Lysmd2 (LysM domain containing 2)

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Gene: Lysmd2 (LysM domain containing 2) Rattus norvegicus

Analyze

Symbol:

Lysmd2

Name:

LysM domain containing 2

RGD ID:

1304585

Description:

Orthologous to human LYSMD2 (LysM domain containing 2); INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC300839; lysM and putative peptidoglycan-binding domain-containing protein 2; LysM, putative peptidoglycan-binding, domain containing 2; RGD1304585; similar to RIKEN cDNA 2210402C18

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	8	76,378,984 - 76,394,395 (+)	NCBI
Rnor_6.0 Ensembl	8	82,560,761 - 82,577,019 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	8	82,560,363 - 82,576,662 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	8	82,160,974 - 82,178,174 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	80,446,544 - 80,462,607 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	80,465,376 - 80,482,027 (+)	NCBI
Celera	8	76,169,272 - 76,184,220 (+)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

COVID-19 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP,ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2,4-dinitrotoluene (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

cadmium dichloride (ISO)

caffeine (EXP)

carbon nanotube (ISO)

choline (ISO)

cisplatin (ISO)

clothianidin (ISO)

copper atom (EXP)

copper(0) (EXP)

cyclosporin A (ISO)

cypermethrin (ISO)

dibenz[a,h]anthracene (ISO)

dichloroacetic acid (ISO)

dorsomorphin (ISO)

flutamide (EXP)

folic acid (ISO)

furan (ISO)

glafenine (EXP)

L-methionine (ISO)

lead(0) (ISO)

lead(2+) (ISO)

methoxyacetic acid (EXP)

methylmercury chloride (EXP)

Monobutylphthalate (EXP)

N-nitrosodiethylamine (ISO)

nickel atom (ISO)

ozone (ISO)

panobinostat (ISO)

paracetamol (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

propiconazole (ISO)

quercetin (ISO)

SB 431542 (ISO)

sodium dichromate (EXP)

sodium fluoride (ISO)

sulforaphane (ISO)

sunitinib (ISO)

tamoxifen (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trichloroethene (ISO)

valdecoxib (EXP)

valproic acid (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Molecular Function

protein binding (ISO)

References

References - curated


1.	RGD automated data pipeline
2.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932

Genomics

Comparative Map Data

Lysmd2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	8	76,378,984 - 76,394,395 (+)	NCBI
Rnor_6.0 Ensembl	8	82,560,761 - 82,577,019 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	8	82,560,363 - 82,576,662 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	8	82,160,974 - 82,178,174 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	80,446,544 - 80,462,607 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	80,465,376 - 80,482,027 (+)	NCBI
Celera	8	76,169,272 - 76,184,220 (+)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

LYSMD2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	51,723,011 - 51,751,585 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	51,723,011 - 51,751,451 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	52,015,208 - 52,043,648 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	15	52,015,261 - 52,043,650 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	49,802,553 - 49,817,608 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	15	28,908,680 - 28,937,069 (-)	NCBI
Cytogenetic Map	15	q21.2	NCBI
HuRef	15	28,845,769 - 28,874,158 (-)	NCBI		HuRef
CHM1_1	15	52,133,295 - 52,161,686 (-)	NCBI		CHM1_1

Lysmd2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	75,532,403 - 75,545,055 (+)	NCBI	GRCm39		mm39
GRCm38	9	75,625,121 - 75,637,773 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	75,625,741 - 75,637,771 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	75,473,539 - 75,485,580 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	9	75,411,650 - 75,423,680 (+)	NCBI			mm8
Celera	9	72,789,273 - 72,801,670 (+)	NCBI		Celera
Cytogenetic Map	9	D	NCBI

Lysmd2
(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_004955409	2,862,478 - 2,874,017 (+)	NCBI	ChiLan1.0	ChiLan1.0

LYSMD2
(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	15	48,992,788 - 49,021,152 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	15	30,661,922 - 30,690,653 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

