Mmut (methylmalonyl-CoA mutase) - Rat Genome Database

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Gene: Mmut (methylmalonyl-CoA mutase) Rattus norvegicus

Analyze

Symbol:

Mmut

Name:

methylmalonyl-CoA mutase

RGD ID:

1587662

Description:

Predicted to enable several functions, including cobalamin binding activity; methylmalonyl-CoA mutase activity; and protein homodimerization activity. Predicted to be involved in homocysteine metabolic process and positive regulation of GTPase activity. Predicted to act upstream of or within post-embryonic development. Predicted to be located in mitochondrial matrix. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in methylmalonic aciduria due to methylmalonyl-CoA mutase deficiency. Orthologous to human MMUT (methylmalonyl-CoA mutase); PARTICIPATES IN 3-hydroxy-3-methylglutaryl-CoA lyase deficiency pathway; 3-hydroxyisobutyric aciduria pathway; 3-methylcrotonyl CoA carboxylase 1 deficiency pathway; INTERACTS WITH (+)-schisandrin B; 4,4'-diaminodiphenylmethane; 5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole.

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

LOC301276; LOC688517; methylmalonyl CoA mutase; methylmalonyl-CoA mutase, mitochondrial; methylmalonyl-Coenzyme A mutase; Mut; rCG43751-like; similar to Methylmalonyl-CoA mutase, mitochondrial precursor (MCM) (Methylmalonyl-CoA isomerase)

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):	MMUT (methylmalonyl-CoA mutase)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther
Mus musculus (house mouse):	Mmut (methylmalonyl-Coenzyme A mutase)	HGNC	EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Mmut (methylmalonyl-CoA mutase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	MMUT (methylmalonyl-CoA mutase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	MMUT (methylmalonyl-CoA mutase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Mmut (methylmalonyl-CoA mutase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	MMUT (methylmalonyl-CoA mutase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	MMUT (methylmalonyl-CoA mutase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Mmut (methylmalonyl-CoA mutase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	MMUT (methylmalonyl-CoA mutase)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Mmut (methylmalonyl-Coenzyme A mutase)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	mut (methylmalonyl CoA mutase)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	mmcm-1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

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	9	19,928,720 - 19,956,985 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	9	19,928,727 - 19,957,046 (-)	Ensembl
Rnor_6.0	9	23,323,934 - 23,352,144 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	23,323,936 - 23,352,668 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	9	22,182,975 - 22,211,162 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	16,065,495 - 16,093,956 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	9	17,606,384 - 17,634,555 (-)	NCBI		Celera
Cytogenetic Map	9	q13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

inherited metabolic disorder (ISO)

methylmalonic acidemia (ISO)

methylmalonic aciduria due to methylmalonyl-CoA mutase deficiency (ISO)

obesity (ISO)

peroxisome biogenesis disorder 8A (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-dexrazoxane (ISO)

(+)-schisandrin B (EXP)

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

4,4'-diaminodiphenylmethane (EXP)

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (EXP)

6-propyl-2-thiouracil (EXP)

adefovir (ISO)

aflatoxin B1 (ISO)

amiodarone (EXP)

aristolochic acid (ISO)

atazanavir sulfate (ISO)

benzbromarone (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

Brodifacoum (EXP)

cadmium atom (ISO)

calcitriol (ISO)

carbon nanotube (ISO)

chenodeoxycholic acid (ISO)

cisplatin (ISO)

clofibrate (EXP)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

deoxycholic acid (ISO)

deoxynivalenol (ISO)

dextran sulfate (ISO)

dicrotophos (ISO)

doxorubicin (ISO)

elemental selenium (ISO)

endosulfan (EXP)

ethyl methanesulfonate (ISO)

furan (EXP)

geneticin (ISO)

gentamycin (ISO)

glafenine (EXP)

glycochenodeoxycholic acid (ISO)

glycocholic acid (ISO)

glycodeoxycholic acid (ISO)

hydrogen peroxide (ISO)

ivermectin (ISO)

