Bcas3 (BCAS3, microtubule associated cell migration factor)

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Gene: Bcas3 (BCAS3, microtubule associated cell migration factor) Rattus norvegicus

Analyze

Symbol:

Bcas3

Name:

BCAS3, microtubule associated cell migration factor

RGD ID:

1560788

Description:

Predicted to enable several functions, including acetyltransferase activator activity; beta-tubulin binding activity; and histone acetyltransferase binding activity. Predicted to be involved in several processes, including cellular response to estrogen stimulus; positive regulation of cellular component organization; and regulation of GTPase activity. Predicted to be located in several cellular components, including cytoskeleton; phagophore assembly site; and transcriptionally active chromatin. Orthologous to human BCAS3 (BCAS3 microtubule associated cell migration factor); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

breast carcinoma amplified sequence 3; breast carcinoma-amplified sequence 3; LOC360587; LOC363662; RGD1560788; similar to Breast carcinoma amplified sequence 3 homolog (K20D4)

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Allele / Splice:

Bcas3^em4Mcwi

Genetic Models:

SS-Bcas3^em4Mcwi

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	10	70,213,710 - 70,673,080 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	10	70,214,098 - 70,673,080 (+)	Ensembl
Rnor_6.0	10	72,951,303 - 73,015,309 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0	10	72,756,548 - 73,271,851 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	72,660,671 - 73,177,317 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	73,617,547 - 74,078,190 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	10	69,140,091 - 69,598,397 (+)	NCBI		Celera
Cytogenetic Map	10	q26	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

breast cancer (ISO)

Developmental Disabilities (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (ISO)

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

2-hydroxypropanoic acid (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

3-methylcholanthrene (ISO)

4-hydroxyphenyl retinamide (ISO)

acrolein (ISO)

aflatoxin B1 (ISO)

aflatoxin B2 (ISO)

alpha-pinene (ISO)

aristolochic acid (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (ISO)

butanal (ISO)

C60 fullerene (EXP)

carbon nanotube (ISO)

chlordecone (ISO)

cisplatin (ISO)

clofibrate (ISO)

coumestrol (ISO)

dexamethasone (ISO)

doxorubicin (ISO)

fenvalerate (EXP)

hydrogen peroxide (ISO)

indometacin (ISO)

methapyrilene (ISO)

methyl methanesulfonate (ISO)

N-Nitrosopyrrolidine (ISO)

O-methyleugenol (ISO)

ozone (ISO)

paracetamol (ISO)

perfluorooctanoic acid (ISO)

PhIP (ISO)

phytoestrogen (ISO)

propiconazole (ISO)

rac-lactic acid (ISO)

resveratrol (ISO)

serpentine asbestos (ISO)

sodium dichromate (EXP)

sunitinib (ISO)

thimerosal (ISO)

titanium dioxide (ISO)

triptonide (ISO)

troglitazone (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of GTPase activity (ISO)

biological_process (ND)

cellular response to estrogen stimulus (ISO)

Golgi organization (ISO)

microtubule organizing center organization (ISO)

negative regulation of focal adhesion assembly (ISO)

negative regulation of GTPase activity (ISO)

positive regulation of actin cytoskeleton reorganization (ISO)

positive regulation of catalytic activity (ISO)

positive regulation of endothelial cell migration (ISO)

positive regulation of filopodium assembly (ISO)

positive regulation of GTPase activity (ISO)

positive regulation of intracellular protein transport (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of establishment of cell polarity (ISO)

tube formation (ISO)

Cellular Component

cell leading edge (ISO)

cell periphery (ISO)

cellular_component (ND)

cytoplasm (ISO)

cytoplasmic microtubule (ISO)

intermediate filament cytoskeleton (ISO)

nucleus (ISO)

phagophore assembly site (ISO)

transcriptionally active chromatin (ISO)

Molecular Function

acetyltransferase activator activity (ISO)

beta-tubulin binding (ISO)

chromatin binding (ISO)

histone acetyltransferase binding (ISO)

histone binding (ISO)

molecular_function (ND)

nuclear receptor binding (ISO)

phosphatidylinositol binding (ISO)

protein binding (ISO)

References

References - curated


1.	Gururaj AE, etal., Cell Cycle. 2006 Jul;5(13):1407-10. Epub 2006 Jul 1.
2.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3.	RGD automated import pipeline for gene-chemical interactions
4.	RGD comprehensive gene curation

