Cdo1 (cysteine dioxygenase type 1)

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| FTP Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References FTP Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Cdo1 (cysteine dioxygenase type 1) Rattus norvegicus

Analyze

Symbol:

Cdo1

Name:

cysteine dioxygenase type 1

RGD ID:

69262

Description:

Exhibits cysteine dioxygenase activity and ferrous iron binding activity. Involved in several processes, including L-cysteine catabolic process; lactation; and response to glucagon. Predicted to localize to cytosol. Biomarker of hypertension. Orthologous to human CDO1 (cysteine dioxygenase type 1); PARTICIPATES IN cysteine metabolic pathway; mercaptolactate-cysteine disulfiduria pathway; ocular nonnephropathic cystinosis pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

CDO; CDO-I; cysteine dioxygenase; cysteine dioxygenase 1, cytosolic; cysteine dioxygenase, type I; cytosolic cysteine dioxygenase 1

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):	CDO1 (cysteine dioxygenase type 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Cdo1 (cysteine dioxygenase 1, cytosolic)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Cdo1 (cysteine dioxygenase type 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CDO1 (cysteine dioxygenase type 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CDO1 (cysteine dioxygenase type 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cdo1 (cysteine dioxygenase type 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CDO1 (cysteine dioxygenase type 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	CDO1 (cysteine dioxygenase type 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cdo1 (cysteine dioxygenase type 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CDO1 (cysteine dioxygenase type 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Cdo1 (cysteine dioxygenase 1, cytosolic)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	cdo1 (cysteine dioxygenase, type I)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG5493	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	cdo-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	18	39,432,473 - 39,447,253 (-)	NCBI
Rnor_6.0 Ensembl	18	40,701,984 - 40,716,686 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	40,702,027 - 40,716,901 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	40,348,054 - 40,362,746 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	40,914,028 - 40,928,671 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	40,951,568 - 40,966,212 (-)	NCBI
Celera	18	37,683,907 - 37,698,550 (-)	NCBI		Celera
Cytogenetic Map	18	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

Experimental Liver Cirrhosis (ISO)

Hereditary Neoplastic Syndromes (ISO)

hypertension (IEP)

Neurodevelopmental Disorders (ISO)

obesity (ISO)

type 2 diabetes mellitus (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP)

17beta-estradiol (ISO)

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

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

3-chloropropane-1,2-diol (EXP)

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

4,4'-sulfonyldiphenol (ISO)

4-octylphenol (ISO)

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

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

aflatoxin B1 (ISO)

amiodarone (EXP)

ammonium chloride (EXP)

Aroclor 1254 (EXP)

arsenite(3-) (ISO)

benzbromarone (EXP)

benzo[a]pyrene (EXP,ISO)

bexarotene (EXP)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

bromobenzene (EXP)

carbon nanotube (ISO)

chloroprene (EXP)

choline (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (EXP)

clofibrate (EXP)

clofibric acid (EXP)

copper atom (EXP)

copper(0) (EXP)

corticosterone (EXP)

coumarin (EXP)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dicrotophos (ISO)

Diisodecyl phthalate (ISO)

diuron (EXP)

endosulfan (EXP)

ethanol (ISO)

flutamide (EXP)

folic acid (ISO)

furan (EXP)

glafenine (EXP)

glutathione (EXP)

hypotaurine (EXP)

indometacin (ISO)

iron atom (EXP)

iron(0) (EXP)

isoprenaline (ISO)

L-ethionine (EXP)

L-methionine (ISO)

m-xylene (EXP)

methapyrilene (EXP)

methylisothiazolinone (ISO)

mono(2-ethylhexyl) phthalate (EXP)

N-methyl-4-phenylpyridinium (ISO)

N-nitrosodiethylamine (EXP)

N-nitrosodimethylamine (EXP)

nefazodone (EXP)

nickel sulfate (ISO)

nimesulide (EXP)