L-ethionine (EXP)

methapyrilene (EXP)

methyl methanesulfonate (ISO)

nefazodone (ISO)

O-methyleugenol (ISO)

omeprazole (EXP)

paracetamol (ISO)

perfluorononanoic acid (ISO)

phlorizin (ISO)

pirinixic acid (EXP,ISO)

propiconazole (ISO)

rac-lactic acid (ISO)

resveratrol (ISO)

selenium atom (ISO)

silicon dioxide (ISO)

tartrazine (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

valproic acid (ISO)

vancomycin (ISO)

zidovudine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

homocysteine metabolic process (ISO)

positive regulation of GTPase activity (ISO)

post-embryonic development (ISO)

Cellular Component

cytoplasm (ISO)

mitochondrial matrix (ISO)

mitochondrion (IBA,ISO)

Molecular Function

cobalamin binding (ISO)

GTPase activity (ISO)

identical protein binding (ISO)

metal ion binding (IEA)

methylmalonyl-CoA mutase activity (IBA,ISO)

modified amino acid binding (ISO)

protein binding (ISO)

protein homodimerization activity (ISO)

tetrapyrrole binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

3-hydroxy-3-methylglutaryl-CoA lyase deficiency pathway (ISO)

3-hydroxyisobutyric aciduria pathway (ISO)

3-methylcrotonyl CoA carboxylase 1 deficiency pathway (ISO)

3-methylglutaconic aciduria type 1 pathway (ISO)

3-methylglutaconic aciduria type 3 pathway (ISO)

glyoxylate and dicarboxylate metabolic pathway (IEA)

isobutyryl-CoA dehydrogenase deficiency pathway (ISO)

isovaleric acidemia pathway (ISO)

malonic aciduria pathway (ISO)

maple syrup urine disease pathway (ISO)

methylmalonate semialdehyde dehydrogenase deficiency pathway (ISO)

methylmalonic acidemia pathway (ISO)

methylmalonic aciduria, cobalamin-related pathway (ISO)

propanoate metabolic pathway (IEA,ISO)

propionic acidemia pathway (ISO)

valine, leucine and isoleucine degradation pathway (IEA,ISO)

References

References - curated


1.	Chandler RJ and Venditti CP, Mol Ther. 2010 Jan;18(1):11-6. doi: 10.1038/mt.2009.247. Epub 2009 Oct 27.
2.	Chandler RJ, etal., BMC Med Genet. 2007 Oct 15;8:64.
3.	Forny P, etal., Hum Mutat. 2016 Aug;37(8):745-54. doi: 10.1002/humu.23013. Epub 2016 May 23.
4.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5.	OMIM Disease Annotation Pipeline
6.	Pipeline to import KEGG annotations from KEGG into RGD
7.	Pipeline to import SMPDB annotations from SMPDB into RGD
8.	RGD automated data pipeline
9.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:14555645	PMID:14651853	PMID:18614015	PMID:19699272	PMID:20031578	PMID:20876572	PMID:28101778	PMID:28497574

Genomics

Comparative Map Data

Mmut
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	9	19,928,720 - 19,956,985 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	9	19,928,727 - 19,957,046 (-)	Ensembl
Rnor_6.0	9	23,323,934 - 23,352,144 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	23,323,936 - 23,352,668 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	9	22,182,975 - 22,211,162 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	16,065,495 - 16,093,956 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	9	17,606,384 - 17,634,555 (-)	NCBI		Celera
Cytogenetic Map	9	q13	NCBI

MMUT
(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	49,430,360 - 49,463,253 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	49,430,360 - 49,463,298 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	6	49,398,073 - 49,430,966 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	49,506,950 - 49,538,990 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	6	49,506,956 - 49,538,811	NCBI
Celera	6	50,954,278 - 50,987,247 (-)	NCBI
Cytogenetic Map	6	p12.3	NCBI
HuRef	6	49,126,994 - 49,159,962 (-)	NCBI		HuRef
CHM1_1	6	49,401,109 - 49,434,080 (-)	NCBI		CHM1_1