LYSMD2
(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	30	17,409,326 - 17,419,698 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	30	17,409,338 - 17,424,092 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Lysmd2
(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_004936471	13,555,166 - 13,570,268 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LYSMD2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	120,026,525 - 120,043,146 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	120,009,417 - 120,043,146 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	133,183,213 - 133,216,939 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LYSMD2
(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	26	31,624,953 - 31,652,483 (+)	NCBI
ChlSab1.1 Ensembl	26	31,637,208 - 31,652,547 (+)	Ensembl

Lysmd2
(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_004624731	8,630,551 - 8,644,510 (+)	NCBI

Position Markers

RH130417

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	82,576,321 - 82,576,501	NCBI	Rnor6.0
Rnor_5.0	8	82,177,466 - 82,177,646	UniSTS	Rnor5.0
RGSC_v3.4	8	80,462,267 - 80,462,447	UniSTS	RGSC3.4
Celera	8	76,183,880 - 76,184,060	UniSTS
RH 3.4 Map	8	898.69	UniSTS
Cytogenetic Map	8	q24	UniSTS

UniSTS:224899

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	82,576,449 - 82,576,600	NCBI	Rnor6.0
Rnor_5.0	8	82,177,594 - 82,177,745	UniSTS	Rnor5.0
RGSC_v3.4	8	80,462,395 - 80,462,546	UniSTS	RGSC3.4
Celera	8	76,184,008 - 76,184,159	UniSTS
Cytogenetic Map	8	q24	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
1581557	Eae16	Experimental allergic encephalomyelitis QTL 16	3.8		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	8	9531047	119211942	Rat
631650	Stl6	Serum triglyceride level QTL 6	4	0.0019	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	10938911	120496129	Rat
631271	Lecl1	Lens clarity QTL 1		0.001	lens clarity trait (VT:0001304)	age of onset/diagnosis of cataract (CMO:0001584)	8	21464919	91140553	Rat
731182	Uae24	Urinary albumin excretion QTL 24	6.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	21813070	100873963	Rat
1358892	Kidm26	Kidney mass QTL 26	3.69		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	29867983	106526740	Rat
1358896	Bp262	Blood pressure QTL 262	2.89		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	29867983	106526740	Rat
1358907	Cm40	Cardiac mass QTL 40	1.89		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	29867983	106526740	Rat
8662823	Vetf5	Vascular elastic tissue fragility QTL 5	1.9		artery integrity trait (VT:0010639)	patent ductus arteriosus score (CMO:0002566)	8	30918112	107206309	Rat
1549908	Neudeg1	Neurodegradation QTL 1	5.5	0	nervous system integrity trait (VT:0010566)	logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)	8	32888352	101374135	Rat
2313046	Bss78	Bone structure and strength QTL 78	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	8	33558660	89058369	Rat
2313057	Bss76	Bone structure and strength QTL 76	3	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	8	33558660	89058369	Rat
2313067	Bss77	Bone structure and strength QTL 77	3.1	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	8	33558660	89058369	Rat
2313088	Bss75	Bone structure and strength QTL 75	3.1	0.0001	body length (VT:0001256)	body length, nose to rump (CMO:0000079)	8	33558660	89058369	Rat
1578765	Klgr1	Kidney lesion grade QTL 1	3.3	0.0001	kidney morphology trait (VT:0002135)	organ lesion measurement (CMO:0000677)	8	33558660	109028082	Rat
1578769	Uae31	Urinary albumin excretion QTL 31	3.3	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	33558660	109028082	Rat
1578755	Pur5	Proteinuria QTL 5	3.3	0.0001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	8	33558660	109028082	Rat
2316950	Scl66	Serum cholesterol level QTL 66	4.1		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	33558764	113580387	Rat
1331838	Niddm61	Non-insulin dependent diabetes mellitus QTL 61	3.53	0.0004	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39230130	106506973	Rat
61358	Bp39	Blood pressure QTL 39	2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	39927901	84927901	Rat
61464	Niddm11	Non-insulin dependent diabetes mellitus QTL 11	3.1	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39958022	84958022	Rat
737824	Hcar10	Hepatocarcinoma resistance QTL 10	2.9		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	8	44219197	89542960	Rat
1358906	Bp253	Blood pressure QTL 253	4	0.0004	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	44219197	100873963	Rat
1554321	Bmd3	Bone mineral density QTL 3	7.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	8	44458129	118087517	Rat
