Lama2 (laminin subunit alpha 2) - Rat Genome Database

Name: Lama2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Lama2 (laminin subunit alpha 2) Rattus norvegicus

Analyze

Symbol:

Lama2

Name:

laminin subunit alpha 2

RGD ID:

1308889

Description:

Predicted to be an extracellular matrix structural constituent. Involved in Schwann cell differentiation. Located in basement membrane and dendritic spine. Biomarker of renovascular hypertension. Human ortholog(s) of this gene implicated in autosomal recessive limb-girdle muscular dystrophy; congenital merosin-deficient muscular dystrophy 1A; muscular dystrophy; and myopia. Orthologous to human LAMA2 (laminin subunit alpha 2); PARTICIPATES IN arrhythmogenic right ventricular cardiomyopathy pathway; cell-extracellular matrix signaling pathway; dilated cardiomyopathy pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; amphetamine.

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

laminin subunit alpha-2; laminin, alpha 2; LOC309368

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	LAMA2 (laminin subunit alpha 2)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	Lama2 (laminin, alpha 2)	HGNC	Treefam, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Lama2 (laminin subunit alpha 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LAMA2 (laminin subunit alpha 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LAMA2 (laminin subunit alpha 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lama2 (laminin subunit alpha 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LAMA2 (laminin subunit alpha 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LAMA2 (laminin subunit alpha 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lama2 (laminin subunit alpha 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	LAMA2 (laminin subunit alpha 2)	Alliance	DIOPT (HGNC)

Allele / Splice:

Lama2^{Tn(sb-T2/Bart3)2.2013Mcwi}

Genetic Models:

F344-Lama2^{Tn(sb-T2/Bart3)2.2013Mcwi}

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	1	17,672,675 - 18,320,641 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	1	17,672,536 - 18,320,530 (+)	Ensembl
Rnor_6.0	1	18,491,264 - 19,143,486 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	18,491,384 - 19,143,269 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	20,002,787 - 20,647,256 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	18,203,466 - 18,885,462 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	18,324,930 - 18,885,310 (+)	NCBI
Celera	1	16,078,601 - 16,724,118 (+)	NCBI		Celera
Cytogenetic Map	1	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Autosomal Recessive Limb-Girdle Muscular Dystrophy Type 23 (ISO)

Charcot-Marie-Tooth disease (ISO)

congenital merosin-deficient muscular dystrophy 1A (ISO)

congenital muscular dystrophy (ISO)

Congenital Muscular Dystrophy due to Partial LAMA2 Deficiency (ISO)

COVID-19 (ISO)

dilated cardiomyopathy (ISO)

genetic disease (ISO)

intellectual disability (ISO)

isolated elevated serum creatine phosphokinase levels (ISO)

Muscle Hypotonia (ISO)

muscular dystrophy (ISO)

Myalgia (ISO)

myopia (ISO)

polymicrogyria (ISO)

renovascular hypertension (IEP)

schizophrenia (ISO)

Thyroid Neoplasms (IEP)

urinary bladder cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17alpha-ethynylestradiol (EXP)

17beta-estradiol (ISO)

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

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

9-cis-retinoic acid (ISO)

aflatoxin B1 (ISO)

all-trans-4-oxoretinoic acid (ISO)

all-trans-retinoic acid (ISO)

amiodarone (ISO)

amphetamine (EXP)

arsenite(3-) (ISO)

atrazine (EXP,ISO)

benzo[a]pyrene (ISO)

Benzo[k]fluoranthene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

calcitriol (ISO)

captan (ISO)

carbon nanotube (ISO)

cefaloridine (EXP)

choline (ISO)

chromium(6+) (ISO)

cisplatin (ISO)

Cuprizon (EXP)

dibenz[a,h]anthracene (ISO)

dibutyl phthalate (EXP)

disodium selenite (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

ethanol (ISO)

folic acid (ISO)

fonofos (ISO)

isoprenaline (EXP)

isotretinoin (ISO)

L-methionine (ISO)

lead diacetate (ISO)

methotrexate (ISO)

mifepristone (ISO)

mitoxantrone (ISO)

