Slc39a1 (solute carrier family 39 member 1)

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Gene: Slc39a1 (solute carrier family 39 member 1) Rattus norvegicus

Analyze

Symbol:

Slc39a1

Name:

solute carrier family 39 member 1

RGD ID:

1305241

Description:

Exhibits signaling receptor binding activity. Predicted to be involved in chordate embryonic development; limb development; and zinc ion transmembrane transport. Predicted to localize to plasma membrane. Orthologous to human SLC39A1 (solute carrier family 39 member 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; aldosterone; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC361986; solute carrier family 39 (zinc transporter), member 1; zinc transporter ZIP1

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):	SLC39A1 (solute carrier family 39 member 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther
Mus musculus (house mouse):	Slc39a1 (solute carrier family 39 (zinc transporter), member 1)	HGNC	NCBI, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Slc39a1 (solute carrier family 39 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SLC39A1 (solute carrier family 39 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SLC39A1 (solute carrier family 39 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Slc39a1 (solute carrier family 39 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SLC39A1 (solute carrier family 39 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	SLC39A1 (solute carrier family 39 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Slc39a1 (solute carrier family 39 member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SLC39A1 (solute carrier family 39 member 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Slc39a1 (solute carrier family 39 (zinc transporter), member 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	slc39a1 (solute carrier family 39 member 1)	Alliance	DIOPT (InParanoid\|OMA\|OrthoInspector\|PANTHER)
Saccharomyces cerevisiae (baker's yeast):	ZRT1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Zip42C.1	Alliance	DIOPT (InParanoid\|OMA\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	Zip42C.2	Alliance	DIOPT (InParanoid\|OMA\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	Zip89B	Alliance	DIOPT (InParanoid\|OMA\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	zipt-1	Alliance	DIOPT (InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	ZRT2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|PhylomeDB)
Caenorhabditis elegans (roundworm):	zipt-2.1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	zipt-2.2	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoInspector\|PANTHER)

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	2	175,703,413 - 175,709,063 (+)	NCBI
Rnor_6.0 Ensembl	2	189,609,800 - 189,615,366 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	2	189,609,766 - 189,615,367 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	2	209,042,625 - 209,048,222 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	182,490,501 - 182,496,068 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	182,440,596 - 182,445,640 (+)	NCBI
Celera	2	169,638,848 - 169,644,414 (+)	NCBI		Celera
Cytogenetic Map	2	q34	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autosomal dominant non-syndromic intellectual disability 18 (ISO)

Prostatic Neoplasms (ISO)

respiratory allergy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

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

3,4-methylenedioxymethamphetamine (ISO)

4,4'-diaminodiphenylmethane (ISO)

aflatoxin B1 (ISO)

aldosterone (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

C60 fullerene (EXP)

cadmium atom (ISO)

cadmium dichloride (ISO)

calcitriol (ISO)

carbon nanotube (ISO)

cisplatin (ISO)

clobetasol (ISO)

cobalt dichloride (ISO)

dexamethasone (EXP)

diuron (EXP)

elemental selenium (ISO)

ethanol (EXP)

flavonoids (EXP)

iron dichloride (ISO)

N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (ISO)

nickel dichloride (ISO)

nickel subsulfide (EXP)

ochratoxin A (ISO)

oxaliplatin (EXP)

paracetamol (ISO)

selenium atom (ISO)

Soman (EXP)

spironolactone (EXP)

tetrachloromethane (ISO)

titanium dioxide (ISO)

topotecan (EXP)

vanadium atom (ISO)

vanadium(0) (ISO)

vitamin E (ISO)

zinc atom (ISO)

zinc dichloride (ISO)

zinc sulfate (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

embryonic cranial skeleton morphogenesis (ISO)

in utero embryonic development (ISO)

limb development (ISO)

zinc ion transmembrane transport (IBA,ISO)

zinc ion transport (ISO)

Cellular Component

integral component of membrane (IEA)

membrane (IBA)

plasma membrane (IBA,ISO)

