Agxt2 (alanine-glyoxylate aminotransferase 2)

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Gene: Agxt2 (alanine-glyoxylate aminotransferase 2) Rattus norvegicus

Analyze

Symbol:

Agxt2

Name:

alanine-glyoxylate aminotransferase 2

RGD ID:

621767

Description:

Predicted to enable alanine-glyoxylate transaminase activity and beta-alanine-pyruvate transaminase activity. Predicted to be involved in carboxylic acid metabolic process and positive regulation of nitric oxide biosynthetic process. Predicted to be located in mitochondrion. Orthologous to human AGXT2 (alanine--glyoxylate aminotransferase 2); PARTICIPATES IN alanine, aspartate and glutamate metabolic pathway; glycine, serine and threonine metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,2,2-tetramine; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

(R)-3-amino-2-methylpropionate--pyruvate transaminase; AGT 2; AGT2; alanine--glyoxylate aminotransferase 2, mitochondrial; beta-ALAAT II; beta-alanine-pyruvate aminotransferase; D-AIBAT

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	2	59,336,252 - 59,377,664 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	2	59,336,283 - 59,377,926 (+)	Ensembl
Rnor_6.0	2	60,337,667 - 60,379,144 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	60,337,667 - 60,379,420 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	84,308,289 - 84,348,843 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	59,713,365 - 59,754,876 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	59,641,628 - 59,683,371 (+)	NCBI
Celera	2	59,294,201 - 59,335,576 (-)	NCBI		Celera
Cytogenetic Map	2	q16	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Beta-Aminoisobutyric Acid, Urinary Excretion of (ISO)

inherited metabolic disorder (ISO)

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dichloroethane (ISO)

17beta-estradiol (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

2,2,2-tetramine (EXP)

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine (EXP)

4-hydroxyphenyl retinamide (ISO)

acetamide (EXP)

acrylamide (EXP)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

cadmium atom (EXP)

cadmium dichloride (EXP)

clofibric acid (EXP)

cobalt dichloride (EXP)

copper atom (EXP)

copper(0) (EXP)

cyclosporin A (ISO)

disulfiram (EXP)

endosulfan (EXP,ISO)

ethanol (EXP)

fenofibrate (ISO)

fenvalerate (EXP)

graphene oxide (ISO)

iodide salt (EXP)

N-Nitrosopyrrolidine (ISO)

nefazodone (EXP)

nimesulide (EXP)

nitrofen (EXP)

O-methyleugenol (ISO)

paracetamol (ISO)

PCB138 (ISO)

pirinixic acid (EXP)

Propiverine (EXP)

sodium arsenite (EXP,ISO)

sodium dichromate (EXP)

streptozocin (EXP)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

troglitazone (EXP,ISO)

valproic acid (ISO)

vancomycin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

glycine biosynthetic process, by transamination of glyoxylate (ISO)

glyoxylate catabolic process (IBA,ISO)

L-alanine catabolic process, by transamination (IBA,ISO)

positive regulation of nitric oxide biosynthetic process (IBA,ISO)

Cellular Component

mitochondrial matrix (TAS)

mitochondrion (ISO,ISS)

Molecular Function

(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (IEA)

alanine-glyoxylate transaminase activity (ISO,ISS)

beta-alanine-pyruvate transaminase activity (ISO)

pyridoxal phosphate binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

alanine, aspartate and glutamate metabolic pathway (IEA)

glycine, serine and threonine metabolic pathway (IEA)

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.	Lee IS, etal., J Biochem (Tokyo) 1995 Apr;117(4):856-62.
3.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
4.	Pipeline to import KEGG annotations from KEGG into RGD
5.	RGD automated data pipeline
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
9.	Tamaki N, etal., Eur J Biochem. 1990 Apr 20;189(1):39-45.
10.	Tamaki N, etal., Methods Enzymol 2000;324:376-89.

