Slc15a4 (solute carrier family 15 member 4)

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| FTP Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References FTP Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Slc15a4 (solute carrier family 15 member 4) Rattus norvegicus

Analyze

Symbol:

Slc15a4

Name:

solute carrier family 15 member 4

RGD ID:

708469

Description:

Exhibits L-histidine transmembrane transporter activity. Involved in histidine transport. Predicted to localize to endosome membrane and integral component of lysosomal membrane. Orthologous to human SLC15A4 (solute carrier family 15 member 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; ammonium chloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC246280; MGC105315; peptide transporter 4; peptide/histidine transporter; peptide/histidine transporter 1; rPHT1; solute carrier family 15 (oligopeptide transporter), member 4; solute carrier family 15, member 4

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	29,048,634 - 29,082,480 (+)	NCBI
Rnor_6.0 Ensembl	12	32,753,824 - 32,773,277 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	32,753,824 - 32,773,277 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	34,660,965 - 34,680,418 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	30,111,863 - 30,131,134 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	29,975,250 - 29,994,522 (+)	NCBI
Celera	12	30,749,254 - 30,768,706 (+)	NCBI		Celera
Cytogenetic Map	12	q14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

systemic lupus erythematosus (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-demecolcine (ISO)

17alpha-ethynylestradiol (ISO)

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

2,6-dinitrotoluene (EXP)

2-methylcholine (ISO)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

bromobenzene (EXP)

cadmium atom (ISO)

carbon nanotube (ISO)

cobalt dichloride (EXP)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dexamethasone (EXP,ISO)

dextran sulfate (ISO)

dichlorine (EXP)

dimethylarsinic acid (ISO)

fipronil (EXP)

fonofos (ISO)

menadione (ISO)

ozone (EXP)

paracetamol (ISO)

parathion (ISO)

perfluorononanoic acid (ISO)

phenobarbital (ISO)

sodium arsenite (ISO)

terbufos (ISO)

testosterone (EXP)

titanium dioxide (ISO)

tungsten (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vincristine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

dipeptide import across plasma membrane (IEA,ISO,ISS)

histidine transport (IBA,IMP)

innate immune response (IEA)

L-histidine transmembrane export from vacuole (IEA,ISO)

L-histidine transmembrane transport (IEA)

mast cell homeostasis (IEA,ISO,ISS)

peptidoglycan transport (IEA,ISO,ISS)

positive regulation of innate immune response (IEA,ISO,ISS)

positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (IEA,ISO,ISS)

positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (IEA,ISO,ISS)

positive regulation of toll-like receptor 7 signaling pathway (IEA,ISO,ISS)

positive regulation of toll-like receptor 8 signaling pathway (IEA,ISO,ISS)

positive regulation of toll-like receptor 9 signaling pathway (IEA,ISO,ISS)

protein transport (IEA)

proton transmembrane transport (IEA)

regulation of isotype switching to IgG isotypes (IEA,ISO,ISS)

regulation of nucleotide-binding oligomerization domain containing signaling pathway (ISO,ISS)

Cellular Component

early endosome membrane (IEA,ISO)

endolysosome membrane (IEA,ISO,ISS)

endosome membrane (ISO)

integral component of endosome membrane (IEA,ISO)

integral component of lysosomal membrane (IEA,ISO,ISS)

lysosomal membrane (ISO)

Molecular Function

dipeptide transmembrane transporter activity (IEA,ISO,ISS)

L-histidine transmembrane transporter activity (IBA,IEA,IMP,ISO,ISS)

peptide:proton symporter activity (IEA,ISO,ISS)

peptidoglycan transmembrane transporter activity (IEA,ISO,ISS)

protein binding (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.	MGD data from the GO Consortium
3.	RGD automated data pipeline
4.	RGD automated import pipeline for gene-chemical interactions
5.	Yamashita T, etal., J Biol Chem 1997 Apr 11;272(15):10205-11.