Molecular Function

protein binding (ISO)

signaling receptor binding (IPI)

zinc ion transmembrane transporter activity (IBA,ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Kim OJ, etal., J Neurochem. 2008 Jul;106(1):83-95. Epub 2008 Jul 1.
3.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:11301334	PMID:12477932	PMID:12888280	PMID:14525987	PMID:16652366	PMID:19530166	PMID:26463958

Genomics

Comparative Map Data

Slc39a1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	2	175,703,413 - 175,709,063 (+)	NCBI
Rnor_6.0 Ensembl	2	189,609,800 - 189,615,366 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	2	189,609,766 - 189,615,367 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	2	209,042,625 - 209,048,222 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	182,490,501 - 182,496,068 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	182,440,596 - 182,445,640 (+)	NCBI
Celera	2	169,638,848 - 169,644,414 (+)	NCBI		Celera
Cytogenetic Map	2	q34	NCBI

SLC39A1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	153,959,099 - 153,968,184 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	153,959,110 - 153,968,184 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	153,931,586 - 153,940,660 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	152,198,212 - 152,206,812 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	150,744,661 - 150,753,261	NCBI
Celera	1	127,003,339 - 127,011,938 (-)	NCBI
Cytogenetic Map	1	q21.3	NCBI
HuRef	1	125,294,161 - 125,303,246 (-)	NCBI		HuRef
CHM1_1	1	155,327,888 - 155,336,973 (-)	NCBI		CHM1_1

Slc39a1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	3	90,155,497 - 90,160,922 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	3	90,155,479 - 90,160,919 (+)	Ensembl
GRCm38	3	90,248,190 - 90,253,613 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	3	90,248,172 - 90,253,612 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	3	90,052,114 - 90,057,534 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	3	90,334,157 - 90,339,539 (+)	NCBI			mm8
MGSCv36	3	91,093,484 - 91,099,116 (+)	NCBI			mm8
Celera	3	90,285,048 - 90,290,812 (+)	NCBI		Celera
Cytogenetic Map	3	F1	NCBI

Slc39a1
(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_004955545	554,947 - 560,336 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955545	556,210 - 559,732 (-)	NCBI	ChiLan1.0	ChiLan1.0

SLC39A1
(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	1	132,944,346 - 132,952,955 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	132,944,346 - 132,952,951 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	129,315,964 - 129,324,571 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

SLC39A1
(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	7	43,171,287 - 43,174,036 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	7	43,171,219 - 43,174,876 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Slc39a1
(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_004936580	3,704,738 - 3,708,671 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLC39A1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	4	95,728,999 - 95,733,824 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	4	95,729,480 - 95,733,824 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	104,630,406 - 104,635,131 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SLC39A1
(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	20	9,847,928 - 9,852,998 (+)	NCBI
ChlSab1.1 Ensembl	20	9,847,968 - 9,853,413 (+)	Ensembl

Slc39a1
(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_004624885	3,260,673 - 3,264,636 (+)	NCBI