Additional References at PubMed

PMID:15489334	PMID:18614015	PMID:20018850	PMID:24586340	PMID:24766736

Genomics

Comparative Map Data

Agxt2
(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	59,336,252 - 59,377,664 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	2	59,336,283 - 59,377,926 (+)	Ensembl
Rnor_6.0	2	60,337,667 - 60,379,144 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	60,337,667 - 60,379,420 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	84,308,289 - 84,348,843 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	59,713,365 - 59,754,876 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	59,641,628 - 59,683,371 (+)	NCBI
Celera	2	59,294,201 - 59,335,576 (-)	NCBI		Celera
Cytogenetic Map	2	q16	NCBI

AGXT2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	5	34,998,101 - 35,048,135 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	34,998,099 - 35,048,188 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	34,998,207 - 35,048,054 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	35,033,963 - 35,083,756 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	35,033,962 - 35,083,756	NCBI
Celera	5	34,880,411 - 34,930,420 (-)	NCBI
Cytogenetic Map	5	p13.2	NCBI
HuRef	5	34,946,958 - 34,996,974 (-)	NCBI		HuRef
CHM1_1	5	35,000,510 - 35,050,560 (-)	NCBI		CHM1_1

Agxt2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	10,358,602 - 10,410,244 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	15	10,358,618 - 10,410,239 (+)	Ensembl
GRCm38	15	10,358,516 - 10,410,158 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	10,358,532 - 10,410,153 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	10,288,334 - 10,339,493 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	15	10,303,304 - 10,354,463 (+)	NCBI			mm8
Celera	15	10,155,885 - 10,206,282 (+)	NCBI		Celera
Cytogenetic Map	15	A1	NCBI

Agxt2
(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_004955426	20,101,620 - 20,142,620 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955426	20,102,368 - 20,142,596 (-)	NCBI	ChiLan1.0	ChiLan1.0

AGXT2
(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	5	80,601,554 - 80,652,575 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	80,601,554 - 80,652,575 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	75,322,351 - 75,373,261 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

AGXT2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	4	73,292,117 - 73,327,769 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	4	73,292,101 - 73,327,962 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	4	72,908,514 - 72,944,184 (+)	NCBI
ROS_Cfam_1.0	4	73,797,662 - 73,833,439 (+)	NCBI
UMICH_Zoey_3.1	4	73,545,393 - 73,581,098 (+)	NCBI
UNSW_CanFamBas_1.0	4	73,668,622 - 73,704,659 (+)	NCBI
UU_Cfam_GSD_1.0	4	74,202,253 - 74,237,942 (+)	NCBI

Agxt2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024407213	224,827,079 - 224,863,177 (-)	NCBI
SpeTri2.0	NW_004936518	6,508,928 - 6,544,324 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

AGXT2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	16	20,576,660 - 20,617,017 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	16	20,576,661 - 20,617,008 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	16	21,478,686 - 21,519,012 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

AGXT2
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	4	33,889,615 - 33,933,500 (-)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	4	33,888,533 - 33,933,449 (-)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666071	24,192,128 - 24,237,014 (-)	NCBI	Vero_WHO_p1.0

Agxt2
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624759	19,858,255 - 19,909,516 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

