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	60875260	105875260	Rat
2312672	Insul15	Insulin level QTL 15		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	10	60875260	105875260	Rat
2293698	Bss43	Bone structure and strength QTL 43	5.33	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	10	62096293	107096293	Rat
1331839	Eae18b	Experimental allergic encephalomyelitis QTL 18b	5.8	0.03	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	10	64550912	70202084	Rat
70363	Bp71	Blood pressure QTL 71		0.04	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	64648175	84601269	Rat
2306970	Anxrr22	Anxiety related response QTL 22	5.95		fear/anxiety-related behavior trait (VT:1000241)	number of periods of voluntary immobility (CMO:0001045)	10	64648175	101691360	Rat
1558643	Cm44	Cardiac mass QTL 44	4.8	0.0000368	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	64648175	102149713	Rat
6893336	Cm75	Cardiac mass QTL 75	0.1	0.87	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	64648175	102149713	Rat
631526	Bp76	Blood pressure QTL 76		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	64648311	69123603	Rat
61402	Niddm3	Non-insulin dependent diabetes mellitus QTL 3	4.58		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	64648311	85513822	Rat
61449	Ciaa2	CIA Autoantibody QTL 2	7.1		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	10	65590122	110590122	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	525
Count of miRNA genes:	246
Interacting mature miRNAs:	287
Transcripts:	ENSRNOT00000013698
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			17	17		17			17	14	25
Low	3	43	40	24	19	24	8	11	57	21	16	11	8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001013969	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC089868	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ231269	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000013698 ⟹ ENSRNOP00000013698

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	65,733,991 - 65,740,828 (+)	Ensembl

RefSeq Acc Id:

NM_001013969 ⟹ NP_001013991

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	63,361,504 - 63,367,940 (+)	NCBI
Rnor_6.0	10	65,734,391 - 65,740,827 (+)	NCBI
Rnor_5.0	10	65,902,790 - 65,915,107 (-)	NCBI
RGSC_v3.4	10	64,576,068 - 64,582,504 (+)	RGD
Celera	10	62,338,075 - 62,344,511 (+)	RGD

Sequence:

show sequence

CAGCTGGTTCCGAGGTGTCAGCCCCTCGGTGTTCGCGCATGGAGGGGCGCGTGAGCCCCGTGGG
CTCGTCCCACCGTCTCCTCACCGCCGCCGTGCTGTTCCGCGGCCCCGTGGAGCCCCTCGTTTTC
CTAGCCAACTTTGCGCTGGTTCTACAGGGACCGCTCACCACACAGTACATTTGGCACCGCATCA
GCACCGAGCTCGGATACAATGGCACCCGCCACCGGGAGAACTGTGGCAACCAGAGCGCGGATCC
CGTCCTGAAGGAAGTGGAGACCCTGACATCCCACTGGACCCTCTACATGAACGTGGGAGGCTTC
CTGGTGGGACTCTTCTGGTCCACCCTCCTGGGAGCCTGGAGTGACCGCGTGGGTCGCCGCCCAT
TGCTGGTGCTGGCCTCTCTTGGTCTGCTGCTCCAGGCCGTGGTGTCCATCTTTGTGGTGCAACT
ACAACTGCACATCGGGTTCTTCGTGCTCGGCCGAGCCCTTTGTGCCCTTCTGGGAGATTTCAAC
GGCCTTCTTGCTGCTAGCTTTGCCTCTGTGGCTGATGTTAGCTCTAATCACAGTCGCACCTTCC
GGATGGCTCTGCTGGAAGCATGCATTGGTGTGGCCGGGACCCTGGCAAGCCTTCTTGGGGGTCA
CTGGCTCCGGGCCCAGGGTTATGCCAACCCTTTCTGGCTGGCTTTGGCTGTGCTGATCGTTATG
ACTCTATATGCAGCATTCTGTTTTGGTGAGACAGTGAAGGAGCCAAAGTCCACGAGGCTTTTCA
CGCTCCGCCATCACCGATCCATTGTCCAGCTGTATGTGGTCCCAGCCCCAGAGAAGTCCAGGAT
GCATCTAGCCCTGTACTCATTGGCCATATTCGTGGTGGTCACTGTGCACTTTGGGGCTCAAGAC
ATCCTGACGCTCTATGAGCTAAGCACACCCCTCTGCTGGGACTCCAAGCTGATTGGCTATGGCT
CAGCAGCCCAGCACTTACCCTACCTCACCAGCCTGCTGGGCCTGAGACTTCTGCAGTTCTGCCT
GGCCGACACCTGGGTGGCTGAGATTGGCCTGGCCTTCAACATCCTGGGAATGGTGGTCTTTGCG
TTCGCAACCATCACACCCCTCATGTTCACAGGGTACGGATTACTCTTCCTGTCATTGGTCACTA
CGCCTGTGATCCGGGCCAAGCTCTCCAAGCTAGTGAGCGAGTCGGAGCAGGGTGCTCTCTTTTC
GGCTGTGGCCTGTGTGAATAGCTTGGCCATGTTGATGGCCTCCGGCATCTTCAACTCACTCTAC
CCGGCCACTCTGAACTTCATGAAGGGCTTCCCCTTCCTCCTGGGAGCTGGCCTCCTCTTTATCC
CGGCCATTCTGATTGGGGTACTGGAGAAGGTTAATCCACACCCAGAGTTCCAGCAGTTTCCTCA
GAACTCCTGAGCTGCCAGAAGCCATGAGAAGCAGTGGCTCCACACCGACTACATACCTAAAGCC
CAGTGCACCAGCGTCTCTAAGGACAGTACTCACTTTGGAAACGGTGTTCAAGCCAGTTATGGGC
AACACCTATTCTCTGACTGAGCCAGTCTCTGCTAGATACAGAATCTAGTCAGGAGAGGTCCACT
CAGGGCAGGCTGCAGGGAGCCATCATGCAGAACCTTCCAGAGTAAAGGAGATGGCATTTAGGGG
ACTAAGCATGAGAATCTTTCTAGCCCATGGTACTAGGTCCCTGCTGTGTTCCGTGGCCTCTAGG
CACCCCTTAATGCTAACTGTGGTACCTGGGAGAGCGGTTTTGACACAGAAGCCTGTCTATGGTT
GGGGATCAGTCCTTGACCACAGCCTATCCACCTTTGACCTCAGCCGTGCCAATTGTCACAGTAA
ATTGTTTGAATCAGTCTGAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006246939 ⟹ XP_006247001