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
2293843	Kiddil6	Kidney dilation QTL 6	3.1		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42776916	195645082	Rat
1598805	Memor8	Memory QTL 8	3		exploratory behavior trait (VT:0010471)	average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)	2	157914311	204022555	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	140566078	217498545	Rat
71113	Cari2	Carrageenan-induced inflammation QTL 2	2.7	0.009	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	2	147522550	217498710	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46537589	217498710	Rat
61457	Niddm8	Non-insulin dependent diabetes mellitus QTL 8	4.1	0.01	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	2	188449158	189857032	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43133606	217498545	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43133606	217498545	Rat
61469	Bp16	Blood pressure QTL 16	5.64		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	2	184730446	229730446	Rat
61473	Bp19	Blood pressure QTL 19	6.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	186611811	189857032	Rat
70162	Bp63	Blood pressure QTL 63	5.64		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	2	184730446	229730446	Rat
724568	Uae13	Urinary albumin excretion QTL 13	4.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	2	149114878	225501939	Rat
1331734	Bp204	Blood pressure QTL 204	3.61192		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	181990297	240020001	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	56244671	217498710	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
1298076	Bp166	Blood pressure QTL 166		0.0009	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	141583337	217498710	Rat
1298080	Bp163	Blood pressure QTL 163		0.02	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66828049	217498710	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
1331794	Bp202	Blood pressure QTL 202	3.66819		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	147122993	240020001	Rat
1331805	Cm29	Cardiac mass QTL 29	3.50746		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	2	147122993	240020001	Rat
2307174	Activ3	Activity QTL 3	4.83	0.000058	locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	2	183984665	228984665	Rat
1581502	Esta3	Estrogen-induced thymic atrophy QTL 3			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	2	142053350	204585731	Rat
631501	Bp101	Blood pressure QTL 101	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	157914409	217498545	Rat
631507	Bp105	Blood pressure QTL 105		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	116075644	228737869	Rat
631522	Bp74	Blood pressure QTL 74		0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	186611811	198704485	Rat
1302793	Bw16	Body weight QTL 16	5	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	2	169852800	217498545	Rat
1641891	Alcrsp17	Alcohol response QTL 17			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	155965557	254121739	Rat
1641925	Alcrsp2	Alcohol response QTL 2			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	155965557	237742948	Rat
1598833	Bp295	Blood pressure QTL 295	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	161745602	206745602	Rat
1598838	Bp290	Blood pressure QTL 290	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	181522444	226522444	Rat
2301415	Cm67	Cardiac mass QTL 67		0.003	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	2	172795683	189857032	Rat
634308	Sach6	Saccharin preference QTL 6	4.9		taste sensitivity trait (VT:0001986)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	2	116075644	228737869	Rat
1358356	Srcrt1	Stress Responsive Cort QTL1	3.66		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	2	175403337	239166203	Rat
1578648	Bss11	Bone structure and strength QTL 11	4.7		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	2	118446646	227707979	Rat
1300165	Rf9	Renal function QTL 9	3.28		kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	2	138901276	217498710	Rat
1354601	Slep1	Serum leptin concentration QTL 1	5.39		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	2	43149788	198704485	Rat
1354605	Rf48	Renal function QTL 48	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	2	75687495	221880419	Rat
1354609	Niddm62	Non-insulin dependent diabetes mellitus QTL 62	4.72	0.000006	insulin secretion trait (VT:0003564)	plasma insulin level (CMO:0000342)	2	158159186	217498710	Rat
1354622	Kidm16	Kidney mass QTL 16	3		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	2	83819608	239166203	Rat