Additional References at PubMed

PMID:12477932	PMID:19913073	PMID:24548120

Genomics

Comparative Map Data

Slc15a4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	29,048,634 - 29,082,480 (+)	NCBI
Rnor_6.0 Ensembl	12	32,753,824 - 32,773,277 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	32,753,824 - 32,773,277 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	34,660,965 - 34,680,418 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	30,111,863 - 30,131,134 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	29,975,250 - 29,994,522 (+)	NCBI
Celera	12	30,749,254 - 30,768,706 (+)	NCBI		Celera
Cytogenetic Map	12	q14	NCBI

SLC15A4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	12	128,793,194 - 128,823,958 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	12	128,793,194 - 128,823,966 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	12	129,277,739 - 129,308,503 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	127,843,713 - 127,874,494 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	12	127,802,644 - 127,833,421	NCBI
Celera	12	128,891,861 - 128,922,740 (-)	NCBI
Cytogenetic Map	12	q24.33	NCBI
HuRef	12	126,263,573 - 126,285,425 (-)	NCBI		HuRef
CHM1_1	12	129,098,609 - 129,129,417 (-)	NCBI		CHM1_1

Slc15a4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	127,668,795 - 127,710,356 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	5	127,672,728 - 127,709,961 (-)	Ensembl
GRCm38	5	127,594,545 - 127,633,292 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	127,595,664 - 127,632,897 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	128,076,036 - 128,097,762 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	5	127,884,869 - 127,906,595 (-)	NCBI			mm8
Celera	5	124,625,149 - 124,646,865 (-)	NCBI		Celera
Cytogenetic Map	5	G1.2	NCBI

Slc15a4
(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	NW_004955482	2,327,137 - 2,343,980 (+)	NCBI	ChiLan1.0	ChiLan1.0

SLC15A4
(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	12	130,639,525 - 130,669,822 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	12	126,418,071 - 126,448,917 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

SLC15A4
(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	26	2,802,724 - 2,831,530 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	26	2,803,798 - 2,832,057 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Slc15a4
(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_004936660	481,772 - 493,567 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLC15A4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	26,122,363 - 26,154,786 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	26,122,362 - 26,154,414 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	27,770,845 - 27,803,186 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SLC15A4
(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	11	124,170,785 - 124,204,358 (-)	NCBI
ChlSab1.1 Ensembl	11	124,169,732 - 124,204,200 (-)	Ensembl

Slc15a4
(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_004624747	26,252,788 - 26,275,273 (-)	NCBI

Position Markers

AA987064

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	32,773,056 - 32,773,218	NCBI	Rnor6.0
Rnor_5.0	12	34,680,197 - 34,680,359	UniSTS	Rnor5.0
RGSC_v3.4	12	30,130,913 - 30,131,075	UniSTS	RGSC3.4
Celera	12	30,768,485 - 30,768,647	UniSTS
Cytogenetic Map	12	q14	UniSTS