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	65,728,508 - 65,741,708 (+)	NCBI
Rnor_5.0	10	65,902,790 - 65,915,107 (-)	NCBI

Sequence:

show sequence

TCCGGCCCCTGGCCCACGGCCGTCACACAGGATGGTTTTGGTAATGAGGAGCCCTGAATATCAG
GTCACGGCTTTACGGCTCAGGAGGGAGGGCTGCAGCAAGGTGGTATCTTTGCGGTGCCTGAAGT
GACGTCACACCACAGGGATTCTAACTCAACTACACCCATCCCAGAGAGCAGCGGACCAAAGCTT
TAGAGACTGTCTCACGCTCCGCCCCTCCAGACTTTAACAGAAGGAGTCGAAGCCCGCGCAGGCG
CAGAGAGCGCAGACTGGTCCGCCTCTCGCAGCTGGTTCCGAGGTGTCAGCCCCTCGGTGTTCGC
GCATGGAGGGGCGCGTGAGCCCCGTGGGCTCGTCCCACCGTCTCCTCACCGCCGCCGTGCTGTT
CCGCGGCCCCGTGGAGCCCCTCGTTTTCCTAGCCAACTTTGCGCTGGTTCTACAGGGACCGCTC
ACCACACAGTACATTTGGCACCGCATCAGCACCGAGCTCGGATACAATGGCACCCGCCACCGGG
AGAACTGTGGCAACCAGAGCGCGGATCCCGTCCTGAAGGAAGTGGAGACCCTGACATCCCACTG
GACCCTCTACATGAACGTGGGAGGCTTCCTGGTGGGACTCTTCTGGTCCACCCTCCTGGGAGCC
TGGAGTGACCGCGTGGGTCGCCGCCCATTGCTGGTGCTGGCCTCTCTTGGTCTGCTGCTCCAGG
CCGTGGTGTCCATCTTTGTGGTGCAACTACAACTGCACATCGGGTTCTTCGTGCTCGGCCGAGC
CCTTTGTGCCCTTCTGGGAGATTTCAACGGCCTTCTTGCTGCTAGCTTTGCCTCTGTGGCTGAT
GTTAGCTCTAATCACAGTCGCACCTTCCGGATGGCTCTGCTGGAAGCATGCATTGGTGTGGCCG
GGACCCTGGCAAGCCTTCTTGGGGGTCACTGGCTCCGGGCCCAGGGTTATGCCAACCCTTTCTG
GCTGGCTTTGGCTGTGCTGATCGTTATGACTCTATATGCAGCATTCTGTTTTGGTGAGACAGTG
AAGGAGCCAAAGTCCACGAGGCTTTTCACGCTCCGCCATCACCGATCCATTGTCCAGCTGTATG
TGGTCCCAGCCCCAGAGAAGTCCAGGATGCATCTAGCCCTGTACTCATTGGCCATATTCGTGGT
GGTCACTGTGCACTTTGGGGCTCAAGACATCCTGACGCTCTATGAGCTAAGCACACCCCTCTGC
TGGGACTCCAAGCTGATTGGCTATGGCTCAGCAGCCCAGCACTTACCCTACCTCACCAGCCTGC
TGGGCCTGAGACTTCTGCAGTTCTGCCTGGCCGACACCTGGGTGGCTGAGATTGGCCTGGCCTT
CAACATCCTGGGAATGGTGGTCTTTGCGTTCGCAACCATCACACCCCTCATGTTCACAGGGTAC
GGATTACTCTTCCTGTCATTGGTCACTACGCCTGTGATCCGGGCCAAGCTCTCCAAGCTAGTGA
GCGAGTCGGAGCAGGGTGCTCTCTTTTCGGCTGTGGCCTGTGTGAATAGCTTGGCCATGTTGAT
GGCCTCCGGCATCTTCAACTCACTCTACCCGGCCACTCTGAACTTCATGAAGGGCTTCCCCTTC