O-methyleugenol (ISO)

ochratoxin A (EXP)

omeprazole (EXP)

oxaliplatin (EXP)

paracetamol (EXP,ISO)

paraquat (EXP)

perfluorooctane-1-sulfonic acid (EXP)

perfluorooctanoic acid (EXP,ISO)

phenobarbital (EXP)

piperonyl butoxide (EXP)

pirinixic acid (EXP,ISO)

potassium dichromate (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

progesterone (EXP,ISO)

quercetin (ISO)

quinolin-8-ol (ISO)

raloxifene (ISO)

serpentine asbestos (ISO)

sodium arsenite (ISO)

sodium fluoride (EXP)

succimer (ISO)

sunitinib (ISO)

tamoxifen (ISO)

tetrachloromethane (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

topotecan (EXP)

tunicamycin (ISO)

valdecoxib (EXP)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cysteine metabolic process (TAS)

L-cysteine catabolic process (IBA,IDA)

L-cysteine metabolic process (NAS)

lactation (IDA)

obsolete oxidation-reduction process (IEA)

response to amino acid (IDA)

response to cAMP (IDA)

response to ethanol (IDA)

response to glucagon (IDA)

response to glucocorticoid (IDA)

response to organonitrogen compound (IDA)

taurine biosynthetic process (IEA)

Cellular Component

cytosol (ISO,TAS)

Molecular Function

cysteine dioxygenase activity (IBA,IDA,TAS)

ferrous iron binding (IBA,IDA)

oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (IBA)

Molecular Pathway Annotations Click to see Annotation Detail View

cysteine and methionine metabolic pathway (IEA)

cysteine metabolic pathway (ISO)

mercaptolactate-cysteine disulfiduria pathway (ISO)

ocular nonnephropathic cystinosis pathway (ISO)

taurine and hypotaurine metabolic pathway (IEA,ISO)

transsulfuration pathway of homocysteine metabolism (ISO)

References

References - curated


1.	Chai SC, etal., J Biol Chem. 2006 Jun 9;281(23):15774-9. Epub 2006 Apr 11.
2.	Cresenzi CL, etal., J Nutr 2003 Sep;133(9):2697-702.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	GOA data from the GO Consortium
5.	Hosokawa Y, etal., Biochem Biophys Res Commun 1990 Apr 30;168(2):473-8.
6.	Hosokawa Y, etal., J Biochem. 1978 Aug;84(2):419-24.
7.	Hosokawa Y, etal., J Biochem. 1980 Aug;88(2):389-94.
8.	Jung YS, etal., Adv Exp Med Biol. 2003;526:245-52.
9.	KEGG
10.	Kuo SM and Stipanuk MH, Biol Neonate. 1984;46(5):237-48.
11.	Kuriyama K, etal., J Neurochem. 1984 Jun;42(6):1600-6.
12.	Kwon YH and Stipanuk MH, Am J Physiol Endocrinol Metab. 2001 May;280(5):E804-15.
13.	MGD data from the GO Consortium
14.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
15.	Parsons RB, etal., J Hepatol. 1998 Oct;29(4):595-602.
16.	Pipeline to import KEGG annotations from KEGG into RGD
17.	Pipeline to import SMPDB annotations from SMPDB into RGD
18.	RGD automated data pipeline
19.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20.	RGD automated import pipeline for gene-chemical interactions
21.	Stipanuk MH and Ueki I, J Inherit Metab Dis. 2011 Feb;34(1):17-32. doi: 10.1007/s10545-009-9006-9. Epub 2010 Feb 17.
22.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
23.	Tsuboyama N, etal., Gene 1996 Nov 28;181(1-2):161-5.
24.	Tsuboyama-Kasaoka N, etal., Endocrinology. 2006 Jul;147(7):3276-84. Epub 2006 Apr 20.

Additional References at PubMed

PMID:11602353	PMID:15489334	PMID:15623508	PMID:16262602	PMID:16325423	PMID:16511222	PMID:16611640	PMID:17153587	PMID:17634260	PMID:18308719	PMID:18847220	PMID:21839860
PMID:22122511	PMID:24084026	PMID:24929188	PMID:25390690

Genomics

Comparative Map Data

Cdo1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	18	39,432,473 - 39,447,253 (-)	NCBI
Rnor_6.0 Ensembl	18	40,701,984 - 40,716,686 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	40,702,027 - 40,716,901 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	40,348,054 - 40,362,746 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	40,914,028 - 40,928,671 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	40,951,568 - 40,966,212 (-)	NCBI
Celera	18	37,683,907 - 37,698,550 (-)	NCBI		Celera
Cytogenetic Map	18	q11	NCBI