N,N-diethyl-m-toluamide (EXP)

N-ethyl-N-nitrosourea (ISO)

nickel atom (ISO)

paclitaxel (ISO)

panobinostat (ISO)

parathion (ISO)

permethrin (EXP)

phenytoin (EXP)

pioglitazone (ISO)

potassium dichromate (ISO)

progesterone (ISO)

propanal (ISO)

Ptaquiloside (ISO)

SB 431542 (ISO)

silicon dioxide (EXP,ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

sodium dichromate (EXP)

sodium fluoride (ISO)

terbufos (ISO)

tetrachloromethane (ISO)

topotecan (ISO)

trichloroethene (EXP)

trichostatin A (ISO)

triclosan (ISO)

valproic acid (ISO)

vincristine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

animal organ morphogenesis (IBA)

axon guidance (IBA,ISO)

cell adhesion (IEA)

positive regulation of synaptic transmission, cholinergic (ISO)

regulation of cell adhesion (IEA)

regulation of cell migration (IEA)

regulation of embryonic development (IEA)

Schwann cell differentiation (IEP)

tissue development (IBA)

Cellular Component

basement membrane (IBA,IDA,ISO)

dendritic spine (IDA)

neuromuscular junction (ISO)

sarcolemma (ISO)

synaptic cleft (ISO)

Molecular Function

extracellular matrix structural constituent (IBA)

molecular_function (ND)

signaling receptor binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

arrhythmogenic right ventricular cardiomyopathy pathway (IEA)

cell-extracellular matrix signaling pathway (IEA)

dilated cardiomyopathy pathway (IEA)

Entamoebiasis pathway (IEA)

hypertrophic cardiomyopathy pathway (IEA)

myocarditis pathway (IEA)

small cell lung carcinoma pathway (IEA)

toxoplasmosis 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.	GOA data from the GO Consortium
3.	Helbling-Leclerc A, etal., Nat Genet. 1995 Oct;11(2):216-8.
4.	Kemaladewi DU, etal., Nat Med. 2017 Aug;23(8):984-989. doi: 10.1038/nm.4367. Epub 2017 Jul 17.
5.	Lekmine F, etal., Virchows Arch. 1999 Apr;434(4):325-32.
6.	Masaki T, etal., Acta Neuropathol (Berl). 2001 Feb;101(2):174-8.
7.	Masaki T, etal., Exp Neurol. 2002 Mar;174(1):109-17.
8.	MGD data from the GO Consortium
9.	Oliviero P, etal., Cardiovasc Res. 2000 May;46(2):346-55.
10.	OMIM Disease Annotation Pipeline
11.	Pipeline to import KEGG annotations from KEGG into RGD
12.	RGD automated data pipeline
13.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14.	RGD automated import pipeline for gene-chemical interactions
15.	RGD comprehensive gene curation
16.	Tian M, etal., Brain Res. 1997 Aug 1;764(1-2):28-38.
17.	Tideman JW, etal., Genet Epidemiol. 2016 Dec;40(8):756-766. doi: 10.1002/gepi.21999. Epub 2016 Sep 9.

Additional References at PubMed

PMID:2099832	PMID:8568931	PMID:9264260	PMID:9396756	PMID:9524190	PMID:11115849	PMID:12051813	PMID:14557481	PMID:15895400	PMID:18757743	PMID:19295126	PMID:19739104
PMID:22654118	PMID:23376485	PMID:24006456	PMID:27068509	PMID:27559042	PMID:27815338

Genomics

Comparative Map Data

Lama2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	17,672,675 - 18,320,641 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	1	17,672,536 - 18,320,530 (+)	Ensembl
Rnor_6.0	1	18,491,264 - 19,143,486 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	18,491,384 - 19,143,269 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	20,002,787 - 20,647,256 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	18,203,466 - 18,885,462 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	18,324,930 - 18,885,310 (+)	NCBI
Celera	1	16,078,601 - 16,724,118 (+)	NCBI		Celera
Cytogenetic Map	1	p12	NCBI