1298079	Activ2	Activity QTL 2	9.5	0.000001	voluntary movement trait (VT:0003491)	rearing measurement (CMO:0001515)	8	45712344	90712344	Rat
70161	Bp62	Blood pressure QTL 62	2.9	0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	46588437	96998640	Rat
12879882	Am8	Aortic mass QTL 8		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	8	47200750	106394378	Rat
12879878	Bw183	Body weight QTL 183		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	8	47200750	106394378	Rat
12879879	Cm99	Cardiac mass QTL 99		0.001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	47200750	106394378	Rat
12879880	Cm100	Cardiac mass QTL 100		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	8	47200750	106394378	Rat
12879881	Cm101	Cardiac mass QTL 101		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	8	47200750	106394378	Rat
12879883	Kidm65	Kidney mass QTL 65		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	47200750	106394378	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	50529480	128036471	Rat
1331837	Bw23	Body weight QTL 23	4.19	0.00007	body mass (VT:0001259)	body weight (CMO:0000012)	8	50529563	106506973	Rat
2313086	Bss60	Bone structure and strength QTL 60	4.1	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	8	54065044	89058369	Rat
4889938	Bss89	Bone structure and strength QTL 89	3.8		tibia size trait (VT:0100001)	tibia cortical bone volume (CMO:0001725)	8	54065044	89058369	Rat
5684973	Bss100	Bone structure and strength QTL 100	4.7		tibia area (VT:1000281)	tibia area measurement (CMO:0001382)	8	54065044	89058369	Rat
1358912	Bw51	Body weight QTL 51	2.95		body mass (VT:0001259)	body weight (CMO:0000012)	8	55435004	115812386	Rat
2303570	Gluco48	Glucose level QTL 48	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	55659105	100659105	Rat
2293697	Bmd39	Bone mineral density QTL 39			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	8	58230766	106394378	Rat
1582243	Bw66	Body weight QTL 66	3.4	0.0048	body mass (VT:0001259)	body weight (CMO:0000012)	8	58425510	91990535	Rat
1582254	Kidm31	Kidney mass QTL 31	3		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	8	58425510	91990535	Rat
631664	Hcar3	Hepatocarcinoma resistance QTL 3	2.9	0.0005	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	8	58425510	106526740	Rat
1300177	Cm2	Cardiac mass QTL 2	3.65		heart mass (VT:0007028)	heart weight (CMO:0000017)	8	59234112	108068306	Rat
2301402	Bp316	Blood pressure QTL 316		0.005	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	61394378	106394378	Rat
10402857	Bp380	Blood pressure QTL 380		0.95	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	61394378	106394378	Rat
2303171	Bp331	Blood pressure QTL 331	5.57	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	65717449	128033050	Rat
631653	Bp125	Blood pressure QTL 125	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	72849686	117849686	Rat
631210	Bw3	Body weight QTL3	5.9		mesenteric fat pad mass (VT:0010427)	mesenteric fat pad weight as a percentage of body weight (CMO:0000654)	8	74917593	121080545	Rat
1300171	Bp184	Blood pressure QTL 184	3.66		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	8	76103982	127182642	Rat
9590292	Uminl3	Urine mineral level QTL 3	3.62	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	8	78805083	123805083	Rat
8694446	Bw170	Body weight QTL 170	12.07	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	8	78805083	123805083	Rat
8694200	Abfw4	Abdominal fat weight QTL 4	9.07	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	8	78805083	123805083	Rat
8694392	Bw161	Body weight QTL 161	8.06	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	8	78805083	123805083	Rat
1549909	Stresp11	Stress response QTL 11	6.83	0.0019	stress-related behavior trait (VT:0010451)	number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)	8	80697934	125697934	Rat
10450865	Bw175	Body weight QTL 175	4.1		total fat pad mass (VT:0015008)	adipose tissue molecular composition measurement (CMO:0000484)	8	81413898	91140553	Rat
634332	Pia18	Pristane induced arthritis QTL 18	4		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	8	81414058	89542815	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	67
Count of miRNA genes:	53
Interacting mature miRNAs:	65
Transcripts:	ENSRNOT00000014301
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	2	40	10		12			1	46	20	25	11
Low	1	3	47	41	7	41	8	10	28	15	16		8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106839	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006243406	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC167017	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473954	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000199	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000014301 ⟹ ENSRNOP00000014301