1354648	Bp239	Blood pressure QTL 239		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66828236	243550655	Rat
1354649	Kidm17	Kidney mass QTL 17	2.9		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	2	83819608	243901375	Rat
2301966	Bp322	Blood pressure QTL 322	3.58		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	158159186	217498710	Rat
1359022	Ppulsi1	Prepulse inhibition QTL 1	3.63		prepulse inhibition trait (VT:0003088)	acoustic startle response measurement (CMO:0001519)	2	142053350	228984665	Rat
1549833	Bp257	Blood pressure QTL 257		0.003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	181987080	199696953	Rat
1554319	Bmd2	Bone mineral density QTL 2	13.4	0.0001	lumbar vertebra area (VT:0010570)	lumbar vertebra cross-sectional area (CMO:0001689)	2	118446793	228582621	Rat
2306901	Bp337	Blood pressure QTL 337		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	177680772	243901375	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	118446646	200453484	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	118446646	200453484	Rat
1359032	Hrtrt18	Heart rate QTL 18			heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	2	169852670	207612467	Rat
2293084	Iddm26	Insulin dependent diabetes mellitus QTL 26	2.9		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	188838511	228984665	Rat
61374	Edpm2	Estrogen-dependent pituitary mass QTL 2	4.42	0.86	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	2	78321410	217498710	Rat
61401	Niddm2	Non-insulin dependent diabetes mellitus QTL 2	4.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	159585731	204585731	Rat
6903312	Bw112	Body weight QTL 112	3.2	0.0013	body mass (VT:0001259)	body weight (CMO:0000012)	2	149614623	198704357	Rat
7488904	Bp363	Blood pressure QTL 363		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	186889035	189857032	Rat
7488925	Bp364	Blood pressure QTL 364		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	174160958	219160958	Rat
7488927	Bp365	Blood pressure QTL 365		0.008	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	177339806	222339806	Rat
8662843	Vetf9	Vascular elastic tissue fragility QTL 9	2.05		thoracic aorta molecular composition trait (VT:0010568)	aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)	2	169852670	243026643	Rat
8662832	Vetf7	Vascular elastic tissue fragility QTL 7	3.5		aorta elastin amount (VT:0003905)	aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)	2	83754907	237610852	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	2	149614466	205573168	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	149614466	205573168	Rat
12879846	Cm90	Cardiac mass QTL 90		0.011	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	2	172795683	189857032	Rat
12879836	Kidm61	Kidney mass QTL 61		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	172795683	199696953	Rat
10755499	Bp389	Blood pressure QTL 389	2.61		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	16679272	245624402	Rat
12879839	Cm85	Cardiac mass QTL 85		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	2	172795683	199696953	Rat
11565181	Bw176	Body weight QTL 176		0.002	body mass (VT:0001259)	body weight (CMO:0000012)	2	172795683	189857032	Rat
12879838	Cm86	Cardiac mass QTL 86		0.002	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	172795683	199696953	Rat
12879840	Bw179	Body weight QTL 179		0.005	body mass (VT:0001259)	body weight (CMO:0000012)	2	172795683	199696953	Rat
12879845	Cm89	Cardiac mass QTL 89		0.008	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	172795683	189857032	Rat
11565180	Kidm56	Kidney mass QTL 56		0.003	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	172795683	189857032	Rat
12879837	Am2	Aortic mass QTL 2		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	2	172795683	199696953	Rat
12879847	Am4	Aortic mass QTL 4		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	2	172795683	189857032	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	533
Count of miRNA genes:	254
Interacting mature miRNAs:	316
Transcripts:	ENSRNOT00000021904
Prediction methods:	Microtar, Miranda, 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	3	43	57	41	19	41	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001134577	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006232707	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC128440	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC168649	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473976	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000069	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000089016 ⟹ ENSRNOP00000071120