CDO1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	5	115,804,733 - 115,816,659 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	115,804,733 - 115,816,659 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	115,140,430 - 115,152,356 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	5	115,140,430 - 115,152,405 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	115,168,329 - 115,180,304 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	115,168,330 - 115,180,304	NCBI
Celera	5	111,088,830 - 111,100,805 (-)	NCBI
Cytogenetic Map	5	q22.3	NCBI
HuRef	5	110,321,120 - 110,333,095 (-)	NCBI		HuRef
CHM1_1	5	114,573,041 - 114,585,035 (-)	NCBI		CHM1_1

Cdo1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	18	46,846,260 - 46,861,569 (-)	NCBI	GRCm39		mm39
GRCm38	18	46,713,193 - 46,728,502 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	46,713,193 - 46,728,395 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	18	46,872,859 - 46,887,996 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	18	46,838,536 - 46,853,673 (-)	NCBI			mm8
Celera	18	48,072,450 - 48,087,588 (-)	NCBI		Celera
Cytogenetic Map	18	C	NCBI
cM Map	18	24.75	NCBI

Cdo1
(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_004955408	35,593,767 - 35,605,189 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955408	35,593,981 - 35,605,189 (-)	NCBI	ChiLan1.0	ChiLan1.0

CDO1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	5	116,955,295 - 116,967,506 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	116,955,295 - 116,967,506 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	111,159,041 - 111,170,965 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

CDO1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	11	5,371,378 - 5,524,562 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	11	5,512,996 - 5,524,556 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Cdo1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936742	981,863 - 993,271 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CDO1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	119,892,691 - 119,940,665 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	119,927,768 - 119,940,690 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	124,815,757 - 124,827,728 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CDO1
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	23	19,049,612 - 19,061,783 (-)	NCBI
ChlSab1.1 Ensembl	23	19,049,262 - 19,061,740 (-)	Ensembl

Cdo1
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624733	6,062,716 - 6,074,583 (+)	NCBI

Position Markers

D18Wox19

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	40,702,827 - 40,702,970	NCBI	Rnor6.0
Rnor_5.0	18	40,348,854 - 40,348,997	UniSTS	Rnor5.0
RGSC_v3.4	18	40,914,821 - 40,914,964	UniSTS	RGSC3.4
Celera	18	37,684,700 - 37,684,843	UniSTS
Cytogenetic Map	18	q11	UniSTS

D18Wox20

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	40,712,166 - 40,712,301	NCBI	Rnor6.0
Rnor_5.0	18	40,358,193 - 40,358,328	UniSTS	Rnor5.0
RGSC_v3.4	18	40,924,160 - 40,924,295	UniSTS	RGSC3.4
Celera	18	37,694,039 - 37,694,174	UniSTS
Cytogenetic Map	18	q11	UniSTS

RH127714

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	40,702,179 - 40,702,362	NCBI	Rnor6.0
Rnor_5.0	18	40,348,206 - 40,348,389	UniSTS	Rnor5.0
RGSC_v3.4	18	40,914,173 - 40,914,356	UniSTS	RGSC3.4
Celera	18	37,684,052 - 37,684,235	UniSTS
Cytogenetic Map	18	q11	UniSTS