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	8	82,560,761 - 82,576,661 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000083410 ⟹ ENSRNOP00000071697

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	8	82,560,971 - 82,577,019 (+)	Ensembl

RefSeq Acc Id:

NM_001106839 ⟹ NP_001100309

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	76,379,314 - 76,394,395 (+)	NCBI
Rnor_6.0	8	82,560,761 - 82,576,661 (+)	NCBI
Rnor_5.0	8	82,160,974 - 82,178,174 (+)	NCBI
RGSC_v3.4	8	80,446,544 - 80,462,607 (+)	RGD
Celera	8	76,169,272 - 76,184,220 (+)	RGD

Sequence:

show sequence

GGCACGGCCAGCCGCAGCCCTAGTGAGGAGGAAGAGGCGGAGGAGGAGGCGCCGCCCCCTTGGC
GAGCTCGGCGCCCCGGCGGCCTTGGCAGGACCCATGGCGGATCTCTCGCCTGCGCCGGCCCTGC
GGGAAGGCGGCCCCCGTGCGCACCGGCCCTCGGCGCCCTCCCCTCCGCTGCGCTCTCGCTCCAC
CTCGGAGCCCGAGGAGGCTGAGCTGTCGCTGAGCCTGGCCCGCACCAAGACCCGCTCGTACGGC
AGCACGGCCAGCGTGCGGGCGCCTCTGGGCGCCGGCGTCATCGAGCGCCATGTGGAGCACCGGG
TCCGCGCCGGGGACACGCTTCAGGGCATCGCGCTCAAGTACGGAGTCACGATGGAACAGATCAA
AAGGGCCAACAAACTGTTTACCAATGACTGTATATTTCTGAAGAAAACGCTGAGCATCCCAATT
CTGTCAGAGAAGCCTTTGGTGTTTAATGGACTTAACTCCATTGATTCTCCAGAAAGTGAAACTG
TTGACAGCAGTTTTTGTCATGAAGAGGAGCCTGTAGTGTCTGAGGAAGAACTACCCCCTCCCAG
TCCTCAGGACACGGACCCCAAGCCTGCGCAGCCTGAGGAAGTGTCTGCCAGAGATTTTCTGCAA
AGACTTGACTTACAGATTAAACTATCAACACAGGCAGCCAGGAAACTCAAAGAAGAGAACAGGG
ATGAAGAGAGTCCCTATGCTGCTTCTCTTTATCACAGTTAGTGTCTGGCCGACGGACTGAGCCA
GATCACAGAACGTCTGGACCCTAAAGAATCCACTGGCCCTGCTTCAGAAGCAACGCCGCTCCTG
GACTCCCATAGTGCACCTTTGAGTAGACCAACTGCAGCTGCCCTGAAGTGAGCAGCTCCTCTGG
CTTTCTATAGTTAAGTCTTACTAGGGCATGACAGCAACACTGTATTTATTCCAAAGCCTTTCAC
TTTTGTAGATGGTGGTAGTTTTAGACCGGCTTTTGTAGATACAAAAGGCATCAGAGACTCTTTA
TATATTTAAGCCAAAAGCTATGTTTATTTCCTGATGAGATCCTAAATGTATGGAGAACATGGTG
ATTGTGAAGTGATAATGCATTTGCTGTGTGTTTATAACTCAAGTGATATAATATATATTTCAAT
ATCACATATTCTGTACTAATGTAAAGAACCAAATTTTGTCTGTTATTTTGTAAAAGTAAACTAC
AGATGTCTGGATGAGAGAATAAACTATGTTTTCACATAGG