Additional References at PubMed

PMID:12477932	PMID:16099728	PMID:17505058	PMID:18030336	PMID:22300583

Genomics

Comparative Map Data

Bcas3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	70,213,710 - 70,673,080 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	10	70,214,098 - 70,673,080 (+)	Ensembl
Rnor_6.0	10	72,951,303 - 73,015,309 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0	10	72,756,548 - 73,271,851 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	72,660,671 - 73,177,317 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	73,617,547 - 74,078,190 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	10	69,140,091 - 69,598,397 (+)	NCBI		Celera
Cytogenetic Map	10	q26	NCBI

BCAS3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	17	60,677,453 - 61,392,838 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	17	60,677,851 - 61,392,831 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	17	58,755,212 - 59,470,192 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	56,109,954 - 56,824,981 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	17	56,110,014 - 56,824,973	NCBI
Celera	17	57,855,963 - 58,571,253 (+)	NCBI
Cytogenetic Map	17	q23.2	NCBI
HuRef	17	54,124,413 - 54,839,845 (+)	NCBI		HuRef
CHM1_1	17	58,819,940 - 59,534,717 (+)	NCBI		CHM1_1

Bcas3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	85,243,611 - 85,716,884 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	11	85,243,993 - 85,716,884 (+)	Ensembl
GRCm38	11	85,353,110 - 85,826,058 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	85,353,167 - 85,826,058 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	85,166,666 - 85,639,560 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	85,169,409 - 85,642,246 (+)	NCBI			mm8
Celera	11	94,976,839 - 95,452,393 (+)	NCBI		Celera
Cytogenetic Map	11	C	NCBI

Bcas3
(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_004955451	1,929,543 - 2,449,523 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955451	1,929,857 - 2,450,225 (+)	NCBI	ChiLan1.0	ChiLan1.0

BCAS3
(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	17	59,901,417 - 60,614,445 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	59,901,453 - 60,613,732 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	54,776,768 - 55,494,917 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

BCAS3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	35,253,617 - 35,845,206 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	35,253,917 - 35,843,328 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	34,482,988 - 35,073,854 (-)	NCBI
ROS_Cfam_1.0	9	36,064,944 - 36,656,494 (-)	NCBI
UMICH_Zoey_3.1	9	34,845,828 - 35,437,477 (-)	NCBI
UNSW_CanFamBas_1.0	9	35,131,472 - 35,722,494 (-)	NCBI
UU_Cfam_GSD_1.0	9	35,219,300 - 35,811,204 (-)	NCBI

Bcas3
(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_024405602	34,313,061 - 34,885,621 (-)	NCBI
SpeTri2.0	NW_004936490	2,189,693 - 2,761,989 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

BCAS3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	36,895,053 - 37,475,187 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	36,894,727 - 37,475,221 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	38,345,061 - 39,039,973 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

BCAS3
(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	16	31,912,523 - 32,620,308 (+)	NCBI	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666077	2,660,424 - 3,371,778 (+)	NCBI	Vero_WHO_p1.0

Bcas3
(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_004624871	2,444,262 - 3,036,148 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

D10Got89

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	70,325,559 - 70,325,682 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	72,766,459 - 72,766,581	NCBI	Rnor6.0
Rnor_5.0	10	72,670,514 - 72,670,636	UniSTS	Rnor5.0
RGSC_v3.4	10	73,728,933 - 73,729,055	RGD	RGSC3.4
RGSC_v3.4	10	73,728,934 - 73,729,056	UniSTS	RGSC3.4
RGSC_v3.1	10	73,743,303 - 73,743,425	RGD
Celera	10	69,251,939 - 69,252,061	UniSTS
RH 2.0 Map	10	715.4	RGD
Cytogenetic Map	10	q26	UniSTS

D10Chm138

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	70,193,411 - 70,193,658 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	72,930,356 - 72,930,606	NCBI	Rnor6.0
Rnor_5.0	10	72,834,326 - 72,834,576	UniSTS	Rnor5.0
RGSC_v3.4	10	73,596,411 - 73,596,657	UniSTS	RGSC3.4
Celera	10	69,119,463 - 69,119,676	UniSTS
Cytogenetic Map	10	q26	UniSTS