RH139615

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	40,715,157 - 40,715,370	NCBI	Rnor6.0
Rnor_5.0	18	40,361,184 - 40,361,397	UniSTS	Rnor5.0
RGSC_v3.4	18	40,927,151 - 40,927,364	UniSTS	RGSC3.4
Celera	18	37,697,030 - 37,697,243	UniSTS
Cytogenetic Map	18	q11	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2299160	Iddm35	Insulin dependent diabetes mellitus QTL 35	2.79		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	18	4407513	62570466	Rat
2312568	Glom21	Glomerulus QTL 21	2	0.005	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	18	5430134	41781619	Rat
2313082	Bss85	Bone structure and strength QTL 85	0.8	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	18	14678852	59678852	Rat
1331753	Bp231	Blood pressure QTL 231	3.643		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	15539427	53861431	Rat
1358358	Sradr6	Stress Responsive Adrenal Weight QTL 6	2.49		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	18	15539427	61499684	Rat
6903359	Bp355	Blood pressure QTL 355	3.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	15539671	61985648	Rat
2293708	Bss46	Bone structure and strength QTL 46	8.8	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	18	15695872	68524999	Rat
1578661	Bss20	Bone structure and strength QTL 20	3.7		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	18	15695872	87080053	Rat
1578667	Bss21	Bone structure and strength QTL 21	3.5		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	18	15695872	87080053	Rat
1358193	Emca2	Estrogen-induced mammary cancer QTL 2	1.6		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	18	19031030	68436105	Rat
1600373	Mamtr6	Mammary tumor resistance QTL 6			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	18	20285758	87080053	Rat
7387267	Uae42	Urinary albumin excretion QTL 42		0.61	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	14	21639491	66639491	Rat
1331741	Bp232	Blood pressure QTL 232	3.59112		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	22603736	87074531	Rat
6903353	Bp353	Blood pressure QTL 353	2.8		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	22604764	61985648	Rat
1641923	Colcr8	Colorectal carcinoma resistance QTL 8	3.1	0.0014	intestine integrity trait (VT:0010554)	poorly differentiated malignant colorectal tumor number (CMO:0002076)	18	23184227	53861431	Rat
1331733	Bp233	Blood pressure QTL 233	3.97196		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	25961026	81761656	Rat
2325839	Bp348	Blood pressure QTL 348		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	26743404	43659626	Rat
2301413	Bp318	Blood pressure QTL 318		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	27743024	48499517	Rat
12904673	Cm127	Cardiac mass QTL 127		0.005	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	18	27743024	48499517	Rat
12904675	Am19	Aortic mass QTL 19		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	18	27743024	48499517	Rat
12904677	Kidm72	Kidney mass QTL 72		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	18	27743024	48499517	Rat
12904668	Bw188	Body weight QTL 188		0.03	body mass (VT:0001259)	body weight (CMO:0000012)	18	27743024	48499517	Rat
12904669	Cm125	Cardiac mass QTL 125		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	18	27743024	48499517	Rat
12904670	Cm126	Cardiac mass QTL 126		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	18	27743024	48499517	Rat
2300157	Bmd66	Bone mineral density QTL 66	13.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	18	30533614	75533614	Rat
2300177	Bmd65	Bone mineral density QTL 65	19.7	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	18	30533614	75533614	Rat
2293704	Bss35	Bone structure and strength QTL 35	4.59	0.0002	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	18	30533614	75533614	Rat
9590318	Scort22	Serum corticosterone level QTL 22	7.64	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	18	31361341	76361341	Rat
1331754	Bp230	Blood pressure QTL 230	4.61609		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	31361341	76361341	Rat
9589816	Gluco68	Glucose level QTL 68	7.25	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	18	31361341	76361341	Rat
8694378	Bw157	Body weight QTL 157	3.59	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	18	31361341	76361341	Rat
738005	Anxrr11	Anxiety related response QTL 11	3.4		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	18	31608424	76608424	Rat
61383	Bp47	Blood pressure QTL 47	17.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	31728373	62570429	Rat
1331776	Bp225	Blood pressure QTL 225	2.829		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	32670352	61985812	Rat
1331774	Bp226	Blood pressure QTL 226	4.41065		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	61985812	Rat
1331742	Bp228	Blood pressure QTL 228	3.88752		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	61985812	Rat
1331798	Bp224	Blood pressure QTL 224	3.53873		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	61985812	Rat
1331727	Bp237	Blood pressure QTL 237	3.053		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	63897621	Rat
61429	Cia17	Collagen induced arthritis QTL 17	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	18	32670352	73016546	Rat
2303120	Mamtr8	Mammary tumor resistance QTL 8		0.001	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	18	32670352	87080053	Rat
6903347	Bp350	Blood pressure QTL 350	4.4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670473	61985648	Rat
631274	Sprol1	Serum protein level QTL 1	5.3		blood total protein amount (VT:0005567)	serum total protein level (CMO:0000661)	18	32704022	80696226	Rat
631518	Bw11	Body weight QTL 11	2.8		body mass (VT:0001259)	body weight (CMO:0000012)	18	38221919	83221919	Rat
61367	Iddm4	Insulin dependent diabetes mellitus QTL 4	2.33	0.0074	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	18	40375769	85375769	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	435
Count of miRNA genes:	237
Interacting mature miRNAs:	274
Transcripts:	ENSRNOT00000000172
Prediction methods:	Microtar, Miranda, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High			8	8		8
Medium	1	9	49	33	9	33	5	5	74	35	36	11	5
Low	2	34			10		3	6			5		3
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_052809	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006254698	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC070509	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473971	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D83481	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ210572	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ218376	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219057	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219282	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000301	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M35266	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000000172 ⟹ ENSRNOP00000000172