Mmut
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	41,245,576 - 41,272,880 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	17	41,245,576 - 41,272,879 (+)	Ensembl
GRCm38	17	40,934,685 - 40,961,990 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	40,934,685 - 40,961,988 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	41,071,634 - 41,098,938 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	17	40,398,258 - 40,425,133 (+)	NCBI			mm8
Celera	17	44,347,903 - 44,375,209 (+)	NCBI		Celera
Cytogenetic Map	17	B2	NCBI
cM Map	17	19.55	NCBI

Mmut
(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_004955411	8,363,142 - 8,399,216 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955411	8,363,142 - 8,397,839 (+)	NCBI	ChiLan1.0	ChiLan1.0

MMUT
(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	50,269,644 - 50,302,593 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	50,269,644 - 50,302,593 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	49,007,500 - 49,040,470 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

MMUT
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	12	17,306,074 - 17,339,921 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	17,307,522 - 17,339,897 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	17,207,742 - 17,239,948 (-)	NCBI
ROS_Cfam_1.0	12	17,803,522 - 17,836,150 (-)	NCBI
UMICH_Zoey_3.1	12	17,323,580 - 17,355,905 (-)	NCBI
UNSW_CanFamBas_1.0	12	17,428,613 - 17,461,241 (-)	NCBI
UU_Cfam_GSD_1.0	12	17,558,439 - 17,590,821 (-)	NCBI

Mmut
(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	52,718,554 - 52,751,973 (-)	NCBI
SpeTri2.0	NW_004936476	11,208,251 - 11,241,648 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

MMUT
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	43,597,292 - 43,624,609 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	43,597,313 - 43,624,603 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	50,107,559 - 50,128,711 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

MMUT
(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	17	22,922,262 - 22,957,742 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	17	22,922,307 - 22,957,879 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666044	49,420,412 - 49,455,585 (-)	NCBI	Vero_WHO_p1.0

Mmut
(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_004624799	14,404,873 - 14,433,803 (-)	NCBI	HetGla_female_1.0		hetGla2

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
70226	Eae4	Experimental allergic encephalomyelitis QTL 4			nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	9	1	25661317	Rat
9589055	Scfw5	Subcutaneous fat weight QTL 5	5.55	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	9	1	37999212	Rat
7411592	Foco8	Food consumption QTL 8	7.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	9	1	37999212	Rat
9589158	Gluco65	Glucose level QTL 65	6.82	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	9	1	37999212	Rat
1300124	Cm4	Cardiac mass QTL 4	3.55		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	9	1	40594091	Rat
1298088	Edpm11	Estrogen-dependent pituitary mass QTL 11	2.5		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	9	1	43718459	Rat
1641911	Alcrsp13	Alcohol response QTL 13			response to alcohol trait (VT:0010489)	brain neurotensin receptor 1 density (CMO:0002068)	9	1	43718459	Rat
10054125	Srcrt7	Stress Responsive Cort QTL 7	3.33	0.0011	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	9	1	87073594	Rat
1331757	Cdexp1	CD45RC expression in CD8 T cells QTL 1	4.3		CD8-positive T cell quantity (VT:0008077)	blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)	9	1024537	67509080	Rat
1354650	Despr5	Despair related QTL 5	4.01	0.0017	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	9	1254084	46254084	Rat
2303559	Gluco54	Glucose level QTL 54	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	9	1254084	46254084	Rat
61425	Cia15	Collagen induced arthritis QTL 15	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	9	5109826	42921101	Rat
631211	Bw4	Body weight QTL4	5.31		retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	9	5109826	50109826	Rat
11353947	Bp392	Blood pressure QTL 392			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	7283252	52283252	Rat
61450	Ciaa3	CIA Autoantibody QTL 3	6.5		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	9	7954720	22071169	Rat
9589133	Insul26	Insulin level QTL 26	17.96	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	9	8952560	53952560	Rat
7411609	Foco16	Food consumption QTL 16	25.6	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	9	8952560	53952560	Rat
1600365	Mcs20	Mammary carcinoma susceptibility QTL 20	3		mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	9	13533770	42791750	Rat
724543	Cm20	Cardiac mass QTL 20	3.9		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	9	16961398	40594091	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	9
Count of miRNA genes:	9
Interacting mature miRNAs:	9
Transcripts:	ENSRNOT00000075279
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	43	57	41	19	41	8	10	74	35	35	11	8
Low								1			6
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_001067239	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003754495	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039084505	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039084506	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473987	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000213	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000075279 ⟹ ENSRNOP00000064363