D10Chm139

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	70,253,424 - 70,253,671 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	72,989,913 - 72,990,157	NCBI	Rnor6.0
Rnor_5.0	10	72,893,869 - 72,894,113	UniSTS	Rnor5.0
RGSC_v3.4	10	73,656,922 - 73,657,166	UniSTS	RGSC3.4
Celera	10	69,179,404 - 69,179,568	UniSTS
Cytogenetic Map	10	q26	UniSTS

RH132054

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	70,672,814 - 70,673,009 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	73,271,586 - 73,271,780	NCBI	Rnor6.0
Rnor_5.0	10	73,177,052 - 73,177,246	UniSTS	Rnor5.0
RGSC_v3.4	10	74,077,925 - 74,078,119	UniSTS	RGSC3.4
Celera	10	69,598,132 - 69,598,326	UniSTS
Cytogenetic Map	10	q26	UniSTS

BF398745

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	70,666,593 - 70,666,839 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	73,265,365 - 73,265,610	NCBI	Rnor6.0
Rnor_5.0	10	73,170,831 - 73,171,076	UniSTS	Rnor5.0
RGSC_v3.4	10	74,071,704 - 74,071,949	UniSTS	RGSC3.4
Celera	10	69,591,909 - 69,592,154	UniSTS
Cytogenetic Map	10	q26	UniSTS

RH134882

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	70,524,251 - 70,524,447 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	73,123,786 - 73,123,981	NCBI	Rnor6.0
Rnor_5.0	10	73,029,249 - 73,029,444	UniSTS	Rnor5.0
RGSC_v3.4	10	73,929,375 - 73,929,570	UniSTS	RGSC3.4
Celera	10	69,450,128 - 69,450,323	UniSTS
Cytogenetic Map	10	q26	UniSTS

RH134984

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	70,656,518 - 70,656,713 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	73,255,290 - 73,255,484	NCBI	Rnor6.0
Rnor_5.0	10	73,160,756 - 73,160,950	UniSTS	Rnor5.0
RGSC_v3.4	10	74,061,629 - 74,061,823	UniSTS	RGSC3.4
Celera	10	69,581,824 - 69,582,018	UniSTS
Cytogenetic Map	10	q26	UniSTS