RH127689

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	2	59,377,694 - 59,377,884 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	60,379,175 - 60,379,364	NCBI	Rnor6.0
Rnor_5.0	2	84,308,069 - 84,308,258	UniSTS	Rnor5.0
RGSC_v3.4	2	59,754,907 - 59,755,096	UniSTS	RGSC3.4
Celera	2	59,293,981 - 59,294,170	UniSTS
Cytogenetic Map	2	q16	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
61355	Bp36	Blood pressure QTL 36	2.9		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	2	5873687	102844969	Rat
731184	Mamtr4	Mammary tumor resistance QTL 4		0.0003	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	2	16491740	61491740	Rat
1357990	Ael1	Aortic elastin QTL 1	3.1	0.00091	aorta elastin amount (VT:0003905)	aortic elastin	2	19076825	64076825	Rat
731167	Glom4	Glomerulus QTL 4	2.4	0.0082	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	2	20304672	65304672	Rat
2300168	Bmd47	Bone mineral density QTL 47	6.6	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	2	20662448	65662448	Rat
10402051	Gdil2	Gastrointestinal dilation QTL 2			enteric ganglion morphology trait (VT:0001045)	length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)	2	24903853	74786777	Rat
1302794	Stl27	Serum triglyceride level QTL 27	4.4	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	2	25413423	143657569	Rat
1358894	Kidm24	Kidney mass QTL 24	4.03		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358899	Kidm23	Kidney mass QTL 23	3.88		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358901	Cm38	Cardiac mass QTL 38	2		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358904	Cm39	Cardiac mass QTL 39	2.26		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358910	Kidm27	Kidney mass QTL 27	5.77		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358911	Kidm28	Kidney mass QTL 28	5.42		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358887	Bw50	Body weight QTL 50	2.39		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
1358908	Bw49	Body weight QTL 49	3.36		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	26917817	81754745	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	26917817	81754745	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26917817	81754745	Rat
1354603	Bp243	Blood pressure QTL 243	3.9		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26917817	127469484	Rat
2290453	Scl55	Serum cholesterol level QTL 55	2.83		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	2	26917817	136917119	Rat
9590095	Sffal3	Serum free fatty acids level QTL 3	6.78	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	2	27157160	72157160	Rat
10755434	Coatc7	Coat color QTL 7		0.04794	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	30648065	75648065	Rat
10755436	Coatc8	Coat color QTL 8		0.02431	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	35023117	80023117	Rat
61371	Edpm1	Estrogen-dependent pituitary mass QTL 1	4	0.05	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	2	35134841	88029593	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	2	40067944	102785628	Rat
1300155	Bp174	Blood pressure QTL 174	4.09		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	2	42804607	60653831	Rat
2293835	Kiddil5	Kidney dilation QTL 5	3.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42804607	157142209	Rat
2293843	Kiddil6	Kidney dilation QTL 6	3.1		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42804607	182042367	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43154682	202446871	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43154682	202446871	Rat
2293676	Bmd19	Bone mineral density QTL 19	10.7	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	2	43162366	111362592	Rat
2293682	Bmd24	Bone mineral density QTL 24	8.9	0.0001	femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	2	43162366	111362592	Rat
2293671	Bss44	Bone structure and strength QTL 44	10.97	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	2	43162366	148478373	Rat
631208	Bw1	Body weight QTL1	5.09		mesenteric fat pad mass (VT:0010427)	mesenteric fat pad weight to body weight ratio (CMO:0000654)	2	43171017	83575226	Rat
1354601	Slep1	Serum leptin concentration QTL 1	5.39		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	2	43171017	184114403	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46123260	202447032	Rat
1354592	Rf50	Renal function QTL 50	3.5		urine output (VT:0003620)	timed urine volume (CMO:0000260)	2	53822747	74786777	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	56043031	202447032	Rat
6480225	Gdil1	Gastrointestinal dilation QTL 1			enteric ganglion morphology trait (VT:0001045)	length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)	2	56660879	74786777	Rat
1582246	Cm60	Cardiac mass QTL 60	5.8		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	57605612	76539510	Rat
1558648	Smcn1	Smooth muscle cell number QTL 1		0.039	blood vessel smooth muscle cell quantity (VT:0010525)	aorta smooth muscle cell count per unit vessel length (CMO:0001646)	2	59134147	127460910	Rat
5684990	Bmd82	Bone mineral density QTL 82	2.8		tibia mineral mass (VT:1000283)	bone mineral content (CMO:0001554)	2	59324377	103795077	Rat
5684996	Bmd85	Bone mineral density QTL 85	4.7	0.024	tibia mineral mass (VT:1000283)	bone mineral density (CMO:0001226)	2	59324377	103795077	Rat
61438	Cia7	Collagen induced arthritis QTL 7	4.6	0.0001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	2	59324377	141596857	Rat
631500	Bp99	Blood pressure QTL 99	2.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	59324719	102755241	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	266
Count of miRNA genes:	164
Interacting mature miRNAs:	191
Transcripts:	ENSRNOT00000024035
Prediction methods:	Microtar, Miranda, Rnahybrid
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium			37	35		35				31	3
Low	1	2	19	6	12	6	3	3	5		27	8	3
Below cutoff		16	1		5		5	5	11	4	3		5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031835	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006232069	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB002584	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC128789	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC081765	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474058	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D38100	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219625	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000066	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000024035 ⟹ ENSRNOP00000024035

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	2	59,336,283 - 59,377,926 (+)	Ensembl
Rnor_6.0 Ensembl	2	60,337,667 - 60,379,420 (+)	Ensembl

RefSeq Acc Id:

NM_031835 ⟹ NP_114023

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	59,336,252 - 59,377,664 (+)	NCBI
Rnor_6.0	2	60,337,732 - 60,379,144 (+)	NCBI
Rnor_5.0	2	84,308,289 - 84,348,843 (-)	NCBI
RGSC_v3.4	2	59,713,365 - 59,754,876 (+)	RGD
Celera	2	59,294,201 - 59,335,576 (-)	RGD