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	2	189,609,800 - 189,615,366 (+)	Ensembl

RefSeq Acc Id:

NM_001134577 ⟹ NP_001128049

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	175,703,483 - 175,709,060 (+)	NCBI
Rnor_6.0	2	189,609,800 - 189,615,367 (+)	NCBI
Rnor_5.0	2	209,042,625 - 209,048,222 (+)	NCBI
RGSC_v3.4	2	182,490,501 - 182,496,068 (+)	RGD
Celera	2	169,638,848 - 169,644,414 (+)	RGD

Sequence:

show sequence

CGAGGCCGGAACCGAGCCACAGCGATGGAGTGAGACCCTCCGGAGGTCGAAGAGTCACTGAGTT
ATCCCAACCACCATGGGGCCCTGGGGGGAGCCCGAGCTCCTGGTGTGGCGCCCAGAAGCGATCG
CATCGGAGCCCTCGGTGCCAGTGGGGCTGGAGGTGAAGCTGGGGGCCCTGGTGCTGCTGTTGCT
GCTGACACTCATCTGCAGCCTGGTACCTGTCTGTGTGCTTCGAAGGTCAGGCGCTAACCATGAA
GCCTCTGCTTCAGGCCAGAAAGCTTTAAGCCTAGTGAGCTGCTTCGCAGGAGGAGTCTTCCTGG
CTACCTGTCTTCTGGACTTGCTGCCTGACTACCTGGCTGCCATAGATGAGGCCTTGGAGGCTCT
TCATGTGACGCTTCAGTTCCCCTTGCAAGAGTTCATCCTGGCCATGGGTTTCTTCCTGGTGTTG
GTGATGGAGCAGATCACACTGGCTTATAAGGAGCAGTCCAGTCCACCACATCCGGAAGAGACGA
GAGCTCTACTGGGAACAGTGAATGGTGGGCCTCAACATTGGCATGATGGACCAGGGATCCCCCA
GGCCAGCGGAACCCCAGCAGCTCCCTCAGCCCTGCGTGCCTGTGTACTGGTCTTCTCCTTAGCC
TTGCACTCTGTATTTGAGGGCCTGGCTGTAGGGTTGCAGAGAGACAGGGCTCGAGCAATGGAGC
TGTGCCTAGCTTTGCTGCTCCACAAGGGTATCCTGGCAGTCAGTCTGTCCCTGCGGCTTCTACA
GAGCCACCTACGAGCGCAGGTGGTGGCTGGCTGTGGGATCCTCTTCTCCTGTATGACACCTCTG
GGCATTGGGCTGGGTGCAGCTCTGGCAGAGTCAGCTGGGCCTCTCCACCAGCTGGCCCAGTCTG
TTCTGGAGGGCATGGCAGCTGGCACCTTCCTCTATATCACCTTCCTGGAAATCCTACCCCAGGA
GTTGGCCACGTCTGAGCAGAGGATCCTCAAGGTCATTCTGCTCCTAGCAGGCTTTGCCCTGCTC
ACCGGCCTGCTCTTTGTCCAAGTCTAAGGTGCTTCGAGAGAAAAGGCAGGGGAGGTTGACTATC
AGGTGCCCCTGTCCTCCCTGCCCTTCTCAATTTGTGGGAAATTGAAAGGAATGGAGAAAGGAAG
TAGTGAGGACCAAAGAGTTCTCTTGAGAGGTAGGGATGGGACATTTGGACTACGAATAATGAGA
TGGAAGTGAGCAGAGAAGAGGCAAGCCCCAGACCCAAAGAATTAAGTGATAGCCAAGTTACTAC
GGACATGATCAGTGGGCATTAAAATGAGGCAGACCGCTACAATCAGAGGTCAGGCTCTACATCT
AAGAGACAAGCTGACAGAAGAACTGAGTTAGGTATCCAGCTGCTTTGGGATAAAGATGCAGAGG
CTATAAGTCAAAGCCAGTATCCTATTGGTTCTAGCCCATTTCACCACTCTGCTGATTGAAGTGG
TTCCTCCTACTGTCTTGTCTCCTAATCTTCTATTTCTCTCTTGTCTTCCACCAAGGGACTAGTG
CCAAATGGTCTCTTTGCCATTTTTCGTAATTTATCTGGCCCTTCTTGTCCTTGGGTTTCTCTGT
GTAGCCTTGGCTGTCCTGGAACTCACTCTGTAGACCAGCCTGGGCTTCAGTTTACAGAGATCCA
TCTGCCTCTGCCTCCCTAATGCTGGGATTAAAGGGGTGCTGGGCCACCACTGCCTAGCTCACTA
GTCTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTCTGGAGCTGGGGACCGAAC
CCAGGGCCTTGCGCATGCTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCACTAGTC
TGTTTTTAAAGTGCCAAATACCCGTCCACCCACTCACCCTTTGGGTTTTTGTTTGCTTTCTACC
CCCCCCCCCCCCCCCCCCCGCCAGGGTTTCTCTGTATAGCTCTGGTTGTCCTGGCCTCAAACTC
AGAGCTCTGACTGCCTCTGCCTCCTGAGCACTGGGATTAAAGGTGTGCAGCACCATGGGTTGCT
CACCTGCCCCTTTTCTGAAAGCACAGTGATGAGGTGATGGGTCAGTGGAGGAGACCTATTTGCT
CTTTATTTAGGCCCCACAATTTGGGGTGGGGCAGAAATGTTTGCTGAACTGGTCTGGAATGAGA
AAAGTAGGTACTGATACCAGCCACTACAGAAAGTGGACATGGTGGGCCAAACCTAGATAATAAC
AATAACCTGCCAAAACTTTATATCTGAGGAGCCCGGGGTGGGGAGACAGATTCCCCCCACCCCC
AGGATTATTTTTGGGGAGGGAGGGCTGTGCATAGGGCTGTACTCTGTAGAATCTATTTTACTAA
CTGACCTGTTTTGGGACATATTACCCAAATAAAGATGTTTCTATACAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006232707 ⟹ XP_006232769