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	9	19,928,727 - 19,957,046 (-)	Ensembl
Rnor_6.0 Ensembl	9	23,323,936 - 23,352,668 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000097764 ⟹ ENSRNOP00000083975

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	9	19,928,727 - 19,955,108 (-)	Ensembl

RefSeq Acc Id:

XM_001067239 ⟹ XP_001067239

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	19,928,720 - 19,956,985 (-)	NCBI
Rnor_6.0	9	23,323,934 - 23,352,144 (-)	NCBI
Rnor_5.0	9	22,182,975 - 22,211,162 (-)	NCBI
RGSC_v3.4	9	16,065,495 - 16,093,956 (-)	RGD

Sequence:

show sequence

CGGAGTTGGCTACGCCCCCTGAGTTGACTGGCTCCGGAGCTCCAGCGGCGAGCGCCAGTGGCTC
TAGGGCATTGGGGTTCGATCTGCGCGGTCGACCCCCAACACTGTTCGTTCTCATTTTCGTTTGG
GAGTATTCATGCTTCACCATGTTGAGAGCTAAGAATCAGCTTTTTTTGTTATCGCCCCATTACC
TGAAGCAGCTAAAAGATGCATCATCCTACAGATGGAAACGGCTCCTACATCAGCAGCAACCCCT
TCACCCAGAATGGGCTGTCCTGGCCAAAAAACAGCTGAAAGGCAAAAACCCAGAGGATCTAATA
TGGCACACCCCAGAAGGGATCTCTATAAAGCCCTTATATTCCAGGGCTGATACTATGGACTTAC
CTGAAGAACTGCCGGGAGTGAAGCCATTCACACGTGGACCATATCCCACCATGTATACCTATAG
ACCCTGGACCATCCGTCAGTATGCGGGCTTTAGTACTGTGGAGGAAAGCAATAAATTCTATAAG
GACAATATTAAGGCTGGTCAGCAGGGGTTGTCTGTTGCCTTCGACCTGGCAACCCATCGTGGTT
ATGATTCAGACAATCCCCGAGTTCGTGGCGATGTCGGAATGGCGGGAGTTGCTATTGACACCGT
AGAAGACACCAAAATCCTATTTGATGGTATTCCTTTAGAAAAAATGTCTGTTTCCATGACCATG
AATGGAGCCGTCATCCCAGTCCTGGCAACATTTATAGTAACTGGGGAGGAGCAAGGTGTACCGA
AGGAGAAGCTCACCGGCACAATTCAGAATGACATCCTAAAGGAGTTCATGGTCAGAAATACTTA
TATTTTCCCCCCAGAGCCATCCATGAAGATTATCGCTGACATTTTCCAATACACAGCACAGCAC
ATGCCAAAATTTAATTCCATTTCGATTAGCGGGTACCACATGCAGGAAGCAGGAGCTGATGCCA
TTTTAGAACTGGCCTATACCATCGCGGATGGGTTGGAGTACTGCAGAACTGGACTCCAGGCTGG
ACTCACAATTGATGAATTTGCGCCAAGGTTGTCTTTCTTTTGGGGAATTGGAATGAACTTCTAC
ATGGAAATAGCGAAGATGCGAGCTGGGAGAAGACTGTGGGCTCACTTAATAGAAAAAATGTTCC
AGCCTAAAAACTCCAAATCTCTCCTTCTAAGAGCACATTGTCAGACATCAGGGTGGTCCCTTAC
TGAGCAGGATCCTTACAATAACATTGTCCGCACTGCTATCGAAGCCATGGCAGCTGTGTTTGGA
GGAACACAGTCCTTGCATACGAACTCTTTTGATGAAGCTCTAGGCTTGCCCACTGTGAAAAGTG
CTCGGATTGCCCGGAACACACAAATCATCATTCAGGAAGAGTCTGGGATCCCAAAAGTGGCTGA
TCCTTGGGGAGGATCATACATGATGGAGTCTCTCACAAATGATGTTTATGAAGCTGCTCTGAAG
TTGATATATGAAGTTGAAGAAATGGGTGGAATGGCCAAAGCTGTAGCTGAAGGAATCCCTAAAC
TTCGCATTGAAGAATGTGCTGCCCGAAGACAAGCTAGAATAGATTCTGGTTCTGAAGTAATTGT
TGGAGTAAATAAGTATCAGTTGGAAAAAGAAGACTCTGTGGAGGTCCTGGCCATTGATAATACT
TCAGTGCGTAAGAAGCAGATTGAAAAACTTAAGAAGATCAAATCCAGCCGGGATCAGGCTTTGG
CTGAGCGGTCCCTCAATGCACTTACCCAGTGTGCTGCCAGTGGAGATGGCAATATTCTAGCTCT
TGCAGTGGATGCAGCTCGTGCAAGATGTACAGTTGGAGAAATCACAGATGCTTTGAAGAAAGTA
TTTGGTGAGCATAAAGCTAATGATCGTATGGTGAGTGGAGCATATCGGCAGGAGTTTGGAGAAA
GCAAAGAGATCACATCTGCCATCAAGAGAGTTAATAAATTCATGGAACGTGAAGGTCGCAGACC
TCGTCTTCTTGTGGCAAAAATGGGACAAGATGGCCATGACAGAGGAGCCAAGGTCATTGCTACA
GGCTTTGCTGATCTTGGTTTTGATGTGGACATAGGCCCTCTTTTTCAGACTCCCCGTGAAGTGG
CGCAGCAAGCCGTGGATGCAGATGTCCATGCTGTGGGTGTCAGCACACTCGCTGCTGGTCATAA
AACCCTCGTTCCTGAGCTCATCAAAGAACTTAGTGCCCTGGGACGGCCAGATATCCTTGTCATG
TGTGGGGGTGTGATCCCACCACAGGATTATGAATTTTTATATGAAGTTGGTGTTTCCAACGTAT
TTGGTCCTGGAACCCGGATTCCCAAGGCTGCCGTTCAAGTGCTTGATGATATTGAGAAATCTTT
GGCAGAGAAGCAGCAATCTGTATAACATCTGGACCTTTAGTTATGACCAAAGAAAGTAGTAGTC
AGACTATGTCTACAGGTAATCCCAACATCTGTTAGTATGCTTGCTTTAGAAACCGTATATTAAA
GGACTCTGATTATAAATGTGCAATCATGCCAACACACGTGTTTAAAGAATCTGAGTTATAAAAA
AATCTCTGAAAATCATCTAAACCAAATATTTTTCAAGTACATTATTTTAGAAATTAAAATGGTA
TACTGCTTTGAAATAGCTAATAATACAATTCTTATAAATAATTAAACTTTTGTTTTGTCCTTTG
AGATGGGGTCTCACTATGTAGCTCTGGCTGTCTTGGAGCTCACTCTCGCCAGTCTGGCCTCAAA
CTCACAGAGACCCACCTGCCTCTGCATCCCTAGTACAGGGTTAAAAGGTATGTGCCACATGCCC
AGCCAATAATTAAACTTTACATTTAAAATTTTGGCTGATTCTTTCTTCAATTTAAGTGTTGATT
TGAGTACTAGAAACTCAAGTTTCTGTGTTAATATATTAATAAAATAATAACATTTATCTTATAA
GAGATAGTGGATGGTATTTATGGATGGCAATAGACTGGGGTTATGATCCTCAGCCAGATCTACT
ATTGCTTCAATAAAAGTAGTATTTATCATCTCCTGTACAATGGAGTAGAGGGCATGGCAGTTAT
GCCTTCCAGGATTGCTTCAACTCCTTCTCAGCATGGGAGTGATATTGCCAATGTCAGAGCTGAC
CCCAAATTCTGGAAAAGATGTTTGTGAACACTTCCCTAAATGAAGTGCTGATGGACATAGGAAT
TTGCTATAATGGCAATCTAAGTCTATTACACAAAATAAATGAATTTTCAGATCTAGAAACATGC
TTATCTGTATAGATTTTTTTATGAAAGATGTTACAAAAATAAAGATGGTCTGAAGAACCCTTGT
AGTGTGATGTTAAGAAATGTACTCATTGAAGGAAGAGAATCACTCTGTGTTAACATAAGGTATT
CAATGAAGGTAAGCTGAGCAAAAGGATTCTTTGGTAATTTTCTACATTGTAGATCAGATAATAG
TGTGGAGGAAAAATCATATATTGTTGTAGAATTAATACACTGTACTATAATATTGTTTTCAGAA
CATGATTCTTGGGGAGGGTATCATGATTATTGTTTCCATTTTAAAGAAAAGCAGTTTGACTTCT
AGGTCAGCAATGTATTCACTTTGTCATGTACTCACTTATGTACTGTGTATAAAGAAATACATAT
TCAATAAATGTGATGTTCCTATCATGTGTCATCCAGCACTATGTGCTGGTGACATGGCATATAC

hide sequence

RefSeq Acc Id:

XM_039084505 ⟹ XP_038940433

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	19,929,110 - 19,956,804 (-)	NCBI

RefSeq Acc Id:

XM_039084506 ⟹ XP_038940434

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	19,935,876 - 19,956,985 (-)	NCBI

Protein Sequences


Protein RefSeqs	XP_001067239	(Get FASTA)	NCBI Sequence Viewer
	XP_038940433	(Get FASTA)	NCBI Sequence Viewer
	XP_038940434	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM18677	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

XP_001067239 ⟸ XM_001067239

- Peptide Label:

isoform X1

- Sequence:

show sequence

MLRAKNQLFLLSPHYLKQLKDASSYRWKRLLHQQQPLHPEWAVLAKKQLKGKNPEDLIWHTPEG
ISIKPLYSRADTMDLPEELPGVKPFTRGPYPTMYTYRPWTIRQYAGFSTVEESNKFYKDNIKAG
QQGLSVAFDLATHRGYDSDNPRVRGDVGMAGVAIDTVEDTKILFDGIPLEKMSVSMTMNGAVIP
VLATFIVTGEEQGVPKEKLTGTIQNDILKEFMVRNTYIFPPEPSMKIIADIFQYTAQHMPKFNS
ISISGYHMQEAGADAILELAYTIADGLEYCRTGLQAGLTIDEFAPRLSFFWGIGMNFYMEIAKM
RAGRRLWAHLIEKMFQPKNSKSLLLRAHCQTSGWSLTEQDPYNNIVRTAIEAMAAVFGGTQSLH
TNSFDEALGLPTVKSARIARNTQIIIQEESGIPKVADPWGGSYMMESLTNDVYEAALKLIYEVE
EMGGMAKAVAEGIPKLRIEECAARRQARIDSGSEVIVGVNKYQLEKEDSVEVLAIDNTSVRKKQ
IEKLKKIKSSRDQALAERSLNALTQCAASGDGNILALAVDAARARCTVGEITDALKKVFGEHKA
NDRMVSGAYRQEFGESKEITSAIKRVNKFMEREGRRPRLLVAKMGQDGHDRGAKVIATGFADLG
FDVDIGPLFQTPREVAQQAVDADVHAVGVSTLAAGHKTLVPELIKELSALGRPDILVMCGGVIP
PQDYEFLYEVGVSNVFGPGTRIPKAAVQVLDDIEKSLAEKQQSV

hide sequence

RefSeq Acc Id:

ENSRNOP00000064363 ⟸ ENSRNOT00000075279

RefSeq Acc Id:	XP_038940433 ⟸ XM_039084505
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038940434 ⟸ XM_039084506
- Peptide Label:	isoform X2

RefSeq Acc Id:

ENSRNOP00000083975 ⟸ ENSRNOT00000097764

Protein Domains

B12-binding

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:1587662	AgrOrtholog
Ensembl Genes	ENSRNOG00000050843	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000064363	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000075279	UniProtKB/TrEMBL
InterPro	Acid_CoA_mut_C	UniProtKB/TrEMBL
	Cbl-dep_enz_cat	UniProtKB/TrEMBL
	Cobalamin-bd	UniProtKB/TrEMBL
	Cobalamin-bd_sf	UniProtKB/TrEMBL
	MeMalonylCoA_mutase_a/b_cat	UniProtKB/TrEMBL
	MMCoA_mutase_a_cat	UniProtKB/TrEMBL
NCBI Gene	688517	ENTREZGENE
Pfam	B12-binding	UniProtKB/TrEMBL
	MM_CoA_mutase	UniProtKB/TrEMBL
PhenoGen	Mmut	PhenoGen
PROSITE	B12_BINDING	UniProtKB/TrEMBL
	METMALONYL_COA_MUTASE	UniProtKB/TrEMBL
Superfamily-SCOP	Cbl-bd	UniProtKB/TrEMBL
	Cbl-dep_enz_cat	UniProtKB/TrEMBL
TIGRFAMs	acid_CoA_mut_C	UniProtKB/TrEMBL
	acid_CoA_mut_N	UniProtKB/TrEMBL
UniProt	D3ZKG1_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2018-11-02	Mmut	methylmalonyl-CoA mutase	Mut	methylmalonyl CoA mutase	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-05-24	Mut	methylmalonyl CoA mutase	LOC100361295	methylmalonyl-Coenzyme A mutase	Data Merged	1643240	APPROVED
2011-08-02	Mut	methylmalonyl CoA mutase	Mut	methylmalonyl-Coenzyme A mutase	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2010-05-05	LOC100361295	methylmalonyl-Coenzyme A mutase			Symbol and Name status set to provisional	70820	PROVISIONAL
2008-03-05	Mut	methylmalonyl-Coenzyme A mutase	LOC688517	similar to Methylmalonyl-CoA mutase, mitochondrial precursor (MCM) (Methylmalonyl-CoA isomerase)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-01-09	LOC688517	similar to Methylmalonyl-CoA mutase, mitochondrial precursor (MCM) (Methylmalonyl-CoA isomerase)	RGD1564912_predicted	similar to Mut protein (predicted)	Data Merged	1643240	APPROVED
2006-11-19	LOC688517	similar to Methylmalonyl-CoA mutase, mitochondrial precursor (MCM) (Methylmalonyl-CoA isomerase)			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-03-07	RGD1564912_predicted	similar to Mut protein (predicted)	LOC301276	similar to Mut protein	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC301276	similar to Mut protein			Symbol and Name status set to provisional	70820	PROVISIONAL

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

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

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

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

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Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)