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	18	40,701,984 - 40,716,686 (-)	Ensembl

RefSeq Acc Id:

NM_052809 ⟹ NP_434696

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	18	39,432,480 - 39,447,124 (-)	NCBI
Rnor_6.0	18	40,702,034 - 40,716,677 (-)	NCBI
Rnor_5.0	18	40,348,054 - 40,362,746 (-)	NCBI
RGSC_v3.4	18	40,914,028 - 40,928,671 (-)	RGD
Celera	18	37,683,907 - 37,698,550 (-)	RGD

Sequence:

show sequence

GAGGGTTTAGGCTGGTCTCCGGTGACCTCCTAGTCCTAAATCTTGATACCCTTGCAAGAGCTTT
GAGCGTGTGGGGTCCCGGGCGTTCGGGGTCCCGGGTGTGTGCGGTTTGTATAGCCTGAAGCCGG
GGTCCTCCGCGCTCGCGTCCTCCGCAGCTGGACTGAAGAGACGCGTCCCAGCCCTGCGGGGATG
GAACGGACCGAGCTGCTGAAGCCCCGGACCCTGGCCGACCTCATCCGAATCTTGCATGAGCTCT
TCGCCGGGGACGAAGTCAATGTGGAGGAGGTGCAGGCTGTGCTGGAAGCCTACGAGAGCAATCC
TGCCGAGTGGGCTTTGTATGCCAAATTCGATCAATACAGGTATACCCGAAACCTTGTGGATCAA
GGAAATGGGAAGTTTAATCTGATGATTCTGTGCTGGGGTGAAGGGCATGGCAGCAGTATTCACG
ATCACACGGACTCCCACTGCTTTTTGAAGCTGCTGCAAGGAAATCTAAAGGAGACATTGTTTGA
CTGGCCTGACAAGAAATCCAACGAGATGATCAAGAAGTCTGAAAGAACTTTGAGGGAAAATCAG
TGTGCCTACATTAATGATTCTATTGGCTTACATCGAGTAGAGAACGTCAGCCACACAGAGCCTG
CTGTGAGCCTTCACTTGTACAGTCCACCTTTCGATACATGCCATGCCTTTGACCAACGAACAGG
GCATAAAAACAAAGTCACCATGACATTCCACAGCAAATTTGGAATCAGAACTCCATTTACAACT
TCAGGTTCACTGGAGAACAACTAAGACCTGCCAAGCCTTTCAAAGTTTTGCTTCTGGGTCGTTG
GAATGTTTTACCTTGGATAAGAGAGGCCACCCATCATTTGCTGTCCAGTTATACATTTTAATAA
GTCCATGCTCAGTGTGTATACTAAGGAAGCAAACCATCCCCTGAGCTATGCAGGAGAAAAATCC
CACTAAAGAAAAAGTCACTTGATTTTTAATAGCCAAATCACCTTGCTCCCAGTTCTTCTGTCTT
CTAACTCCATGGAAATTCTATTGGGAGTTCTCAGTGGGGTTTTTTTTCAACCTTAGGAAAGCAC
TTCTGGTCTCTGAACTCTAATAATCAATAAGTAAAAATGAAGAAACCACAAGCTATCACATGTC
TGTTTTCATACCTGGAAGTCTAAGTGTGGAAATCTTTAATTTACTTTGTATGTTCTTAATGTTT
GACAAGAATTTTTTTAAATCTTGGTTTTCAGTTTTTTCAACCCTGTTTGACAAATTCCTATGCT
GTGGAGACTAGGGATGCAGATAGCAGTTTGGTGTTTGGTAGTGAACAGCAGTGGGGCCAGAAAT
GTGCATGTATCCAGACCTCCTGCAAATAAAAACTGAAACTCATGTGTAATGTGTGCCACCACCT
TAAGCTGCCACCAAAATTGCCAAACGACTTTAATAAAACTGGATTTGAGA

hide sequence

RefSeq Acc Id:

XM_006254698 ⟹ XP_006254760

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	18	39,432,473 - 39,447,253 (-)	NCBI
Rnor_6.0	18	40,702,027 - 40,716,901 (-)	NCBI
Rnor_5.0	18	40,348,054 - 40,362,746 (-)	NCBI

Sequence:

show sequence

AAGTATGAGGCAAGGGCAACAGTGGGGCTTCTGAGGGTTGGCGCGTACACACAGTGCTGTGCCA
GGGCCCTCCCTCTGGCTCTCTCCACCTCTGGCCCCTTTCTCGGGTCTCTCCCCGCCTCACTCCA
CCCCCTTAAGGCGGTTGGTACGTTCTAGATGGCTCCAAGAGCTTAAAAAGGGCCCGGGAGGGCG
GATTCCTCAGATTTGGTCTTGACTGATCAGTCGAGGGTTTAGGCTGGTCTCCGGTGACCTCCTA
GTCCTAAATCTTGATACCCTTGCAAGAGCTTTGAGCGTGTGGGGTCCCGGGCGTTCGGGGTCCC
GGGTGTGTGCGGTTTGTATAGCCTGAAGCCGGGGTCCTCCGCGCTCGCGTCCTCCGCAGCTGGA
CTGAAGAGACGCGTCCCAGCCCTGCGGGGATGGAACGGACCGAGCTGCTGAAGCCCCGGACCCT
GGCCGACCTCATCCGAATCTTGCATGAGCTCTTCGCCGGGGACGAAGTCAATGTGGAGGAGGTG
CAGGCTGTGCTGGAAGCCTACGAGAGCAATCCTGCCGAGTGGGCTTTGTATGCCAAATTCGATC
AATACAGGTATACTCGAAACCTTGTGGATCAAGGAAATGGGAAGTTTAATCTGATGATTCTGTG
CTGGGGTGAAGGGCATGGCAGCAGTATTCACGATCACACGGACTCCCACTGCTTTTTGAAGCTG
CTGCAAGGAAATCTAAAGGAGACATTGTTTGACTGGCCTGACAAGAAATCCAACGAGATGATCA
AGAAGTCTGAAAGAACTTTGAGGGAAAATCAGTGTGCCTACATTAATGACAACTTCAGGTTCAC
TGGAGAACAACTAAGACCTGCCAAGCCTTTCAAAGTTTTGCTTCTGGGTCGTTGGAATGTTTTA
CCTTGGATAAGAGAGGCCACCCATCATTTGCTGTCCAGTTATACATTTTAATAAGTCCATGCTC
AGTGTGTATACTAAGGAAGCAAACCATCCCCTGAGCTATGCAGGAGAAAAATCCCACTAAAGAA
AAAGTCACTTGATTTTTAATAGCCAAATCACCTTGCTCCCAGTTCTTCTGTCTTCTAACTCCAT
GGAAATTCTATTGGGAGTTCTCAGTGGGGTTTTTTTTCAACCTTAGGAAACACTTCTGGTCTCT
GAACTCTAATAATCAATAAGTAAAAATGAAGAAACCACAAGCTATCACATGTCTGTTTTCATAC
CTGGAAGTCTAAGTGTGGAAATCTTTAATTTACTTTGTATGTTCTTAATGTTTGACAAGAATTT
TTTTAAATCTTGGTTTTCAGTTTTTTCAACCCTGTTTGACAAATTCCTATGCTGTGGAGACTAG
GGATGCAGATAGCAGTTTGGTGTTTGGTAGTGAACAGCAGTGGGGCCAGAAATGTGCATGTATC
CAGACCTCCTGCAAATAAAAACTGAAACTCATGTGTAATGTGTGCCACCACCTTAAGCTGCCAC
CAAAATTGCCAAACGACTTTAATAAAACTGGATTTGAGAAGAAGTA