hide sequence

RefSeq Acc Id:

XM_006243406 ⟹ XP_006243468

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	76,378,984 - 76,392,448 (+)	NCBI
Rnor_6.0	8	82,560,363 - 82,574,715 (+)	NCBI
Rnor_5.0	8	82,160,974 - 82,178,174 (+)	NCBI

Sequence:

show sequence

AAGGTTTCCTGCCACTAAGATTTTGATGTTATGAAGTGGGTACTACTGAGTAAGCAGGCCCCTC
ACTGAGGAATCAGTAATGGCAAGCAAAGCTTGATGGGGGGTAGGGGGGGATGTACTGTGGCTAG
GTCAGGCTTTAGTCGGACTCTTTCTCGTCTGCACGGATCTGAGGTCCACATGGGATCTAGGACA
CCTCCGTGGGCCTCTGTCGGCCCACAGGCCTCGGCGCGCTCCCGCAGGGCCTTCTCTGGCAGGA
CCCGCACACTACAGCCCAGGCTCAGCTCCCTTATCGCCATCAGCACGGGGACCTCTGGTGCCTG
GGAAAAGCTGGCTCAGAGCGGCGCACGCCATGCAGGTCCCGCAGCTCCCCGCCTCGGCCTCGCG
CCTGCCGCCCCCGCGGCACGGCCAGCCGCAGCCCTAGTGAGGAGGAAGAGGCGGAGGAGGAGGC
GCCGCCCCCTTGGCGAGCTCGGCGCCCCGGCGGCCTTGGCAGGACCCATGGCGGATCTCTCGCC
TGCGCCGGCCCTGCGGGAAGGCGGCCCCCGTGCGCACCGGCCCTCGGCGCCCTCCCCTCCGCTG
CGCTCTCGCTCCACCTCGGAGCCCGAGGAGGCTGAGCTGTCGCTGAGCCTGGCCCGCACCAAGA
CCCGCTCGTACGGCAGCACGGCCAGCGTGCGGGCGCCTCTGGGCGCCGGCGTCATCGAGCGCCA
TGTGGAGCACCGGGTCCGCGCCGGGGACACGCTTCAGGGCATCGCGCTCAAGTACGGAGTCACG
GGGAACTGGAGCTTGTATTGCAACCTGGAGCTTATTCAGGGTCCGTTTCTGGACACAATGCCCA
TGATCAACCTGATTTGGAGAAACAACAAGATATCTGAGATGAAGAATGGTTCATTTTCAGGATC
AAGTCTCAATCTTAGTGAGGATTTCTATTGCTACCATGAAACATTGTGACCAAAATATGGAACA
GATCAAAAGGGCCAACAAACTGTTTACCAATGACTGTATATTTCTGAAGAAAACGCTGAGCATC
CCAATTCTGTCAGAGAAGCCTTTGGTGTTTAATGGACTTAACTCCATTGATTCTCCAGAAAGTG
AAACTGTTGACAGCAGTTTTTGTCATGAAGAGGAGCCTGTA

hide sequence

RefSeq Acc Id:

XM_017595572 ⟹ XP_017451061

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	8	82,560,456 - 82,576,662 (+)	NCBI