CTCCTGGGAGCTGGCCTCCTCTTTATCCCGGCCATTCTGATTGGGGTACTGGAGAAGGTTAATC
CACACCCAGAGTTCCAGCAGTTTCCTCAGAACTCCTGAGCTGCCAGAAGCCATGAGAAGCAGTG
GCTCCACACCGACTACATACCTAAAGCCCAGTGCACCAGCGTCTCTAAGGACAGTACTCACTTT
GGAAACGGTGTTCAAGCCAGTTATGGGCAACACCTATTCTCTGACTGAGCCAGTCTCTGCTAGA
TACAGAATCTAGTCAGGAGAGGTCCACTCAGGGCAGGCTGCAGGGAGCCATCATGCAGAACCTT
CCAGAGTAAAGGAGATGGCATTTAGGGGACTAAGCATGAGAATCTTTCTAGCCCATGGTACTAG
GTCCCTGCTGTGTTCCGTGGCCTCTAGGCACCCCTTAATGCTAACTGTGGTACCTGGGAGAGCG
GTTTTGACACAGAAGCCTGTCTATGGTTGGGGATCAGTCCTTGACCACAGCCTATCCACCTTTG
ACCTCAGCCGTGCCAATTGTCACAGTAAATTGTTTGAATCAGTCTGAAAAGTTTACTGGGCTTT
GGGGCTTTCTGTCTTCTCACTCTCTCCCTGTTTGGCACCAGCACCATCTGGGCTGGAGCTCCTG
AGTTGCCTACGGGGTAGTTACTGGGTAGTCCTATCCCTCCAGGCTCCAGCTGGTTTCTCCCTAC
ACTGCTGAGGGATAAAGGACTTTTGAGGCTTCATCAGCCCCATGGAGACACTTGGGCCCAAGCC
CTGGCTGCCCCTTGCTGATAGTCAGATGATTCATTCCCTGGCTGGCTTCATGGCTATACCAGCC
CCAGAAGGATCTCCTTTGGTTGCCATTTGGCCCCACCCATGTAGCTCAGTGTTGAGCAGTGTCA
TGTACAGAGACTACCCTTCATGCTTTGGGGAAGTGAGCAGAGGTTGGGAAGACCTGGGCTCAAA
GCTGAAAGGCAGAATCTTACCTAATGGGAAGCCACTGTCTTTGATGACTAACGGTCTTCTCCAA
GCTGACCCAAAGCAGGAGGTTTGTCATTCTTCAAAGTGGAACTGCCCATGAGAGCTAGACCCTG
CAGCTGTCTCTTCCTGCCCAAACCGTAAGCTAGTTTCCCTGCTGGAAGCCATACAGGTGAAAGA
GATGTATCCCAGAGAAAACTAAGGCTCACTGAACTGCACCAGGGTCCATCTGACTTCCACACTC
CTGCCTCACTGTCCCTCTGGAGATAGGAAAGTCTAAGCAAGAAGAGGCTTCCGGGCTGGAGAGA
TGGCTCAGTGGTTAAGAGCACCCGATTGCTCTTCCAGGGGTCCTGAGTTCAATTCCCAGCAACC
ACATGGTGGCTCACAACCATCTGTAAAGAGATCCGATGCCCCCTTCTGGTGTATCTGAAGACAG
CTACAGTGTGTGTGTATATATATATAATTAATTAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001013991	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH89868	(Get FASTA)	NCBI Sequence Viewer
	EDM05355	(Get FASTA)	NCBI Sequence Viewer
	EDM05356	(Get FASTA)	NCBI Sequence Viewer
	Q5EBA8	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001013991 ⟸ NM_001013969

