Mt-co2 (mitochondrially encoded cytochrome c oxidase II)

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Gene: Mt-co2 (mitochondrially encoded cytochrome c oxidase II) Rattus norvegicus

Analyze

Symbol:

Mt-co2

Name:

mitochondrially encoded cytochrome c oxidase II

RGD ID:

621872

Description:

Predicted to contribute to cytochrome-c oxidase activity. Involved in several processes, including lactation; positive regulation of cellular biosynthetic process; and positive regulation of necrotic cell death. Predicted to localize to mitochondrial inner membrane and respiratory chain complex IV. Biomarker of type 2 diabetes mellitus. Orthologous to several human genes including MTCO2P12 (MT-CO2 pseudogene 12); INTERACTS WITH 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether; atrazine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Co2; COII; Cox2; cytochrome c oxidase 2, mitochondrial; cytochrome c oxidase II, mitochondrial; cytochrome c oxidase subunit 2; cytochrome c oxidase subunit II

RGD Orthologs

Human

Mouse

Dog

Pig

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	MT	7,006 - 7,689 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	MT	7,006 - 7,689 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	MT	7,006 - 7,689 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	MT	7,006 - 7,689 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Cytogenetic Map	MT		NCBI

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Brain Injuries (IEP)

cerebral infarction (ISO)

colon cancer (ISO)

cytochrome-c oxidase deficiency disease (ISO)

dilated cardiomyopathy (ISO)

Experimental Diabetes Mellitus (ISO)

Huntington's disease (ISO)

Leigh disease (ISO)

MELAS syndrome (ISO)

mitochondrial metabolism disease (ISO)

neuroblastoma (ISO)

Subacute Necrotizing Encephalopathy of Leigh, Infantile (ISO)

tetralogy of Fallot (ISO)

type 2 diabetes mellitus (IEP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

(+)-epicatechin-3-O-gallate (ISO)

(-)-epigallocatechin 3-gallate (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP)

17beta-estradiol (ISO)

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

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

2,6-di-tert-butyl-4-methylphenol (ISO)

3,3'-diindolylmethane (ISO)

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

5-methyl-4-oxido-2-pyrazin-4-iumcarboxylic acid (ISO)

aldehydo-D-glucose (ISO)

all-trans-retinoic acid (ISO)

arsane (ISO)

arsenic atom (ISO)

atrazine (EXP,ISO)

bexarotene (ISO)

bisphenol A (EXP,ISO)

butylated hydroxyanisole (ISO)

cadmium atom (EXP,ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

chloramphenicol (ISO)

chlorogenic acid (ISO)

chromium(6+) (ISO)

cis-caffeic acid (ISO)

cisplatin (EXP)

clarithromycin (ISO)

copper atom (ISO)

copper(0) (ISO)

D-glucose (ISO)

desferrioxamine B (ISO)

dexamethasone (EXP,ISO)

didanosine (ISO)

doxorubicin (EXP,ISO)

ethidium (ISO)

flutamide (ISO)

fructose (EXP)

gallic acid (ISO)

gallocatechin (ISO)

glucose (ISO)

hydrogen peroxide (ISO)

hydrogen sulfide (ISO)

josamycin (ISO)

lamivudine (ISO)

lead nitrate (EXP)

Licarin A (ISO)

microcystin-LR (EXP)

Mitotane (ISO)

N-methyl-4-phenylpyridinium (ISO)

okadaic acid (ISO)

oxaloacetic acid (ISO)

paraquat (EXP)

perfluorooctanoic acid (EXP)

pirinixic acid (EXP)

Propiverine (EXP)

puerarin (EXP)

quercetin (ISO)

reactive oxygen species (ISO)

resveratrol (EXP,ISO)

sodium arsenite (EXP,ISO)

sodium fluoride (ISO)

sodium hydrogensulfite (EXP)

sulfur dioxide (EXP)

T-2 toxin (EXP)

tenofovir disoproxil fumarate (ISO)

thapsigargin (ISO)

trans-caffeic acid (ISO)

tungsten (ISO)

tunicamycin (ISO)

valproic acid (ISO)

zalcitabine (EXP)

zidovudine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

ATP synthesis coupled electron transport (IBA)

lactation (IEP)

positive regulation of ATP biosynthetic process (IMP)

positive regulation of hydrogen peroxide biosynthetic process (IMP)

positive regulation of necrotic cell death (IMP)

positive regulation of vasoconstriction (ISO)

proton transmembrane transport (IEA)

response to cold (IEP)

Cellular Component

cellular_component (ND)

integral component of membrane (IEA)

mitochondrial inner membrane (ISO)

mitochondrion (ISO)

respiratory chain complex IV (ISO,ISS)

Molecular Function

copper ion binding (IEA)

cytochrome-c oxidase activity (IBA,ISO,ISS)

molecular_function (ND)

protein binding (ISO)

References

References - curated


1.	Brown GG and Simpson MV, Proc Natl Acad Sci U S A 1982 May;79(10):3246-50.
2.	Freshwater JD, etal., Diabetes 2002 Jul;51(7):2249-55.
3.	Gadaleta G, etal., J Mol Evol 1989 Jun;28(6):497-516.
4.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5.	Harris LK, etal., J Neurotrauma. 2001 Oct;18(10):993-1009.
6.	Huttemann M, etal., Gene 2003 Jul 17;312:95-102.
7.	Jove M, etal., J Lipid Res. 2004 Jan;45(1):113-23. Epub 2003 Oct 16.
8.	KEGG
9.	Kim J, etal., Hum Mol Genet. 2010 Oct 15;19(20):3919-35. doi: 10.1093/hmg/ddq306. Epub 2010 Jul 21.
10.	Martin I, etal., Biochem J. 1989 Nov 1;263(3):965-8.
11.	Martin I, etal., Biochem J. 1993 Nov 15;296 ( Pt 1):231-4.
12.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
13.	Pepe G, etal., Biochem Int 1983 Apr;6(4):553-63.
14.	RGD automated data pipeline
15.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16.	RGD automated import pipeline for gene-chemical interactions
17.	RGD comprehensive gene curation
18.	Singh S, etal., Glia. 2009 Nov 1;57(14):1480-91. doi: 10.1002/glia.20864.

Additional References at PubMed

PMID:16626973	PMID:16677768	PMID:17540723	PMID:17559081	PMID:17600550	PMID:17881916	PMID:17885826	PMID:17963755	PMID:18349208	PMID:18456673	PMID:21335517	PMID:21717513
PMID:21863308	PMID:22043833	PMID:22082260	PMID:25727371	PMID:27592455	PMID:29227865	PMID:29476059	PMID:30528878	PMID:31799638

Genomics

Comparative Map Data

Mt-co2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	MT	7,006 - 7,689 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	MT	7,006 - 7,689 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	MT	7,006 - 7,689 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	MT	7,006 - 7,689 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Cytogenetic Map	MT		NCBI

MT-CO2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	MT	7,586 - 8,269 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	MT	7,586 - 8,269 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	MT	7,586 - 8,269 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	MT	7,587 - 8,270 (+)	NCBI	NCBI36		hg18	NCBI36

mt-Co2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	MT	7,013 - 7,696 (+)	NCBI	GRCm39		mm39
GRCm38	MT	7,013 - 7,696 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	MT	7,013 - 7,696 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	MT	7,013 - 7,696 (+)	NCBI	GRCm37		mm9	NCBIm37

MT-CO2
(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	MT	7,034 - 7,717 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	MT	7,034 - 7,717 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

MT-CO2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	MT	8,203 - 8,890 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	MT	8,203 - 8,890 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	MT	8,203 - 8,890 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	64
Count of miRNA genes:	57
Interacting mature miRNAs:	61
Transcripts:	ENSRNOT00000043693
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


GenBank Nucleotide	AJ428514	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY172581	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DQ673907	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DQ673911	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DQ673912	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DQ673913	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DQ673916	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ919759	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ919760	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ919765	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ919766	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ919767	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ919768	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ919769	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ919770	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ919771	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GU997609	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GU997610	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	HM152027	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	HM152028	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KJ530565	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KJ939360	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KJ939361	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM114606	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM114607	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM114608	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM577635	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM657952	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM657953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM820832	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM820834	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM820835	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM820836	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KP099715	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KP233832	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KP241960	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000043693 ⟹ ENSRNOP00000046414

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	MT	7,006 - 7,689 (+)	Ensembl