RH136813

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	70,207,552 - 70,207,760 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	72,944,830 - 72,945,037	NCBI	Rnor6.0
Rnor_5.0	10	72,848,800 - 72,849,007	UniSTS	Rnor5.0
RGSC_v3.4	10	73,611,010 - 73,611,217	UniSTS	RGSC3.4
Celera	10	69,133,542 - 69,133,749	UniSTS
Cytogenetic Map	10	q26	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
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	1	80676123	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6154182	73453136	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6357896	96121100	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9658275	104670812	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14487011	89062041	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14487011	104060283	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14487011	107057807	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	19816042	99406971	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22427500	90627625	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	26521957	98003205	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	26521957	98952741	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	26944628	71944628	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	27606468	72606468	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	27606468	72606468	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	28453136	73453136	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	29299504	107211142	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	30632053	75632053	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31224026	75632053	Rat
1578779	Tcas10	Tongue tumor susceptibility QTL 10	3.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	10	31297439	76297439	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	33973921	78973921	Rat
2317042	Aia20	Adjuvant induced arthritis QTL 20	3.38		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	37565079	82565079	Rat
2317043	Aia7	Adjuvant induced arthritis QTL 7	3.82		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	37565079	82565079	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	40035094	102359817	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	40035094	104060283	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	40035094	104060283	Rat
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	41142633	86142633	Rat
61463	Bp12	Blood pressure QTL 12	6.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	41333258	86333258	Rat
8552805	Bw145	Body weight QTL 145	2.2		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	10	41944526	78307017	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	42045676	104670812	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	42323132	87323132	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	42323132	87323132	Rat
6893342	Cm78	Cardiac mass QTL 78	0.1	0.88	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	42876766	79813922	Rat
9589030	Epfw9	Epididymal fat weight QTL 9	19.24	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	10	44441699	89441699	Rat
7411614	Foco18	Food consumption QTL 18		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	44441699	89441699	Rat
8694173	Bw149	Body weight QTL 149	4.38	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	10	44441699	89441699	Rat
2300218	Hpcl2	Hepatic cholesterol level QTL 2			liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	45029650	95600334	Rat
631547	Bp87	Blood pressure QTL 87	4.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	47369470	92369470	Rat
2293705	Bmd25	Bone mineral density QTL 25	7.1	0.0001	femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	10	49444551	81709989	Rat
7207811	Bmd90	Bone mineral density QTL 90	5.2		femur size trait (VT:1000369)	femoral neck cross-sectional area (CMO:0001697)	10	49444551	81709989	Rat
2293652	Bmd22	Bone mineral density QTL 22	4.9	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	49444551	81709989	Rat
2293669	Bmd33	Bone mineral density QTL 33	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	10	49444551	81709989	Rat
2293679	Bmd30	Bone mineral density QTL 30	3.5	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	49444551	81709989	Rat
1549846	Scl47	Serum cholesterol level QTL 47	3.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	50574707	95574707	Rat
70364	Bp72	Blood pressure QTL 72			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	51121100	96121100	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	51770177	107211142	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	51770177	107211142	Rat
1359017	Hrtrt21	Heart rate QTL 21	2.4		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	10	51772940	96772940	Rat
631530	Tls3	T-lymphoma susceptibility QTL 3	0	0.0001	thymus integrity trait (VT:0010555)	percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)	10	51774612	95600334	Rat
631535	Cm51	Cardiac mass QTL 51	3		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	51786282	91669536	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	53797385	107211142	Rat
70164	Bw21	Body weight QTL 21	4.36	0.00005	body mass (VT:0001259)	body weight (CMO:0000012)	10	53797494	98952626	Rat
1354608	Cm33	Cardiac mass QTL 33	2.8		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	10	54809292	99809292	Rat
2312662	Slep8	Serum leptin concentration QTL 8		0.05	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	10	57134272	102134272	Rat
2312668	Scl65	Serum cholesterol level QTL 65		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	57134272	102134272	Rat
2312672	Insul15	Insulin level QTL 15		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	10	57134272	102134272	Rat
1549831	Bss6	Bone structure and strength QTL 6	4		lumbar vertebra strength trait (VT:0010574)	vertebra ultimate force (CMO:0001678)	10	57576521	102576521	Rat
2293698	Bss43	Bone structure and strength QTL 43	5.33	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	10	59209888	104209888	Rat
70363	Bp71	Blood pressure QTL 71		0.04	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	61345276	81714865	Rat
2306970	Anxrr22	Anxiety related response QTL 22	5.95		fear/anxiety-related behavior trait (VT:1000241)	number of periods of voluntary immobility (CMO:0001045)	10	61345276	98211570	Rat
6893336	Cm75	Cardiac mass QTL 75	0.1	0.87	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	61345276	99703528	Rat
1558643	Cm44	Cardiac mass QTL 44	4.8	0.0000368	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	61345276	99703528	Rat
61402	Niddm3	Non-insulin dependent diabetes mellitus QTL 3	4.58		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	61345413	82564856	Rat
2313103	Bss80	Bone structure and strength QTL 80	2	0.0001	tibia strength trait (VT:1000284)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	10	62057807	107057807	Rat
2313105	Bss79	Bone structure and strength QTL 79	1.8	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	10	62057807	107057807	Rat
61449	Ciaa2	CIA Autoantibody QTL 2	7.1		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	10	63221094	107211142	Rat
2298481	Eau9	Experimental allergic uveoretinitis QTL 9		0.0169	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	10	65927233	82565079	Rat
1357344	Bp249	Blood pressure QTL 249		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	66743655	98003205	Rat
631565	Hcuc4	Hepatic copper content QTL 4	4.15		hepatic copper amount (VT:0003065)	liver copper weight to liver dry weight ratio (CMO:0001512)	10	66941813	73452992	Rat
2317029	Aia19	Adjuvant induced arthritis QTL 19	2.98		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	66978955	107211142	Rat
2317039	Aia6	Adjuvant induced arthritis QTL 6	4.31		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	66978955	107211142	Rat
2289985	Bp305	Blood pressure QTL 305			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	67502108	73579767	Rat
10450498	Bp384	Blood pressure QTL 384		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	67750049	107211142	Rat
1642980	Bp300	Blood pressure QTL 300			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	68383129	107211142	Rat
61396	Bp9	Blood pressure QTL 9	4.8	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	68420376	107211142	Rat
2300172	Bmd57	Bone mineral density QTL 57	9.8	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	10	69738412	107211142	Rat
2293646	Bss25	Bone structure and strength QTL 25	10.96	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	10	69738412	107211142	Rat
2293663	Bss33	Bone structure and strength QTL 33	9.34	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	10	69738412	107211142	Rat
6893366	Bw106	Body weight QTL 106	0.3	0.47	body mass (VT:0001259)	body weight (CMO:0000012)	10	70199100	107211142	Rat