RH141739

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	32,772,950 - 32,773,132	NCBI	Rnor6.0
Rnor_5.0	12	34,680,091 - 34,680,273	UniSTS	Rnor5.0
RGSC_v3.4	12	30,130,807 - 30,130,989	UniSTS	RGSC3.4
Celera	12	30,768,379 - 30,768,561	UniSTS
RH 3.4 Map	12	480.3	UniSTS
Cytogenetic Map	12	q14	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
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	36919844	Rat
7387292	Kidm42	Kidney mass QTL 42	3.03	0.0004	kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	12	1	38334225	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	150810	45150810	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	150810	45150810	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	492578	45492578	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	2475687	47475687	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	2513442	47513442	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	2513442	47513442	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	4210051	49210051	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	9223626	52716770	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223630	52716770	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	9789834	52716770	Rat
1300157	Rf21	Renal function QTL 21	4.4		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	12	11764995	37522089	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13127211	50320041	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	14419775	52716770	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	15021986	52716770	Rat
61416	Pia4	Pristane induced arthritis QTL 4	8.4		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	12	15714609	35964508	Rat
61421	Cia12	Collagen induced arthritis QTL 12	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	15714609	41291738	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	15908900	52716770	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	15908900	52716770	Rat
631543	Bp83	Blood pressure QTL 83	5.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	17185580	44098244	Rat
2293684	Bmd26	Bone mineral density QTL 26	4.4	0.0002	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	12	17960865	38409001	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	18342477	52716770	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	18342477	52716770	Rat
2302060	Pia37	Pristane induced arthritis QTL 37	6.1	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	18729043	52716770	Rat
1549902	Bp269	Blood pressure QTL 269			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	18752593	52716770	Rat
1549912	Bp268	Blood pressure QTL 268			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	18752593	52716770	Rat
737822	Alc10	Alcohol consumption QTL 10	2.2		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	12	22650702	45946937	Rat
5684888	Pia42	Pristane induced arthritis QTL 42			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	22650702	48598906	Rat
61324	Eae5	Experimental allergic encephalomyelitis QTL 5	14		nervous system integrity trait (VT:0010566)	percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)	12	22650702	52716770	Rat
1298081	Cia25	Collagen induced arthritis QTL 25	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	22650721	41291738	Rat
70213	Niddm27	Non-insulin dependent diabetes mellitus QTL 27	3.72		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	22876297	43799153	Rat
631560	Apr1	Acute phase response QTL 1	6.1		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	24906590	52716770	Rat
7411643	Foco20	Food consumption QTL 20		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	26098845	52716770	Rat
70169	Eae13	Experimental allergic encephalomyelitis QTL 13		0.032	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	12	27190240	42196641	Rat
1331763	Wbc2	White blood cell count QTL 2	3.162		leukocyte quantity (VT:0000217)	total white blood cell count (CMO:0000365)	12	27285473	36161779	Rat
8693658	Alc33	Alcohol consumption QTL 33	2.1	0.68	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	12	29113609	49560679	Rat
8693635	Alc28	Alcohol consumption QTL 28	2.7	0.439	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	12	29113609	50757185	Rat
1556747	Calcic1	Intracellular calcium level QTL 1		3.6	platelet calcium amount (VT:0010500)	platelet intracellular calcium level (CMO:0000922)	12	31723565	47433663	Rat
1300175	Cm5	Cardiac mass QTL 5	3.78		heart mass (VT:0007028)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	31723565	51955754	Rat
1600386	Calcic2	Intracellular calcium level QTL 2		0.001	platelet physiology trait (VT:0005464)	platelet intracellular calcium level (CMO:0000922)	12	31723565	52716770	Rat
1331787	Rf41	Renal function QTL 41	2.998		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	12	31723688	45946802	Rat
631829	Alc6	Alcohol consumption QTL 6	4.7		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	12	32289782	43305579	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	615
Count of miRNA genes:	279
Interacting mature miRNAs:	350
Transcripts:	ENSRNOT00000001277
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	2	10	19	10	19	10			74	30	41	11
Low	1	33	38	31		31	8	11		5			8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_144758	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089070	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089071	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089072	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005491598	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB000280	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC087709	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473973	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000227	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000001277 ⟹ ENSRNOP00000001277

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	32,753,824 - 32,773,277 (+)	Ensembl

RefSeq Acc Id:

NM_144758 ⟹ NP_653359

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	29,063,027 - 29,082,480 (+)	NCBI
Rnor_6.0	12	32,753,824 - 32,773,277 (+)	NCBI
Rnor_5.0	12	34,660,965 - 34,680,418 (+)	NCBI
RGSC_v3.4	12	30,111,863 - 30,131,134 (+)	RGD
Celera	12	30,749,254 - 30,768,706 (+)	RGD

Sequence:

show sequence

ACCGGGTCCTTAGGGAACCAGCCATGGAGGGCGAGCGGGCGCCGCTGTTAGGTTCGCGGCGTGC
GGCGGCAGCAGCTGGGGTGTTTGCGGGGCGTCGTGCGGCGTGCGGGGCGGTACTGTTGGCCGAA
CTGCTGGAGCGCGCGGCCTTCTACGGCGTCACGGCCAACCTAGTGTTATTCTTGAATGGCGCGC
CGTTCAACTGGGAGGGCGCGCAGGCCAGCCAGGCACTGCTGCTCTTCATGGGCCTCACCTACCT
GGGATCCCCGTTCGGGGGATGGCTCGCTGACGCGCGACTCGGCCGGGCGCGCGCCATCCTGCTC
AGCCTGGCGCTCTACCTGCTGGGCATGCTGGCCTTCCCGCTGCTGGCCGCGCCCCGCTCGCGCT
CTTTTCTCTGCGGGGATCCGCACCCGGAGCTGGTGCGCAACTGCTCGGCTCCCTTCCCTAACGG
AACGGCGGTCTGTCCCGATGCTGCCGCGCGCCGCTGTGCTCCCGCCACCTTCGCGGGTCTAGTG
CTCGTGGGACTCGGTGTGGCCACGGTCAAGGCCAACATCACACCCTTTGGAGCGGATCAGGTCA
AAGATCGAGGTCCAGAGGCCACTCGGAGATTTTTCAATTGGTTTTACTGGAGCATTAATTTGGG
AGCAATCCTGTCATTAGGAGGTATTGCCTATATTCAGCAGAATGTGAGCTTTCTCACAGGCTAC
CTGATTCCTACAGTCTGCGTGGCCATTGCTTTCCTGGTCTTCCTCTGTGGCCAGAGTGTCTTCA
TCACCAAGCCTCCTGATGGCAGTGCCTTCACTGACATGTTCAGGATTCTGACCTACAGCTGCTG
CTCCCAGAGAGGAGGGCAGCGGAGAAGTGGTGAAGGCCTTGGAGTCTTTCAGCAATCTTCTAAA
CACAGTCTGTTTGATTCATGTAAGATGTCGCGTGGAGGGCCGTTCACAGAGGACAAAGTGGAAG
ACGTGAAAGCCCTGGTCAAGATTGTGCCCGTGTTCTTGGCTCTGATTCCTTACTGGACAGTGTA
TTTCCAAATGCAGACCACATATGTTTTACAGAGTCTTCATTTGAAGATTCCAGAAATCTCAAGT
ATCACCACCACCCATCACACGCTGCCTGCAGCTTGGCTCACCATGTTTGATGCGGTGCTCATCC
TCCTGCTCATCCCACTGAAGGACAAGCTAGTGGACCCGGTGCTGAGGAGACACGGCCTGCTCCC
ATCCTCCCTGAAGAGGATTGCCGTGGGGATGTTCTTCGTCACATGCTCTGCCTTTGCTGCAGGA
ATCCTGGAGAGTAAAAGGCTGGACCTGGTGAAGGAGAAGACCATCAACCAGACCATTGGTGGTG
TGGTCTACCATGCTGCTGACCTGCCCATCTGGTGGCAGATCCCACAGTATGTGCTCATTGGCAT
CAGTGAGATATTTGCAAGTATAGCAGGTCTGGAGTTTGCGTACTCGGCTGCCCCCAAGTCCATG
CAGAGTGCCATCATGGGACTCTTCTTCTTCTTCTCTGGCATTGGGTCCTTCGTGGGCTCAGGAC
TGCTGGCCCTGGTGTCTCTCAAGGCCATCGGGTGGATGAGCAGTCATACAGACTTTGGGAACAT
CAACAGCTGCCACCTGCATTACTACTTCTTCCTGCTGGCCGCCATCCAGGGAGCTACGCTGCTG
CTCTTCCTCATTGTGTCTGTGAAGTACGACCGCCAGCGAGCCAGGACAGATGGGGGGACAGCCA
GCACGAGGACCTGATGCAGCCAGCCAGCATGCTCACAGGTTCTGCAGACTATAAGGCCTCAGGG
CTTGCTAACTACCAGGGCACTGCCAGCAAGCAGGTTGAGGCTAGATGGTTGGTGTCCCAACTTC
TGAACTTGCATGTTGTCTGGACTGGCTTCTCCCTCCCTGTGCCCAGATGATGGTGGTGAGTGCC
TTACTGTGGCCCGTCTCATGTGCACTGGGCCTACCAGGAGATGAGAATGTGGCTTCTCTCACTG
AAGGTCTCTGCCCGTTCTGAGCCAGCCATGCTTTCTCTTTTAGAATCCTGAGCAGCCCCTGTCC
TGCTGCTGGGCATCCTTATTCCTTACAAACACTGTTACTTTCATAGCATCTCCTGTAAGATTAG
CAAGCATTTCCATCAAGCGGTAGGAGGATTCTCTTCAGAGATCAAAGTGTGGTTGATGGCGAGA
GAGCCCCATGAGCTGTTTCTGCTCCATTGATGGTCTCTTGTCACAGATCTTGCTGATGCCAAGG
CCTTTGTGGGTCAGTAGTGTAGACTCATCTGCTCAAAAAGTAGTTTTGTTGGCTAAGGTGAAGA
AGTGTTTCTTATTACACTAGGCTGGCCTCACTAGGCTGACCTCAAACTTGGTGCTGCCTCCTGT
CTGCTTCTCAAGTGCTAAGATCTCAGATGTCCATCACCATGGTCAGCAGGACTTAGGTCATGAA
CTACTGATCTGCTTTAAGCACATGCATCAGTGGTGAGTGAGGACACCATGTTCTCACTGAGACC
AGACAGCAGCTGGCAGGAGATTGGCATTTACACCTGGCAGATCTTTTCTGAGAACTTGACTTTG
TGTAGCAGTAAGATTGGAGGCAGGTGGTGAGTGGGGAAAACACGGGAGCTGTTGGGCTGGTCGC
CCACCTTTGTATTGTTACTGACATATCTGGGGTTCTGAGTGTGTCAACTAAACCATTTTATGTG
TTGCTGTGTCTTGTATAATTTGATAAAAGCTTCTCAGACATG

hide sequence

RefSeq Acc Id:

XM_039089070 ⟹ XP_038944998

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	29,067,312 - 29,081,698 (+)	NCBI

RefSeq Acc Id:

XM_039089071 ⟹ XP_038944999

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	29,064,647 - 29,081,698 (+)	NCBI

RefSeq Acc Id:

XM_039089072 ⟹ XP_038945000

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	29,048,634 - 29,081,698 (+)	NCBI

RefSeq Acc Id:

XR_005491598

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	29,063,001 - 29,081,380 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_653359	(Get FASTA)	NCBI Sequence Viewer
	XP_038944998	(Get FASTA)	NCBI Sequence Viewer
	XP_038944999	(Get FASTA)	NCBI Sequence Viewer
	XP_038945000	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH87709	(Get FASTA)	NCBI Sequence Viewer
	BAA20489	(Get FASTA)	NCBI Sequence Viewer
	EDM13532	(Get FASTA)	NCBI Sequence Viewer
	EDM13533	(Get FASTA)	NCBI Sequence Viewer
	O09014	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_653359 ⟸ NM_144758

- UniProtKB:

O09014 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MEGERAPLLGSRRAAAAAGVFAGRRAACGAVLLAELLERAAFYGVTANLVLFLNGAPFNWEGAQ
ASQALLLFMGLTYLGSPFGGWLADARLGRARAILLSLALYLLGMLAFPLLAAPRSRSFLCGDPH
PELVRNCSAPFPNGTAVCPDAAARRCAPATFAGLVLVGLGVATVKANITPFGADQVKDRGPEAT
RRFFNWFYWSINLGAILSLGGIAYIQQNVSFLTGYLIPTVCVAIAFLVFLCGQSVFITKPPDGS
AFTDMFRILTYSCCSQRGGQRRSGEGLGVFQQSSKHSLFDSCKMSRGGPFTEDKVEDVKALVKI
VPVFLALIPYWTVYFQMQTTYVLQSLHLKIPEISSITTTHHTLPAAWLTMFDAVLILLLIPLKD
KLVDPVLRRHGLLPSSLKRIAVGMFFVTCSAFAAGILESKRLDLVKEKTINQTIGGVVYHAADL
PIWWQIPQYVLIGISEIFASIAGLEFAYSAAPKSMQSAIMGLFFFFSGIGSFVGSGLLALVSLK
AIGWMSSHTDFGNINSCHLHYYFFLLAAIQGATLLLFLIVSVKYDRQRARTDGGTASTRT

hide sequence

RefSeq Acc Id:

ENSRNOP00000001277 ⟸ ENSRNOT00000001277

RefSeq Acc Id:	XP_038945000 ⟸ XM_039089072
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038944999 ⟸ XM_039089071
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038944998 ⟸ XM_039089070
- Peptide Label:	isoform X1

Transcriptome

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

Promoters

RGD ID:

13698598

Promoter ID:

EPDNEW_R9122

Type:

multiple initiation site

Name:

Slc15a4_1

Description:

solute carrier family 15 member 4

SO ACC ID:

SO:0000170

Source:

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

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	12	32,753,835 - 32,753,895	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

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

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)

Visual

CSV

TAB

Printer

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)

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

F344/NRrrc (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

FHH/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

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

FHL/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

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

GH/OmrMcwi (MCW)

Visual

CSV

TAB

Printer

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)

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

LE/Stm (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

LEW/Crl (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

LEW/NCrlBR (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

LH/MavRrrc (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

LL/MavRrrc (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

LN/MavRrrc (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

M520/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

MHS/Gib (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

MNS/Gib (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

MR/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

SBH/Ygl (MCW)

Visual

CSV

TAB

Printer

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)

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

SBN/Ygl (MCW)

Visual

CSV

TAB

Printer

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)

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

SHR/NHsd (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

SHRSP/Gcrc (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

SR/JrHsd (MCW)

Visual

CSV

TAB

Printer

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)

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

SS/Jr (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

SS/JrHsdMcwi (MCW)

Visual

CSV

TAB

Printer

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)

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

WAG/Rij (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

WKY/Gcrc (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

WKY/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

WKY/NCrl (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

WKY/NHsd (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

WN/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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:708469	AgrOrtholog
Ensembl Genes	ENSRNOG00000000962	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000001277	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000001277	ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7315369	IMAGE-MGC_LOAD
InterPro	MFS_trans_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	POT_fam	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTR2_symporter_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:246280	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:105315	IMAGE-MGC_LOAD
NCBI Gene	246280	ENTREZGENE
PANTHER	PTHR11654	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	PTR2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Slc15a4	PhenoGen
PROSITE	PTR2_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF103473	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JSH0_RAT	UniProtKB/TrEMBL
	O09014	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q5M931	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-02-25	Slc15a4	solute carrier family 15 member 4	Slc15a4	solute carrier family 15 (oligopeptide transporter), member 4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-08-02	Slc15a4	solute carrier family 15 (oligopeptide transporter), member 4	Slc15a4	solute carrier family 15, member 4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Slc15a4	solute carrier family 15, member 4		peptide/histidine transporter	Name updated	1299863	APPROVED
2004-09-10	Slc15a4	peptide/histidine transporter	LOC246280		Symbol and Name updated	1299863	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in hippocampus, choroid plexus, cerebellum, and pontine nucleus	1299463
gene_regulation	transport inhibited by dipeptides and tripeptides but not by free amino acids	1299463

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 - CTD