Sequence:

show sequence

CCTGCTTCCACTGGATTTTCTTCCTGCCTGGGAAAAGATGTCTCTAGCCTGGAGAACATTGCAG
AAAGCTTTCTACCTGGAGACCTCTCTGAGAATCCTCCAGATGCGTCCATCCCTGAGCTGTGCTT
CTCGGATATATGTACCCAAGCTCACTCTTCATACAAAGCACAACATGCCACCATGTGACTTCTC
ACCTGAGAAATACCAGTCTCTGGCCTACAACCATGTCCTGGAGATTCATAAGCAGCACCTTTCT
CCTGTGAATACAGCCTATTTCCAGAAGCCTTTGCTGCTCCACCAGGGACACATGGAATGGCTCT
TTGATTCGGAAGGAAACAGATACCTGGACTTCTTCTCTGGGATTGTAACTGTTGGTGTTGGTCA
CTGCCACCCGAAGGTAACTGCTGTGGCAAAAAAGCAGATGGACCGCCTGTGGCATACAAGTTCT
GTCTTCTTCCACTCTCCGATGCATGAATATGCAGAGAGGCTGTCAGCACTCCTTCCTGAGCCTC
TTAAGGTCATTTTCTTGGTAAACAGTGGATCAGAAGCCAATGACCTGGCCATGGTGATGGCCAG
GGCATACTCGAACCACACAGACATCATTTCTTTCAGAGGAGCCTATCATGGATGTAGTCCCTAC
ACACTTGGTCTGACGAATGTAGGAATTTACAAGATGAAAGTCCCCAGTACGATAGCCTGCCAAT
CGACAATGTGCCCAGATGTTTTCCGTGGGCCTTGGGGAGGAAGCCACTGTCGGGATTCTCCGGT
GCAAACAGTCAGGAAATGCAGCTGTGCTCCAGATGGCTGCCAAGCTAAAGAACGGTACATTGAA
CAGTTCAAAGACACACTGAACACTTCTGTGGCCACGTCAATTGCTGGATTTTTTGCAGAGCCAA
TTCAAGGTGTGAATGGTGTTGTCCAGTACCCAAAGGAGTTTCTGAAGGAAGCCTTTGCACTGGT
TCGAGAGAGGGGAGGTGTATGCATTGCAGATGAAGTGCAGACAGGCTTTGGAAGGCTGGGCTCT
CACTTCTGGGGTTTCCAAACACATGATACAATGCCTGACATTGTCACCATGGCTAAAGGGATTG
GAAATGGCTTCCCCATGGCAGCAGTTGTGACCACTCCAGAAATTGCGAGCTCTTTGGCTAAACA
CTTACATCACTTCAGCACATTTGGAGGAAGTCCCCTGGCCTGCGCCATTGGATCTGCTGTGCTT
GAGGTGATTGAAGAAGAAAATCTCCAGAGAAACAGTCAAGAAGTTGGCACCTACATGCTGCTAA
AGTTTGCTAAGCTTCGGGATGAATTTGACATCGTTGGGGATGTGCGAGGCAAAGGCCTTATGGT
GGGGATAGAGATGGTTCAAGACAAGATAAGCCGCCAGCCTCTTCCTAAAACAGAAGTCAATCAA
ATCCATGAGGACTGCAAAGACATGGGGCTCCTAGTGGGTAGAGGTGGTAATTTTTCTCAGACTT
TCCGCATTGCGCCCCCGATGCGTGTCACAAAGCTGGAAGTGGATTTTGCATTTGAAGTATTTCG
TTCTGCCTTAACTCAACACATGGAGAGAAGAGCTAAGTAAGAAGAGCCCCAAGCCTCAAGAACT
TCTCAACTATGCTCAGAGTTGGATTGGAGAGATGCTGAAACCACAAGTATTAGATAGAAAAAAA
CCCTGCAGCCCTCTGAAGTAATTGTAAAAGACTCGATGGACTATCTACTGGCTACATTTGTCAA
CTGAGTCCCCATTCTCCTGATAATTCCATCCTTCAGGAGAAGTATCTGTCACTGGCTCACAGAA
TAAGTCTTAGTTTGTGTAGATTAGTCTGGGCTAATGTTATTTCCCGTTGCATTAACTGGTTTGT
AAATGAATACACAGTATATGTGTCGCCGATGAGTCCTGAAGTAAATCCTTTCCGTGACACTAAA
AAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_114023	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH81765	(Get FASTA)	NCBI Sequence Viewer
	BAA07281	(Get FASTA)	NCBI Sequence Viewer
	BAA19549	(Get FASTA)	NCBI Sequence Viewer
	EDL82993	(Get FASTA)	NCBI Sequence Viewer
	EDL82994	(Get FASTA)	NCBI Sequence Viewer
	EDL82995	(Get FASTA)	NCBI Sequence Viewer
	EDL82996	(Get FASTA)	NCBI Sequence Viewer
	EDL82997	(Get FASTA)	NCBI Sequence Viewer
	Q64565	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_114023 ⟸ NM_031835