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	175,703,413 - 175,709,063 (+)	NCBI
Rnor_6.0	2	189,609,766 - 189,614,272 (+)	NCBI
Rnor_5.0	2	209,042,625 - 209,048,222 (+)	NCBI

Sequence:

show sequence

GAGAGGGGTGGGGAGGGGGTGGGAATTCCCGACGCGAGGCCGGAACCGAGCCACAGCGATGGAG
TGAGACCCTCCGGAGTCTTCTCTATATAGGTCGAAGAGTCACTGAGTTATCCCAACCACCATGG
GGCCCTGGGGGGAGCCCGAGCTCCTGGTGTGGCGCCCAGAAGCGATCGCATCGGAGCCCTCGGT
GCCAGTGGGGCTGGAGGTGAAGCTGGGGGCCCTGGTGCTGCTGTTGCTGCTGACACTCATCTGC
AGCCTGGTACCTGTCTGTGTGCTTCGAAGGTCAGGCGCTAACCATGAAGCCTCTGCTTCAGGCC
AGAAAGCTTTAAGCCTAGTGAGCTGCTTCGCAGGAGGAGTCTTCCTGGCTACCTGTCTTCTGGA
CTTGCTGCCTGACTACCTGGCTGCCATAGATGAGGCCTTGGAGGCTCTTCATGTGACGCTTCAG
TTCCCCTTGCAAGAGTTCATCCTGGCCATGGGTTTCTTCCTGGTGTTGGTGATGGAGCAGATCA
CACTGGCTTATAAGGAGCAGTCCAGTCCACCACATCCGGAAGAGACGAGAGCTCTACTGGGAAC
AGTGAATGGTGGGCCTCAACATTGGCATGATGGACCAGGGATCCCCCAGGCCAGCGGAACCCCA
GCAGCTCCCTCAGCCCTGCGTGCCTGTGTACTGGTCTTCTCCTTAGCCTTGCACTCTGTATTTG
AGGGCCTGGCTGTAGGGTTGCAGAGAGACAGGGCTCGAGCAATGGAGCTGTGCCTAGCTTTGCT
GCTCCACAAGGGTATCCTGGCAGTCAGTCTGTCCCTGCGGCTTCTACAGAGCCACCTACGAGCG
CAGGTGGTGGCTGGCTGTGGGATCCTCTTCTCCTGTATGACACCTCTGGGCATTGGGCTGGGTG
CAGCTCTGGCAGAGTCAGCTGGGCCTCTCCACCAGCTGGCCCAGTCTGTTCTGGAGGGCATGGC
AGCTGGCACCTTCCTCTATATCACCTTCCTGGAAATCCTACCCCAGGAGTTGGCCACGTCTGAG
CAGAGGATCCTCAAGGTCATTCTGCTCCTAGCAGGCTTTGCCCTGCTCACCGGCCTGCTCTTTG
TCCAAGTCTAAGGTGCTTCGAGAGAAAAGGCAGGGGAGGTTGACTATCAGGTGCCCCTGTCCTC
CCTGCCCTTCTCAATTTGTGGGAAATTGAAAGGAATGGAGAAAGGAAGTAGTGAGGACCAAAGA
GTTCTCTTGAGAGGTAGGGATGGGACATTTGGACTACGAATAATGAGATGGAAGTGAGCAGAGA
AGAGGCAAGCCCCAGACCCAAAGAATTAAGTGATAGCCAAGTTACTACGGACATGATCAGTGGG
CATTAAAATGAGGCAGACCGC

hide sequence

Protein Sequences


Protein RefSeqs	NP_001128049	(Get FASTA)	NCBI Sequence Viewer
	XP_006232769	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68649	(Get FASTA)	NCBI Sequence Viewer
	EDM00575	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001128049 ⟸ NM_001134577

- UniProtKB:

B5DEF5 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MGPWGEPELLVWRPEAIASEPSVPVGLEVKLGALVLLLLLTLICSLVPVCVLRRSGANHEASAS
GQKALSLVSCFAGGVFLATCLLDLLPDYLAAIDEALEALHVTLQFPLQEFILAMGFFLVLVMEQ
ITLAYKEQSSPPHPEETRALLGTVNGGPQHWHDGPGIPQASGTPAAPSALRACVLVFSLALHSV
FEGLAVGLQRDRARAMELCLALLLHKGILAVSLSLRLLQSHLRAQVVAGCGILFSCMTPLGIGL
GAALAESAGPLHQLAQSVLEGMAAGTFLYITFLEILPQELATSEQRILKVILLLAGFALLTGLL
FVQV

hide sequence

RefSeq Acc Id:	XP_006232769 ⟸ XM_006232707
- Peptide Label:	isoform X1
- UniProtKB:	B5DEF5 (UniProtKB/TrEMBL)
- Sequence:	show sequence MGPWGEPELLVWRPEAIASEPSVPVGLEVKLGALVLLLLLTLICSLVPVCVLRRSGANHEASAS GQKALSLVSCFAGGVFLATCLLDLLPDYLAAIDEALEALHVTLQFPLQEFILAMGFFLVLVMEQ ITLAYKEQSSPPHPEETRALLGTVNGGPQHWHDGPGIPQASGTPAAPSALRACVLVFSLALHSV FEGLAVGLQRDRARAMELCLALLLHKGILAVSLSLRLLQSHLRAQVVAGCGILFSCMTPLGIGL GAALAESAGPLHQLAQSVLEGMAAGTFLYITFLEILPQELATSEQRILKVILLLAGFALLTGLL FVQV hide sequence

RefSeq Acc Id:

ENSRNOP00000071120 ⟸ ENSRNOT00000089016

Transcriptome

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

Promoters

RGD ID:

13691497

Promoter ID:

EPDNEW_R2022

Type:

initiation region

Name:

Slc39a1_1

Description:

solute carrier family 39 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	2	189,609,790 - 189,609,850	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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CSV

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

ACI/EurMcwi (RGD)

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CSV

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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CSV

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

BN/SsN (MCW)

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CSV

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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CSV

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

F344/NRrrc (MCW)

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CSV

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

FHH/EurMcwi (MCW)

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CSV

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

FHH/EurMcwi (RGD)

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CSV

TAB

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

FHL/EurMcwi (MCW)

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CSV

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

FHL/EurMcwi (RGD)

Visual

CSV

TAB

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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CSV

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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CSV

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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CSV

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

M520/N (MCW)

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CSV

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

MHS/Gib (RGD)

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CSV

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

MNS/Gib (RGD)

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CSV

TAB

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

MR/N (MCW)

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CSV

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
2	209046341	209046342	G	A	snv	GH/OmrMcwi (MCW), BBDP/WorN (KNAW), MR/N (KNAW)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
2	189613485	189613486	G	A	snv	GH/OmrMcwi (MCW), BBDP/Wor (RGD), MR/N (MCW)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
2	182494187	182494188	G	A	snv	MR/N (KNAW), BBDP/WorN (ICL), GH/OmrMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305241	AgrOrtholog
Ensembl Genes	ENSRNOG00000059463	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000071120	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000089016	ENTREZGENE, UniProtKB/TrEMBL
InterPro	ZIP	UniProtKB/TrEMBL
KEGG Report	rno:361986	UniProtKB/TrEMBL
NCBI Gene	361986	ENTREZGENE
Pfam	Zip	UniProtKB/TrEMBL
PhenoGen	Slc39a1	PhenoGen
UniProt	B5DEF5	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-03-09	Slc39a1	solute carrier family 39 member 1	Slc39a1	solute carrier family 39 (zinc transporter), member 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Slc39a1	solute carrier family 39 (zinc transporter), member 1	Slc39a1_predicted	solute carrier family 39 (zinc transporter), member 1 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Slc39a1_predicted	solute carrier family 39 (zinc transporter), member 1 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD