Mt-co2 (mitochondrially encoded cytochrome c oxidase II) - Rat Genome Database

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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 enable copper ion binding activity. 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 be located in mitochondrial inner membrane. Predicted to be part of mitochondrial respiratory chain complex IV. Biomarker of colorectal carcinoma and 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; 2,3,7,8-tetrachlorodibenzodioxine.
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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2MT7,006 - 7,689 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblMT7,006 - 7,689 (+)Ensembl
Rnor_6.0MT7,006 - 7,689 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblMT7,006 - 7,689 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0MT7,006 - 7,689 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4MT7,006 - 7,689 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic MapMT NCBI


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  (EXP,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)
aristolochic 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)
gentamycin  (EXP)
glucose  (ISO)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
ivermectin  (ISO)
josamycin  (ISO)
lamivudine  (ISO)
lead nitrate  (EXP)
Licarin A  (ISO)
microcystin-LR  (EXP)
Mitotane  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nimesulide  (ISO)
okadaic acid  (ISO)
oxaloacetic acid  (ISO)
p-menthan-3-ol  (ISO)
paracetamol  (EXP)
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)
trichloroethene  (EXP)
tungsten  (ISO)
tunicamycin  (ISO)
tyrphostin B42  (ISO)
valproic acid  (ISO)
zalcitabine  (EXP)
zidovudine  (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. Huang T, etal., Oxid Med Cell Longev. 2019 Jul 15;2019:5813985. doi: 10.1155/2019/5813985. eCollection 2019.
7. Huttemann M, etal., Gene 2003 Jul 17;312:95-102.
8. Jove M, etal., J Lipid Res. 2004 Jan;45(1):113-23. Epub 2003 Oct 16.
9. KEGG
10. Kim J, etal., Hum Mol Genet. 2010 Oct 15;19(20):3919-35. doi: 10.1093/hmg/ddq306. Epub 2010 Jul 21.
11. Liu JR, etal., Pathol Res Pract. 2015 Jun;211(6):426-34. doi: 10.1016/j.prp.2015.01.007. Epub 2015 Jan 24.
12. Martin I, etal., Biochem J. 1989 Nov 1;263(3):965-8.
13. Martin I, etal., Biochem J. 1993 Nov 15;296 ( Pt 1):231-4.
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. Pepe G, etal., Biochem Int 1983 Apr;6(4):553-63.
16. Rai A, etal., Pharmacol Res. 2018 Jun;132:188-203. doi: 10.1016/j.phrs.2017.12.010. Epub 2017 Dec 8.
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. RGD comprehensive gene curation
21. 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   PMID:34201437  


Genomics

Comparative Map Data
Mt-co2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2MT7,006 - 7,689 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblMT7,006 - 7,689 (+)Ensembl
Rnor_6.0MT7,006 - 7,689 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblMT7,006 - 7,689 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0MT7,006 - 7,689 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4MT7,006 - 7,689 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic MapMT NCBI
MT-CO2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblMT7,586 - 8,269 (+)EnsemblGRCh38hg38GRCh38
GRCh38MT7,586 - 8,269 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37MT7,586 - 8,269 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36MT7,587 - 8,270 (+)NCBINCBI36hg18NCBI36
mt-Co2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39MT7,013 - 7,696 (+)NCBIGRCm39mm39
GRCm39 EnsemblMT7,013 - 7,696 (+)Ensembl
GRCm38MT7,013 - 7,696 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblMT7,013 - 7,696 (+)EnsemblGRCm38mm10GRCm38
MGSCv37MT7,013 - 7,696 (+)NCBIGRCm37mm9NCBIm37
MT-CO2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1MT7,034 - 7,717 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblMT7,034 - 7,717 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaMT7,034 - 7,717 (+)NCBI
MT-CO2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblMT8,203 - 8,890 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1MT8,203 - 8,890 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2MT8,203 - 8,890 (+)NCBISscrofa10.2Sscrofa10.2susScr3

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 9 49 79 41 19 41 8 11 74 35 41 11 8
Medium
Low
Below cutoff

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 AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblMT7,006 - 7,689 (+)Ensembl
Rnor_6.0 EnsemblMT7,006 - 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 (2019)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
F344/Stm (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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)
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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
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)
Visual CSV TAB Printer
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)
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/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)
Visual CSV TAB Printer
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)
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 (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)
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)
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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)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (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)
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
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)
Visual CSV TAB Printer
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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (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)
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)
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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)
Visual CSV TAB Printer
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)
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)
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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)
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 (2020)
Visual CSV TAB Printer
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)
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 (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)
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 (2020)
Visual CSV TAB Printer
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)
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

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