Sequence:

show sequence

TTGATGGGGGGTAGGGGGGGATGTACTGTGGCTAGGTCAGGCTTTAGTCGGACTCTTTCTCGTC
TGCACGGATCTGAGGTCCACATGGGATCTAGGACACCTCCGTGGGCCTCTGTCGGCCCACAGGC
CTCGGCGCGCTCCCGCAGGGCCTTCTCTGGCAGGACCCGCACACTACAGCCCAGGCTCAGCTCC
CTTATCGCCATCAGCACGGGGACCTCTGGTGCCTGGGAAAAGCTGGCTCAGAGCGGCGCACGCC
ATGCAGGTCCCGCAGCTCCCCGCCTCGGCCTCGCGCCTGCCGCCCCCGCGGCACGGCCAGCCGC
AGCCCTAGTGAGGAGGAAGAGGCGGAGGAGGAGGCGCCGCCCCCTTGGCGAGCTCGGCGCCCCG
GCGGCCTTGGCAGGACCCATGGCGGATCTCTCGCCTGCGCCGGCCCTGCGGGAAGGCGGCCCCC
GTGCGCACCGGCCCTCGGCGCCCTCCCCTCCGCTGCGCTCTCGCTCCACCTCGGAGCCCGAGGA
GGCTGAGCTGTCGCTGAGCCTGGCCCGCACCAAGACCCGCTCGTACGGCAGCACGGCCAGCGTG
CGGGCGCCTCTGGGCGCCGGCGTCATCGAGCGCCATGTGGAGCACCGGGTCCGCGCCGGGGACA
CGCTTCAGGGCATCGCGCTCAAGTACGGAGTCACGATGGAACAGATCAAAAGGGCCAACAAACT
GTTTACCAATGACTGTATATTTCTGAAGAAAACGCTGAGCATCCCAATTCTGTCAGAGAAGCCT
TTGGTGTTTAATGGACTTAACTCCATTGATTCTCCAGAAAGTGAAACTGTTGACAGCAGTTTTT
GTCATGAAGAGGAGCCTGTAGTGTCTGAGGAAGAACTACCCCCTCCCAGTCCTCAGGACACGGA
CCCCAAGCCTGCGCAGCCTGAGGAAGTGTCTGCCAGAGATTTTCTGCAAAGACTTGACTTACAG
ATTAAACTATCAACACAGGCAGCCAGGAAACTCAAAGAAGAGAACAGGGATGAAGAGAGTCCCT
ATGCTGCTTCTCTTTATCACAGTTAGTGTCTGGCCGACGGACTGAGCCAGATCACAGAACGTCT
GGACCCTAAAGAATCCACTGGCCCTGCTTCAGAAGCAACGCCGCTCCTGGACTCCCATAGTGCA
CCTTTGAGTAGACCAACTGCAGCTGCCCTGAAGTGAGCAGCTCCTCTGGCTTTCTATAGTTAAG
TCTTACTAGGGCATGACAGCAACACTGTATTTATTCCAAAGCCTTTCACTTTTGTAGATGGTGG
TAGTTTTAGACCGGCTTTTGTAGATACAAAAGGCATCAGAGACTCTTTATATATTTAAGCCAAA
AGCTATGTTTATTTCCTGATGAGATCCTAAATGTATGGAGAACATGGTGATTGTGAAGTGATAA
TGCATTTGCTGTGTGTTTATAACTCAAGTGATATAATATATATTTCAATATCACATATTCTGTA
CTAATGTAAAGAACCAAATTTTGTCTGTTATTTTGTAAAAGTAAACTACAGATGTCTGGATGAG
AGAATAAACTATGTTTTCACATAGGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001100309	(Get FASTA)	NCBI Sequence Viewer
	XP_006243468	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI67017	(Get FASTA)	NCBI Sequence Viewer
	EDL77780	(Get FASTA)	NCBI Sequence Viewer
	EDL77781	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001100309 ⟸ NM_001106839
- UniProtKB:	B2RZ41 (UniProtKB/TrEMBL)
- Sequence:	show sequence MEQIKRANKLFTNDCIFLKKTLSIPILSEKPLVFNGLNSIDSPESETVDSSFCHEEEPVVSEEE LPPPSPQDTDPKPAQPEEVSARDFLQRLDLQIKLSTQAARKLKEENRDEESPYAASLYHS hide sequence