- UniProtKB:

Q5EBA8 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MEGRVSPVGSSHRLLTAAVLFRGPVEPLVFLANFALVLQGPLTTQYIWHRISTELGYNGTRHRE
NCGNQSADPVLKEVETLTSHWTLYMNVGGFLVGLFWSTLLGAWSDRVGRRPLLVLASLGLLLQA
VVSIFVVQLQLHIGFFVLGRALCALLGDFNGLLAASFASVADVSSNHSRTFRMALLEACIGVAG
TLASLLGGHWLRAQGYANPFWLALAVLIVMTLYAAFCFGETVKEPKSTRLFTLRHHRSIVQLYV
VPAPEKSRMHLALYSLAIFVVVTVHFGAQDILTLYELSTPLCWDSKLIGYGSAAQHLPYLTSLL
GLRLLQFCLADTWVAEIGLAFNILGMVVFAFATITPLMFTGYGLLFLSLVTTPVIRAKLSKLVS
ESEQGALFSAVACVNSLAMLMASGIFNSLYPATLNFMKGFPFLLGAGLLFIPAILIGVLEKVNP
HPEFQQFPQNS

hide sequence

RefSeq Acc Id:

XP_006247001 ⟸ XM_006246939

- Peptide Label:

isoform X1

- Sequence:

show sequence

MEGRVSPVGSSHRLLTAAVLFRGPVEPLVFLANFALVLQGPLTTQYIWHRISTELGYNGTRHRE
NCGNQSADPVLKEVETLTSHWTLYMNVGGFLVGLFWSTLLGAWSDRVGRRPLLVLASLGLLLQA
VVSIFVVQLQLHIGFFVLGRALCALLGDFNGLLAASFASVADVSSNHSRTFRMALLEACIGVAG
TLASLLGGHWLRAQGYANPFWLALAVLIVMTLYAAFCFGETVKEPKSTRLFTLRHHRSIVQLYV
VPAPEKSRMHLALYSLAIFVVVTVHFGAQDILTLYELSTPLCWDSKLIGYGSAAQHLPYLTSLL
GLRLLQFCLADTWVAEIGLAFNILGMVVFAFATITPLMFTGYGLLFLSLVTTPVIRAKLSKLVS
ESEQGALFSAVACVNSLAMLMASGIFNSLYPATLNFMKGFPFLLGAGLLFIPAILIGVLEKVNP
HPEFQQFPQNS

hide sequence

RefSeq Acc Id:

ENSRNOP00000013698 ⟸ ENSRNOT00000013698

Transcriptome

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

Promoters

RGD ID:

13697480

Promoter ID:

EPDNEW_R8005

Type:

multiple initiation site

Name:

Slc46a1_1

Description:

solute carrier family 46 member 1

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	10	65,734,362 - 65,734,422	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

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

ACI/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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

ACI/N (MCW)

Visual

CSV

TAB

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

BBDP/Wor (RGD)

Visual

CSV

TAB

Printer

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

BN/SsN (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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:1309472	AgrOrtholog
Ensembl Genes	ENSRNOG00000010291	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000013698	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000013698	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7322786	IMAGE-MGC_LOAD
InterPro	MFS	UniProtKB/Swiss-Prot
	MFS_dom	UniProtKB/Swiss-Prot
	MFS_trans_sf	UniProtKB/Swiss-Prot
	Sugar_transporter_CS	UniProtKB/Swiss-Prot
KEGG Report	rno:303333	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:108986	IMAGE-MGC_LOAD
NCBI Gene	303333	ENTREZGENE
Pfam	MFS_1	UniProtKB/Swiss-Prot
PhenoGen	Slc46a1	PhenoGen
PROSITE	MFS	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF103473	UniProtKB/Swiss-Prot
UniProt	PCFT_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-03-09	Slc46a1	solute carrier family 46 member 1	Slc46a1	solute carrier family 46 (folate transporter), member 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-02-26	Slc46a1	solute carrier family 46, member 1	RGD1309472	similar to DNA segment, Chr 11, ERATO Doi 18, expressed	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	RGD1309472	similar to DNA segment, Chr 11, ERATO Doi 18, expressed	RGD1309472_predicted	similar to DNA segment, Chr 11, ERATO Doi 18, expressed (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1309472_predicted	similar to DNA segment, Chr 11, ERATO Doi 18, expressed (predicted)	LOC303333_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC303333_predicted	similar to DNA segment, Chr 11, ERATO Doi 18, expressed (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

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - SMPDB