LAMA2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	6	128,883,138 - 129,516,566 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	128,883,138 - 129,516,566 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	6	129,204,283 - 129,837,711 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	129,245,979 - 129,879,404 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	6	129,246,034 - 129,879,401	NCBI
Celera	6	129,950,556 - 130,583,793 (+)	NCBI
Cytogenetic Map	6	q22.33	NCBI
HuRef	6	126,785,527 - 127,418,362 (+)	NCBI		HuRef
CHM1_1	6	129,468,357 - 130,101,369 (+)	NCBI		CHM1_1

Lama2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	26,857,281 - 27,493,021 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	26,856,032 - 27,495,754 (-)	Ensembl
GRCm38	10	26,981,285 - 27,617,191 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	26,980,036 - 27,619,758 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	26,701,091 - 27,336,748 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	26,670,819 - 27,306,267 (-)	NCBI			mm8
Celera	10	27,907,208 - 28,541,586 (-)	NCBI		Celera
Cytogenetic Map	10	A4	NCBI
cM Map	10	14.23	NCBI

Lama2
(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_004955436	9,830,030 - 10,399,891 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955436	9,829,777 - 10,400,101 (+)	NCBI	ChiLan1.0	ChiLan1.0

LAMA2
(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	6	130,781,676 - 131,415,549 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	130,781,781 - 131,415,337 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	126,672,013 - 127,307,870 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

LAMA2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	67,645,461 - 68,096,506 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	67,611,122 - 68,095,914 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	68,254,521 - 68,844,637 (+)	NCBI
ROS_Cfam_1.0	1	67,721,690 - 68,305,337 (+)	NCBI
ROS_Cfam_1.0 Ensembl	1	67,721,701 - 68,304,715 (+)	Ensembl
UMICH_Zoey_3.1	1	67,644,723 - 68,228,165 (+)	NCBI
UNSW_CanFamBas_1.0	1	67,427,961 - 68,011,313 (+)	NCBI
UU_Cfam_GSD_1.0	1	68,070,825 - 68,654,877 (+)	NCBI

Lama2
(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_024404946	117,593,991 - 118,159,491 (+)	NCBI
SpeTri2.0	NW_004936639	259,662 - 825,170 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LAMA2
(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	33,867,639 - 34,359,698 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	33,765,412 - 34,359,741 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	37,284,919 - 37,545,503 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LAMA2
(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	13	44,074,128 - 44,688,187 (-)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1	13	44,074,128 - 44,688,187 (-)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	13	44,073,525 - 44,531,889 (-)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666040	16,239,880 - 16,874,460 (-)	NCBI	Vero_WHO_p1.0

Lama2
(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_004624753	3,194,678 - 3,794,145 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

D1Got23

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	18,212,061 - 18,212,241 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	19,034,627 - 19,034,806	NCBI	Rnor6.0
Rnor_5.0	1	20,539,064 - 20,539,243	UniSTS	Rnor5.0
RGSC_v3.4	1	18,776,338 - 18,776,518	RGD	RGSC3.4
RGSC_v3.4	1	18,776,339 - 18,776,518	UniSTS	RGSC3.4
RGSC_v3.1	1	18,776,401 - 18,776,580	RGD
Celera	1	16,616,775 - 16,616,954	UniSTS
RH 3.4 Map	1	179.2	RGD
RH 3.4 Map	1	179.2	UniSTS
RH 2.0 Map	1	105.5	RGD
Cytogenetic Map	1	p12	UniSTS

RH129016

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	18,320,436 - 18,320,616 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	19,143,282 - 19,143,461	NCBI	Rnor6.0
Rnor_5.0	1	20,647,052 - 20,647,231	UniSTS	Rnor5.0
RGSC_v3.4	1	18,885,258 - 18,885,437	UniSTS	RGSC3.4
Celera	1	16,723,914 - 16,724,093	UniSTS
RH 3.4 Map	1	178.2	UniSTS
Cytogenetic Map	1	p12	UniSTS