Genetic Models

This gene Bcas3 is modified in the following models/strains

SS-Bcas3^em4Mcwi

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	77
Count of miRNA genes:	60
Interacting mature miRNAs:	72
Transcripts:	ENSRNOT00000004657
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

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001173430	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086494	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086495	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086496	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086497	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086498	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086499	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086500	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086501	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086502	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC158637	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000095630 ⟹ ENSRNOP00000094777

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	70,214,098 - 70,670,694 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000096172 ⟹ ENSRNOP00000092518

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	70,214,098 - 70,673,080 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000098788 ⟹ ENSRNOP00000097649

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	70,214,098 - 70,673,080 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000099126 ⟹ ENSRNOP00000087925

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	70,214,098 - 70,673,080 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000104458 ⟹ ENSRNOP00000082383

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	70,214,098 - 70,673,080 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000110774 ⟹ ENSRNOP00000084198

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	70,214,098 - 70,373,150 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000119090 ⟹ ENSRNOP00000096642

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	70,214,098 - 70,673,066 (+)	Ensembl

RefSeq Acc Id:

NM_001173430 ⟹ NP_001166901

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,214,102 - 70,673,080 (+)	NCBI
Rnor_6.0	10	72,756,548 - 73,271,851 (+)	NCBI
Rnor_5.0	10	72,660,671 - 73,177,317 (+)	NCBI
Celera	10	69,140,091 - 69,598,397 (+)	NCBI

Sequence:

show sequence

CTGGAGCTGGAGAACAGCGTTTACCGGCGGAGCGGCCGTTTTAAATTATAGGAAGAAAGATTCA
GCAAAAGAGTGAACTGTTCTCACTTTCAGATGTTAGGCAGTTCAAGGCCAGCCTCAATTACAGG
GTCTTATGAATGAAACCATGGCTACAGATTCTCCTAGAAGACCCAGTCGCTGCACTGGTGGAGT
TGTGGTCCGCCCTCAGGCCGTCACGGAGCAGTCCTACATGGAAAGCGTTGTGACTTTTCTGCAG
GATGTCGTGCCACAGGCTTACAGTGGGACACCCCTAACGGAAGAAAAGGAGAAGATAGTTTGGG
TCCGGTTTGAGAATGCAGATCTGAATGATACATCACGGAATCTAGAATTTCATGAACTGCATAG
CACGGGAAATGAGCCTCCTCTGCTGGTTATGATCGGCTACAGTGACGGAATGCAGGTGTGGGGC
ATCCCTATCAGCGGGGAAGCCCAGGAGCTCTTCTCTGTTCGACATGGTCCAGTCCGAGCAGCTA
GAATCTTGCCTGCTCCACAGTTGGGTGCTCAAAAGTGTGATAACTTTGCTGAGAAAAGACCTCT
TCTTGGTGTTTGTAAGAGCATTGGATCTTCAGGCACGACGCCACCATACTGCTGTGTGGATCTG
TACTCACTTCGTACGGGGGAGATGGTCAAGTCCATTCAGTTTAAAACGCCCATTTATGATCTTC
ATTGTAATAAGCGGATCCTCGTCGTAGTCCTGCAGGAGAAAATCGCTGCCTTCGACAGCTGTAC
TTTCACAAAAAAATTTTTTGTCACAAGTTGTTATCCTTGTCCTGGGCCAAACATGAATCCTATT
GCTCTTGGGAGCCGTTGGCTTGCTTATGCAGAAAATAAGCTGATTCGCTGTCACCAGTCCCGTG
GCGGAGCCTGTGGAGACAACATTCAGTCTTACACTGCCACTGTCATTAGTGCTGCTAAAACACT
GAAAAGTGGCCTGACGATGGTTGGGAAAGTGGTGACTCAACTGACAGGCACACTGCCCTCAGGA
GTGACAGATGATGACATAGCCATACACTGCAACTCAAGACGGAGCCCCTTGGTGCCGGGCATCA
TCACAGTCATAGACACTGAGACAGTTGGAGAGGGCCAGGTGCTTGTGAGTGAGGATTCAGACAG
TGATGGCATTGTGGCCCACTTCCCTGCCCACGAGAAGCCAGTGTGCTGTATGGCTTTTAATACA
AGTGGAATGCTTTTAGTCACAACAGATACTCTTGGCCATGACTTTCATGTCTTCCAAATCCTGA
CTCATCCTTGGTCATCCTCACAGTGTGCTGTCCATCACCTGTATACACTTCACAGGGGAGAGAC
CGAGGCCAAAGTTCAGGACATCTGTTTCAGCCATGATTGTCGTTGGGTGGTGGTCAGTACCCTC
CGGGGTACTTCCCACGTTTTCCCCATCAACCCTTATGGTGGCCAGCCTTGTGTCCGCACACACA
TGTCACCGCGAGTAGTGAATCGCATGAGCCGTTTCCAGAAAAGTGCTGGGCTGGAAGAGATTGA
ACAAGAGCTGACATCTAAGCAAGGCGGCCGCTGTAGTCCTGTCCCAGGCCTGTCCAGCAGCCCT
TCCGGCTCCCCGCTGCATGGGAAGCTGAGTAGCCAAGACTCTTACAATAACTTTACCAACAACA
ACCCTGGCAACCCCCGGCTTTCTCCCCTCCCCAGCTTGATGGTAGTGACACCTCTTGCACAAAT
CAAGCAGCCAATGACATTGGGGACCATCACGAAACGAACAGGGCCTTATCTCTTTGGAGCGGGG
TGTTTTTCCATAAAAGCTCCATGCAAAGTTAAACCGCCTCCACAAATTTCTCCAAGCAAATCGA
TGGGCGGGGAGTTTTGCGTGGCCGCAGTGTTTGGGACCTCCAGGTCGTGGTTTGCAAACAATGC
TGGTCTGAAACGGGAAAAAGATCAGTCCAAACAAGTTGTGGTTGAATCTCTTTATATCATCAGT
TGCTACGGGACCTTAGTGGAGCACATGATTGAGCCTCGGCCTATCAGTACTGCTCCCAAGATAA
GTGACGACACACCACTGGAGATAATGACCTCACCTCGTGCCAGCTGGACACTTGTCAGAACGCC
TCAGTGGAACGAACTGCAGCCACCATTCAATGCGAATCACCCCCTGCTCCTTGCGGCAGAAGCA
GTGCAGTATTACCAGCTCCTGCTGGCCGGCTCACTTCCCCCTGGAAGTCCTGGCCCCATTACTC
GACATGGGTCCTATGACAGTTTAGCATCTGACCACAGCGGACAGGAAGATGAAGAATGGCTATC
CCAGGTTGAAATTGTGACACACACTGGACCCCACAGGCGCCTATGGATGGGTCCACAGTTCCAG
TTCAAAACCATCCACCCCTCAGGCCAGACCACGGTCATATCATCTAGTTCTTCTGTGTTACAGT
CTCATGGACCTAGTGACACACCACAGCCGCTCTTGGACTTTGATACAGATGATCTAGATCTTAA
CAGCCTCAGGATCCAGCCGGTCCGCTCTGACCCAGTCAGCATGCCAGGGTCATCCCGTCCAGTC
TCTGATCGAAGGGGAGTTTCCACCGTGATCGATGCTGCCTCAGGTACCTTCGACCGGAGCGTGA
CCCTGTTGGAGGTGTGTGGGAGCTGGCCTGAGGGCTTCGGGCTGCGACATATGTCCTCCATGGA
GCACACAGAAGAGGGCCTCCGGGAACGGCTTGCAGATGCCATGGCCGAGTCACCGAGCCGAGAC
GTTGTGGGATCTGGAACAGAACTTCAGCGAGAGGGAAGCATCGAGACTCTGAGTAACAGCTCAG
GCTCCACCAGTGGCAGCATCCCAAGAAACTTTGATGGCTACCGATCTCCGCTCCCGACCAACGA
GAGCCAGCCGCTCAGCCTCTTCCCCACTGGCTTCCCATAGACACCAGCCACCTGCTTCTGACTG
GCTGGCCTGCTCACCCCCTAGAGGGACTGACAGGGGTGGAGAGAAATGCCCCTATCTCCCTACA
CCCCCACCCCCATAAACCTCTGGTCCCACCCTTTTCAGTCTCCTCAACCCCACCTTCCCGGAGC
TTAGTGACAGCAGCCGCTCATCCCTAACTGGACTGAAGACACCTTCGGAACACCTCAGTACACC
CTGACTTCTCCCACTCCTGTCAGTGGGGGCTGTGGCCTGAAGAGACTGCAGAACTCAGTCCCTT
CTCTCTTTGCACATAATGTCCTGCATTGGATCCGCTTTTGTATTTTCTAACTACCCACAGGGGA
CTGGAACAGTGGCCAGATCTTAGGGCCTTGGGTAGGGAAGAGTTGAAAGGTCCAGCCAGGCATT
TTGGTGGACATCAGCCCTAGCCCAGTTGAGGCTGTGATGCACACTGCCCCCAGGTATCAGTTCT
TTCTAAAAAAGGGGTTAACTGAGGCCTAGAGTGATAGGGAAAAAGGAAAGACCTCCCCTTGCCC
CTGCTTCCCTGTTGGCTCATGGGGAGATTTGTCTGTCTTATCTTTAAACCCTTGTACCCTGGTC
CTGTGCTGTTCAGTGAAGGAAACTGAAGTTACTGAGGCCGTGTCAGAAGTGCACGTCTTGTCCA
ATAAATCTTGCTGCAATTGGTGTTCA

hide sequence

RefSeq Acc Id:

XM_039086494 ⟹ XP_038942422

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,213,714 - 70,673,080 (+)	NCBI

RefSeq Acc Id:

XM_039086495 ⟹ XP_038942423

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,213,713 - 70,673,080 (+)	NCBI

RefSeq Acc Id:

XM_039086496 ⟹ XP_038942424

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,213,716 - 70,673,080 (+)	NCBI

RefSeq Acc Id:

XM_039086497 ⟹ XP_038942425

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,213,716 - 70,673,080 (+)	NCBI

RefSeq Acc Id:

XM_039086498 ⟹ XP_038942426

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,213,717 - 70,673,080 (+)	NCBI

RefSeq Acc Id:

XM_039086499 ⟹ XP_038942427

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,213,713 - 70,673,080 (+)	NCBI

RefSeq Acc Id:

XM_039086500 ⟹ XP_038942428

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,213,720 - 70,673,080 (+)	NCBI

RefSeq Acc Id:

XM_039086501 ⟹ XP_038942429

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,213,710 - 70,473,416 (+)	NCBI

RefSeq Acc Id:

XM_039086502 ⟹ XP_038942430

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	70,213,714 - 70,524,637 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001166901	(Get FASTA)	NCBI Sequence Viewer
	XP_038942422	(Get FASTA)	NCBI Sequence Viewer
	XP_038942423	(Get FASTA)	NCBI Sequence Viewer
	XP_038942424	(Get FASTA)	NCBI Sequence Viewer
	XP_038942425	(Get FASTA)	NCBI Sequence Viewer
	XP_038942426	(Get FASTA)	NCBI Sequence Viewer
	XP_038942427	(Get FASTA)	NCBI Sequence Viewer
	XP_038942428	(Get FASTA)	NCBI Sequence Viewer
	XP_038942429	(Get FASTA)	NCBI Sequence Viewer
	XP_038942430	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI58638	(Get FASTA)	NCBI Sequence Viewer
	EDM05545	(Get FASTA)	NCBI Sequence Viewer
	EDM05546	(Get FASTA)	NCBI Sequence Viewer
	EDM05547	(Get FASTA)	NCBI Sequence Viewer
	EDM05548	(Get FASTA)	NCBI Sequence Viewer
	EDM05549	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001166901 ⟸ NM_001173430

- Sequence:

show sequence

MNETMATDSPRRPSRCTGGVVVRPQAVTEQSYMESVVTFLQDVVPQAYSGTPLTEEKEKIVWVR
FENADLNDTSRNLEFHELHSTGNEPPLLVMIGYSDGMQVWGIPISGEAQELFSVRHGPVRAARI
LPAPQLGAQKCDNFAEKRPLLGVCKSIGSSGTTPPYCCVDLYSLRTGEMVKSIQFKTPIYDLHC
NKRILVVVLQEKIAAFDSCTFTKKFFVTSCYPCPGPNMNPIALGSRWLAYAENKLIRCHQSRGG
ACGDNIQSYTATVISAAKTLKSGLTMVGKVVTQLTGTLPSGVTDDDIAIHCNSRRSPLVPGIIT
VIDTETVGEGQVLVSEDSDSDGIVAHFPAHEKPVCCMAFNTSGMLLVTTDTLGHDFHVFQILTH
PWSSSQCAVHHLYTLHRGETEAKVQDICFSHDCRWVVVSTLRGTSHVFPINPYGGQPCVRTHMS
PRVVNRMSRFQKSAGLEEIEQELTSKQGGRCSPVPGLSSSPSGSPLHGKLSSQDSYNNFTNNNP
GNPRLSPLPSLMVVTPLAQIKQPMTLGTITKRTGPYLFGAGCFSIKAPCKVKPPPQISPSKSMG
GEFCVAAVFGTSRSWFANNAGLKREKDQSKQVVVESLYIISCYGTLVEHMIEPRPISTAPKISD
DTPLEIMTSPRASWTLVRTPQWNELQPPFNANHPLLLAAEAVQYYQLLLAGSLPPGSPGPITRH
GSYDSLASDHSGQEDEEWLSQVEIVTHTGPHRRLWMGPQFQFKTIHPSGQTTVISSSSSVLQSH
GPSDTPQPLLDFDTDDLDLNSLRIQPVRSDPVSMPGSSRPVSDRRGVSTVIDAASGTFDRSVTL
LEVCGSWPEGFGLRHMSSMEHTEEGLRERLADAMAESPSRDVVGSGTELQREGSIETLSNSSGS
TSGSIPRNFDGYRSPLPTNESQPLSLFPTGFP

hide sequence

RefSeq Acc Id:	XP_038942429 ⟸ XM_039086501
- Peptide Label:	isoform X8

RefSeq Acc Id:	XP_038942423 ⟸ XM_039086495
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038942427 ⟸ XM_039086499
- Peptide Label:	isoform X6

RefSeq Acc Id:	XP_038942422 ⟸ XM_039086494
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038942430 ⟸ XM_039086502
- Peptide Label:	isoform X9

RefSeq Acc Id:	XP_038942425 ⟸ XM_039086497
- Peptide Label:	isoform X4

RefSeq Acc Id:	XP_038942424 ⟸ XM_039086496
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038942426 ⟸ XM_039086498
- Peptide Label:	isoform X5

RefSeq Acc Id:	XP_038942428 ⟸ XM_039086500
- Peptide Label:	isoform X7

RefSeq Acc Id:

ENSRNOP00000096642 ⟸ ENSRNOT00000119090

RefSeq Acc Id:

ENSRNOP00000092518 ⟸ ENSRNOT00000096172

RefSeq Acc Id:

ENSRNOP00000084198 ⟸ ENSRNOT00000110774

RefSeq Acc Id:

ENSRNOP00000097649 ⟸ ENSRNOT00000098788

RefSeq Acc Id:

ENSRNOP00000094777 ⟸ ENSRNOT00000095630

RefSeq Acc Id:

ENSRNOP00000087925 ⟸ ENSRNOT00000099126

RefSeq Acc Id:

ENSRNOP00000082383 ⟸ ENSRNOT00000104458

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:1560788	AgrOrtholog
Ensembl Genes	ENSRNOG00000066893	Ensembl
Gene3D-CATH	2.130.10.10	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7456859	IMAGE-MGC_LOAD
InterPro	WD40/YVTN_repeat-like_dom_sf	UniProtKB/TrEMBL
	WD40_repeat_dom_sf	UniProtKB/TrEMBL
MGC_CLONE	MGC:187553	IMAGE-MGC_LOAD
NCBI Gene	363662	ENTREZGENE
PhenoGen	Bcas3	PhenoGen
Superfamily-SCOP	SSF50978	UniProtKB/TrEMBL
UniProt	B0BN06_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2009-06-15	Bcas3	breast carcinoma amplified sequence 3	Bcas3_predicted	breast carcinoma amplified sequence 3 (predicted)	Data Merged	1643240	APPROVED
2008-02-28	Bcas3	breast carcinoma amplified sequence 3	RGD1560788_predicted	similar to Breast carcinoma amplified sequence 3 homolog (K20D4) (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1560788_predicted	similar to Breast carcinoma amplified sequence 3 homolog (K20D4) (predicted)	LOC363662	similar to Breast carcinoma amplified sequence 3 homolog (K20D4)	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC363662	similar to Breast carcinoma amplified sequence 3 homolog (K20D4)			Symbol and Name status set to provisional	70820	PROVISIONAL
2005-01-12	Bcas3_predicted	breast carcinoma amplified sequence 3 (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)

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Imported Disease Annotations - ClinVar