- UniProtKB:

Q64565 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSLAWRTLQKAFYLETSLRILQMRPSLSCASRIYVPKLTLHTKHNMPPCDFSPEKYQSLAYNHV
LEIHKQHLSPVNTAYFQKPLLLHQGHMEWLFDSEGNRYLDFFSGIVTVGVGHCHPKVTAVAKKQ
MDRLWHTSSVFFHSPMHEYAERLSALLPEPLKVIFLVNSGSEANDLAMVMARAYSNHTDIISFR
GAYHGCSPYTLGLTNVGIYKMKVPSTIACQSTMCPDVFRGPWGGSHCRDSPVQTVRKCSCAPDG
CQAKERYIEQFKDTLNTSVATSIAGFFAEPIQGVNGVVQYPKEFLKEAFALVRERGGVCIADEV
QTGFGRLGSHFWGFQTHDTMPDIVTMAKGIGNGFPMAAVVTTPEIASSLAKHLHHFSTFGGSPL
ACAIGSAVLEVIEEENLQRNSQEVGTYMLLKFAKLRDEFDIVGDVRGKGLMVGIEMVQDKISRQ
PLPKTEVNQIHEDCKDMGLLVGRGGNFSQTFRIAPPMRVTKLEVDFAFEVFRSALTQHMERRAK

hide sequence

RefSeq Acc Id:

ENSRNOP00000024035 ⟸ ENSRNOT00000024035

Transcriptome

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

Promoters

RGD ID:

13691182

Promoter ID:

EPDNEW_R1707

Type:

initiation region

Name:

Agxt2_1

Description:

alanine-glyoxylate aminotransferase 2

SO ACC ID:

SO:0000170

Source:

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

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	2	60,337,739 - 60,337,799	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN-Lx/CubMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (MCW)

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

BUF/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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)

DA/OlaHsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (RGD)

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

LEW/Crl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrc (RGD)

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

LN/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (MCW)

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

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (MCW)

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

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621767	AgrOrtholog
Ensembl Genes	ENSRNOG00000017821	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000024035	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000024035	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	3.40.640.10	UniProtKB/Swiss-Prot
	3.90.1150.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7106995	IMAGE-MGC_LOAD
InterPro	Aminotrans_3	UniProtKB/Swiss-Prot
	PyrdxlP-dep_Trfase	UniProtKB/Swiss-Prot
	PyrdxlP-dep_Trfase_dom1	UniProtKB/Swiss-Prot
	PyrdxlP-dep_Trfase_major	UniProtKB/Swiss-Prot
KEGG Report	rno:83784	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:93330	IMAGE-MGC_LOAD
NCBI Gene	83784	ENTREZGENE
Pfam	Aminotran_3	UniProtKB/Swiss-Prot
PhenoGen	Agxt2	PhenoGen
PIRSF	Transaminase_4ab_Lys_Orn	UniProtKB/Swiss-Prot
PROSITE	AA_TRANSFER_CLASS_3	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF53383	UniProtKB/Swiss-Prot
UniProt	AGT2_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	O08616	UniProtKB/Swiss-Prot
	Q642F1	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-09-10	Agxt2	alanine-glyoxylate aminotransferase 2	AGT2	beta-alanine-pyruvate aminotransferase	Symbol and Name updated	1299863	APPROVED
2002-08-07	AGT2	beta-alanine-pyruvate aminotransferase			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in kidney	632008
gene_protein	512 amino acids	632008

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)