RefSeq Acc Id:

XP_006243468 ⟸ XM_006243406

- Peptide Label:

isoform X1

- Sequence:

show sequence

MGGRGGCTVARSGFSRTLSRLHGSEVHMGSRTPPWASVGPQASARSRRAFSGRTRTLQPRLSSL
IAISTGTSGAWEKLAQSGARHAGPAAPRLGLAPAAPAARPAAALVRRKRRRRRRRPLGELGAPA
ALAGPMADLSPAPALREGGPRAHRPSAPSPPLRSRSTSEPEEAELSLSLARTKTRSYGSTASVR
APLGAGVIERHVEHRVRAGDTLQGIALKYGVTGNWSLYCNLELIQGPFLDTMPMINLIWRNNKI
SEMKNGSFSGSSLNLSEDFYCYHETL

hide sequence

RefSeq Acc Id:

XP_017451061 ⟸ XM_017595572

- Peptide Label:

isoform X1

- Sequence:

show sequence

MGGRGGCTVARSGFSRTLSRLHGSEVHMGSRTPPWASVGPQASARSRRAFSGRTRTLQPRLSSL
IAISTGTSGAWEKLAQSGARHAGPAAPRLGLAPAAPAARPAAALVRRKRRRRRRRPLGELGAPA
ALAGPMADLSPAPALREGGPRAHRPSAPSPPLRSRSTSEPEEAELSLSLARTKTRSYGSTASVR
APLGAGVIERHVEHRVRAGDTLQGIALKYGVTMEQIKRANKLFTNDCIFLKKTLSIPILSEKPL
VFNGLNSIDSPESETVDSSFCHEEEPVVSEEELPPPSPQDTDPKPAQPEEVSARDFLQRLDLQI
KLSTQAARKLKEENRDEESPYAASLYHS

hide sequence

RefSeq Acc Id:

ENSRNOP00000014301 ⟸ ENSRNOT00000014301

RefSeq Acc Id:

ENSRNOP00000071697 ⟸ ENSRNOT00000083410

Transcriptome

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

Promoters

RGD ID:

13696131

Promoter ID:

EPDNEW_R6656

Type:

initiation region

Name:

Lysmd2_1

Description:

LysM domain containing 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	8	82,560,845 - 82,560,905	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1304585	AgrOrtholog
Ensembl Genes	ENSRNOG00000010642	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000014301	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000071697	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000014301	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000083410	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7302522	IMAGE-MGC_LOAD
KEGG Report	rno:300839	UniProtKB/TrEMBL
MGC_CLONE	MGC:189223	IMAGE-MGC_LOAD
NCBI Gene	300839	ENTREZGENE
PhenoGen	Lysmd2	PhenoGen
UniProt	A0A0G2K146_RAT	UniProtKB/TrEMBL
	B2RZ41	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	G3V7F2	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-02-10	Lysmd2	LysM domain containing 2	Lysmd2	LysM, putative peptidoglycan-binding, domain containing 2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Lysmd2	LysM, putative peptidoglycan-binding, domain containing 2	Lysmd2_predicted	LysM, putative peptidoglycan-binding, domain containing 2 (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-30	Lysmd2_predicted	LysM, putative peptidoglycan-binding, domain containing 2 (predicted)	RGD1304585_predicted	similar to RIKEN cDNA 2210402C18 (predicted)	Symbol and Name updated	1299863	APPROVED
2005-01-20	RGD1304585_predicted	similar to RIKEN cDNA 2210402C18 (predicted)	LOC300839_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC300839_predicted	similar to RIKEN cDNA 2210402C18 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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

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

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

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