hide sequence

Protein Sequences


Protein RefSeqs	NP_434696	(Get FASTA)	NCBI Sequence Viewer
	XP_006254760	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40904	(Get FASTA)	NCBI Sequence Viewer
	AAH70509	(Get FASTA)	NCBI Sequence Viewer
	BAA11925	(Get FASTA)	NCBI Sequence Viewer
	EDM14395	(Get FASTA)	NCBI Sequence Viewer
	EDM14396	(Get FASTA)	NCBI Sequence Viewer
	EDM14397	(Get FASTA)	NCBI Sequence Viewer
	EDM14398	(Get FASTA)	NCBI Sequence Viewer
	EDM14399	(Get FASTA)	NCBI Sequence Viewer
	P21816	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_434696 ⟸ NM_052809

- UniProtKB:

P21816 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MERTELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVD
QGNGKFNLMILCWGEGHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLREN
QCAYINDSIGLHRVENVSHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPFT
TSGSLENN

hide sequence

RefSeq Acc Id:	XP_006254760 ⟸ XM_006254698
- Peptide Label:	isoform X1
- Sequence:	show sequence MERTELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVD QGNGKFNLMILCWGEGHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLREN QCAYINDNFRFTGEQLRPAKPFKVLLLGRWNVLPWIREATHHLLSSYTF hide sequence

RefSeq Acc Id:

ENSRNOP00000000172 ⟸ ENSRNOT00000000172

Transcriptome

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

Promoters

RGD ID:

13700767

Promoter ID:

EPDNEW_R11291

Type:

single initiation site

Name:

Cdo1_1

Description:

cysteine dioxygenase type 1

SO ACC ID:

SO:0000170

Source:

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

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	18	40,716,701 - 40,716,761	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

ACI/N (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

BN/SsN (MCW)

Visual

CSV

TAB

Printer

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

Buf/N (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

FHH/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

GH/OmrMcwi (MCW)

Visual

CSV

TAB

Printer

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

GK/Ox (RGD)

Visual

CSV

TAB

Printer

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

LE/Stm (RGD)

Visual

CSV

TAB

Printer

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

LEW/Crl (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

LH/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

LL/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

LN/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

M520/N (MCW)

Visual

CSV

TAB

Printer

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

MHS/Gib (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

MR/N (MCW)

Visual

CSV

TAB

Printer

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

SBH/Ygl (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

SHRSP/Gcrc (RGD)

Visual

CSV

TAB

Printer

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

SR/JrHsd (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

SS/JrHsdMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

WKY/Gcrc (RGD)

Visual

CSV

TAB

Printer

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

WKY/N (MCW)

Visual

CSV

TAB

Printer

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

WKY/NCrl (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

WN/N (MCW)

Visual

CSV

TAB

Printer

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:69262	AgrOrtholog
Ensembl Genes	ENSRNOG00000000158	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000000172	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000000172	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.120.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7100321	IMAGE-MGC_LOAD
InterPro	CDO_1	UniProtKB/Swiss-Prot
	RmlC-like_jellyroll	UniProtKB/Swiss-Prot
	RmlC_Cupin_sf	UniProtKB/Swiss-Prot
KEGG Report	rno:81718	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:91599	IMAGE-MGC_LOAD
NCBI Gene	81718	ENTREZGENE
PANTHER	PTHR12918	UniProtKB/Swiss-Prot
Pfam	CDO_I	UniProtKB/Swiss-Prot
PhenoGen	Cdo1	PhenoGen
Superfamily-SCOP	SSF51182	UniProtKB/Swiss-Prot
UniProt	CDO1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	Q6NS32	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-07-09	Cdo1	cysteine dioxygenase type 1	Cdo1	cysteine dioxygenase, type I	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-09	Cdo1	cysteine dioxygenase, type I	Cdo1	cysteine dioxygenase 1, cytosolic	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-11-17	Cdo1	cysteine dioxygenase 1, cytosolic			Name updated	1299863	APPROVED
2002-06-10	Cdo1	cytosolic cysteine dioxygenase 1			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in liver, kidney, lung, and brain	632438
gene_protein	predicted protein consists of 200 aa residues and masses 23 kDa	68765
gene_transcript	gene spans around 15 kb and comprises 5 exons	632438

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)