RH138034

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	17,910,359 - 17,910,570 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	18,730,287 - 18,730,497	NCBI	Rnor6.0
Rnor_5.0	1	20,238,082 - 20,238,292	UniSTS	Rnor5.0
RGSC_v3.4	1	18,442,358 - 18,442,568	UniSTS	RGSC3.4
Celera	1	16,316,149 - 16,316,359	UniSTS
RH 3.4 Map	1	178.3	UniSTS
Cytogenetic Map	1	p12	UniSTS

EST-CFZ97756

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	17,718,112 - 17,718,464 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	18,535,680 - 18,536,031	NCBI	Rnor6.0
Rnor_5.0	1	20,047,158 - 20,047,509	UniSTS	Rnor5.0
RGSC_v3.4	1	18,249,000 - 18,249,351	UniSTS	RGSC3.4
Celera	1	16,124,057 - 16,124,408	UniSTS
Cytogenetic Map	1	p12	UniSTS

AU049510

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	17,870,999 - 17,871,286 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	18,690,967 - 18,691,253	NCBI	Rnor6.0
Rnor_5.0	1	20,199,031 - 20,199,317	UniSTS	Rnor5.0
RGSC_v3.4	1	18,402,537 - 18,402,823	UniSTS	RGSC3.4
Celera	1	16,276,775 - 16,277,061	UniSTS
Cytogenetic Map	1	p12	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
1354647	Despr8	Despair related QTL 8		0.0000341	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	1	24744506	Rat
2298546	Neuinf4	Neuroinflammation QTL 4	5.1		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	1	1	28736750	Rat
2313053	Bss51	Bone structure and strength QTL 51	3.8	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	1	32356093	Rat
2313070	Bss52	Bone structure and strength QTL 52	4.4	0.0001	body length (VT:0001256)	body length (CMO:0000013)	1	1	32356093	Rat
2313090	Bmd69	Bone mineral density QTL 69	4.4	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	1	32356093	Rat
738020	Pia8	Pristane induced arthritis QTL 8	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	1	65833076	Rat
1578650	Bmd6	Bone mineral density QTL 6	12.2		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	1	509108	43284926	Rat
1578651	Bmd7	Bone mineral density QTL 7	14.2		femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	1	509108	43284926	Rat
1578669	Bss9	Bone structure and strength QTL 9	6.3		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	1	509108	43284926	Rat
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	509108	86060548	Rat
1600360	Mcs16	Mammary carcinoma susceptibility QTL 16	2.4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	2244390	43433040	Rat
7421626	Bp360	Blood pressure QTL 360		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	4393289	49393289	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5925874	115540829	Rat
4889451	Eae29	Experimental allergic encephalomyelitis QTL 29	5.51		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	1	5925877	24697545	Rat
631508	Sald1	Serum aldosterone level QTL 1	3.7		blood aldosterone amount (VT:0005346)	serum aldosterone level (CMO:0000487)	1	9856001	54856001	Rat
2302038	Pia31	Pristane induced arthritis QTL 31	5.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	1	10992065	55992065	Rat
1300167	Hrtrt2	Heart rate QTL 2	4.35		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	11481312	75088344	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	11481312	82174945	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11481312	82174945	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	11481312	82174945	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	11481312	82174945	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2317755	Glom22	Glomerulus QTL 22	3.8		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	1	11481482	32355910	Rat
1578756	Iddm22	Insulin dependent diabetes mellitus QTL 22	2.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	11835181	56835181	Rat
70179	Xhs2	X-ray hypersensitivity QTL 2	3.2		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	1	15321100	19121980	Rat
5684998	Bss101	Bone structure and strength QTL 101	3.6		tibia strength trait (VT:1000284)	tibia ultimate force (CMO:0001734)	1	15431621	49361612	Rat
5684999	Bss102	Bone structure and strength QTL 102	5.5	0.00000072	tibia strength trait (VT:1000284)	tibia stiffness (CMO:0001735)	1	15431621	49361612	Rat
631494	Bp95	Blood pressure QTL 95	40	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	16206210	49268520	Rat