Protein Sequences


Protein RefSeqs	YP_665632	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAN77597	(Get FASTA)	NCBI Sequence Viewer
	ABG11764	(Get FASTA)	NCBI Sequence Viewer
	ABG11816	(Get FASTA)	NCBI Sequence Viewer
	ABG11829	(Get FASTA)	NCBI Sequence Viewer
	ABG11842	(Get FASTA)	NCBI Sequence Viewer
	ABG11881	(Get FASTA)	NCBI Sequence Viewer
	ACP50283	(Get FASTA)	NCBI Sequence Viewer
	ACP50296	(Get FASTA)	NCBI Sequence Viewer
	ACP50361	(Get FASTA)	NCBI Sequence Viewer
	ACP50374	(Get FASTA)	NCBI Sequence Viewer
	ACP50387	(Get FASTA)	NCBI Sequence Viewer
	ACP50400	(Get FASTA)	NCBI Sequence Viewer
	ACP50413	(Get FASTA)	NCBI Sequence Viewer
	ACP50426	(Get FASTA)	NCBI Sequence Viewer
	ACP50439	(Get FASTA)	NCBI Sequence Viewer
	ADE05942	(Get FASTA)	NCBI Sequence Viewer
	ADE05955	(Get FASTA)	NCBI Sequence Viewer
	ADG85624	(Get FASTA)	NCBI Sequence Viewer
	ADG85637	(Get FASTA)	NCBI Sequence Viewer
	AHZ60969	(Get FASTA)	NCBI Sequence Viewer
	AIU45578	(Get FASTA)	NCBI Sequence Viewer
	AIU45591	(Get FASTA)	NCBI Sequence Viewer
	AIU45682	(Get FASTA)	NCBI Sequence Viewer
	AIU45695	(Get FASTA)	NCBI Sequence Viewer
	AIU45708	(Get FASTA)	NCBI Sequence Viewer
	AIY51545	(Get FASTA)	NCBI Sequence Viewer
	AIZ58325	(Get FASTA)	NCBI Sequence Viewer
	AIZ58338	(Get FASTA)	NCBI Sequence Viewer
	AJD83435	(Get FASTA)	NCBI Sequence Viewer
	AJE61355	(Get FASTA)	NCBI Sequence Viewer
	AJE61381	(Get FASTA)	NCBI Sequence Viewer
	AJE61394	(Get FASTA)	NCBI Sequence Viewer
	AJJ48380	(Get FASTA)	NCBI Sequence Viewer
	AJK29984	(Get FASTA)	NCBI Sequence Viewer
	AJO99996	(Get FASTA)	NCBI Sequence Viewer
	CAD21562	(Get FASTA)	NCBI Sequence Viewer
	P00406	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

ENSRNOP00000046414 ⟸ ENSRNOT00000043693

Protein Domains

COX2_CUA COX2_TM

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 (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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CSV

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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CSV

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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CSV

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

F344/NCrl (RGD)

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CSV

TAB

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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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CSV

TAB

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

FHH/EurMcwi (MCW)

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CSV

TAB

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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)

Visual

CSV

TAB

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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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CSV

TAB

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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)

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)

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CSV

TAB

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

GK/Ox (RGD)

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CSV

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

LE/Stm (RGD)

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CSV

TAB

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

LEW/Crl (RGD)

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CSV

TAB

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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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CSV

TAB

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

LH/MavRrrc (RGD)

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CSV

TAB

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621872	AgrOrtholog
Ensembl Genes	ENSRNOG00000030371	Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000046414	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000043693	UniProtKB/Swiss-Prot
Gene3D-CATH	1.10.287.90	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	2.60.40.420	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	CcO_II-like_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CcO_II_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Copper_CuA	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Cupredoxin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Cyt_c_oxidase_su2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Cyt_c_oxidase_su2_TM_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Cyt_c_oxidase_su2_TM_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:26198	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	26198	ENTREZGENE
Pfam	COX2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	COX2_TM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Mt-co2	PhenoGen
PROSITE	COX2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	COX2_CUA	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	COX2_TM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF49503	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF81464	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs	CoxB	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	COX2_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q8SEZ5	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	Q37738	UniProtKB/Swiss-Prot
	Q80WI7	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-09	Mt-co2	mitochondrially encoded cytochrome c oxidase II	mt-Co2	cytochrome c oxidase II, mitochondrial	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-02-11	Krt1-9	cytochrome c oxidase II, mitochondrial	mt-Co2	cytochrome c oxidase 2, mitochondrial	Name updated to reflect Human and Mouse nomenclature	625702	APPROVED
2002-08-07	mt-Co2	cytochrome c oxidase 2, mitochondrial			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_protein	one of the three mitochondrial coded subunits, among the 13 subunits of each COX monomer	724423

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