Genetic Models

This gene Lama2 is modified in the following models/strains

F344-Lama2^{Tn(sb-T2/Bart3)2.2013Mcwi}

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	115
Count of miRNA genes:	92
Interacting mature miRNAs:	95
Transcripts:	ENSRNOT00000014917
Prediction methods:	Microtar, 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		33	9	2	10	2	8	10	5	24	30	11	8
Low	3	8	46	37	9	37		1	69	11	11
Below cutoff		2	2	2		2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_017590488	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017590489	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017590910	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017590911	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039098968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039098969	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473994	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000008	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000014917 ⟹ ENSRNOP00000014917

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	17,672,536 - 18,320,530 (+)	Ensembl
Rnor_6.0 Ensembl	1	18,491,384 - 19,143,269 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000079138 ⟹ ENSRNOP00000070049

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	17,672,714 - 18,320,530 (+)	Ensembl
Rnor_6.0 Ensembl	1	18,491,384 - 19,143,269 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000102071 ⟹ ENSRNOP00000078909

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	17,672,536 - 18,320,530 (+)	Ensembl

RefSeq Acc Id:

XM_039098968 ⟹ XP_038954896

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	17,672,675 - 18,320,641 (+)	NCBI

RefSeq Acc Id:

XM_039098969 ⟹ XP_038954897

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	17,672,675 - 18,320,641 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_038954896	(Get FASTA)	NCBI Sequence Viewer
	XP_038954897	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL93824	(Get FASTA)	NCBI Sequence Viewer
	EDL93825	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

ENSRNOP00000070049 ⟸ ENSRNOT00000079138

RefSeq Acc Id:

ENSRNOP00000014917 ⟸ ENSRNOT00000014917

RefSeq Acc Id:	XP_038954896 ⟸ XM_039098968
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038954897 ⟸ XM_039098969
- Peptide Label:	isoform X2

RefSeq Acc Id:

ENSRNOP00000078909 ⟸ ENSRNOT00000102071

Protein Domains

LAM_G_DOMAIN Laminin EGF-like Laminin IV type A Laminin N-terminal

Transcriptome

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

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:1308889	AgrOrtholog
Ensembl Genes	ENSRNOG00000011134	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000014917	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000070049	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000014917	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000079138	ENTREZGENE, UniProtKB/TrEMBL
InterPro	ConA-like_subgrp	UniProtKB/TrEMBL
	EGF-like_dom	UniProtKB/TrEMBL
	EGF_laminin	UniProtKB/TrEMBL
	Growth_fac_rcpt_N_dom	UniProtKB/TrEMBL
	Laminin_B_type_IV	UniProtKB/TrEMBL
	Laminin_G	UniProtKB/TrEMBL
	Laminin_I	UniProtKB/TrEMBL
	Laminin_II	UniProtKB/TrEMBL
	Laminin_N	UniProtKB/TrEMBL
NCBI Gene	309368	ENTREZGENE
Pfam	Laminin_B	UniProtKB/TrEMBL
	Laminin_EGF	UniProtKB/TrEMBL
	Laminin_G_1	UniProtKB/TrEMBL
	Laminin_G_2	UniProtKB/TrEMBL
	Laminin_I	UniProtKB/TrEMBL
	Laminin_II	UniProtKB/TrEMBL
	Laminin_N	UniProtKB/TrEMBL
PhenoGen	Lama2	PhenoGen
PROSITE	EGF_LAM_1	UniProtKB/TrEMBL
	EGF_LAM_2	UniProtKB/TrEMBL
	LAM_G_DOMAIN	UniProtKB/TrEMBL
	LAMININ_IVA	UniProtKB/TrEMBL
	LAMININ_NTER	UniProtKB/TrEMBL
SMART	EGF	UniProtKB/TrEMBL
	EGF_Lam	UniProtKB/TrEMBL
	LamB	UniProtKB/TrEMBL
	LamG	UniProtKB/TrEMBL
	LamNT	UniProtKB/TrEMBL
Superfamily-SCOP	ConA_like_lec_gl	UniProtKB/TrEMBL
	SSF57184	UniProtKB/TrEMBL
Transposagen	Lama2	Transposagen
UniProt	F1M614_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Lama2	laminin, alpha 2	Lama2_predicted	laminin, alpha 2 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Lama2_predicted	laminin, alpha 2 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

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)