Cox5b (cytochrome c oxidase subunit 5B) - Rat Genome Database
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Gene: Cox5b (cytochrome c oxidase subunit 5B) Rattus norvegicus
Analyze
Symbol: Cox5b
Name: cytochrome c oxidase subunit 5B
RGD ID: 620608
Description: Predicted to have cytochrome-c oxidase activity. Involved in response to peptide hormone. Predicted to localize to mitochondrion. Biomarker of hypertension. Orthologous to human COX5B (cytochrome c oxidase subunit 5B); PARTICIPATES IN Alzheimer's disease pathway; Huntington's disease pathway; oxidative phosphorylation pathway; INTERACTS WITH 3H-1,2-dithiole-3-thione; aldehydo-D-glucose; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cytochrome c oxidase polypeptide Vb; cytochrome c oxidase subunit 5B, mitochondrial; cytochrome c oxidase subunit Vb; cytochrome c oxidase subunit VIA*
Orthologs:
Homo sapiens (human) : COX5B (cytochrome c oxidase subunit 5B)  HGNC  Alliance
Mus musculus (house mouse) : Cox5b (cytochrome c oxidase subunit 5B)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : LOC102024993 (cytochrome c oxidase subunit 5B, mitochondrial)
Pan paniscus (bonobo/pygmy chimpanzee) : LOC100972878 (cytochrome c oxidase subunit 5B, mitochondrial)
Canis lupus familiaris (dog) : COX5B (cytochrome c oxidase subunit 5B)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : LOC101965209 (cytochrome c oxidase subunit 5B, mitochondrial)
Sus scrofa (pig) : COX5B (mitochondrial cytochrome c oxidase subunit Vb)
Chlorocebus sabaeus (African green monkey) : COX5B (cytochrome c oxidase subunit 5B)
Heterocephalus glaber (naked mole-rat) : LOC101714602 (cytochrome c oxidase subunit 5B, mitochondrial)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0943,259,706 - 43,262,039 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl943,259,709 - 43,262,040 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0942,912,214 - 42,914,547 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4935,625,478 - 35,627,304 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1935,626,891 - 35,628,718 (+)NCBI
Celera936,688,358 - 36,690,184 (+)NCBICelera
Cytogenetic Map9q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
5-aza-2'-deoxycytidine  (ISO)
aldehydo-D-glucose  (EXP)
ammonium chloride  (EXP)
astaxanthin  (ISO)
atrazine  (EXP,ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
cadmium atom  (ISO)
chloropicrin  (ISO)
cisplatin  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) chloride  (ISO)
crocidolite asbestos  (ISO)
D-glucose  (EXP)
dicrotophos  (ISO)
dioxygen  (EXP)
flutamide  (EXP)
folic acid  (ISO)
genistein  (EXP)
glafenine  (EXP)
glucose  (EXP)
heptachlor  (EXP)
homocysteine  (ISO)
hydrogen peroxide  (ISO)
isoniazide  (ISO)
isotretinoin  (ISO)
L-methionine  (ISO)
lamivudine  (ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
methoxychlor  (EXP)
myricetin  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodiethylamine  (ISO)
ochratoxin A  (EXP,ISO)
paraquat  (EXP)
perfluorododecanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
Pyridostigmine bromide  (EXP)
quercetin  (EXP)
rotenone  (EXP,ISO)
sarin  (EXP)
scopolamine  (EXP)
succimer  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
tetrathiomolybdate(2-)  (ISO)
theophylline  (ISO)
toluene  (EXP)
trichostatin A  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zidovudine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7601105   PMID:12477932   PMID:12865426   PMID:14645204   PMID:14651853   PMID:15489334   PMID:16103131   PMID:17634366   PMID:18408135   PMID:18614015   PMID:23376485   PMID:25002582  
PMID:26316108   PMID:28246552   PMID:29476059   PMID:30361391  


Genomics

Comparative Map Data
Cox5b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0943,259,706 - 43,262,039 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl943,259,709 - 43,262,040 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0942,912,214 - 42,914,547 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4935,625,478 - 35,627,304 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1935,626,891 - 35,628,718 (+)NCBI
Celera936,688,358 - 36,690,184 (+)NCBICelera
Cytogenetic Map9q21NCBI
COX5B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl297,646,062 - 97,648,383 (+)EnsemblGRCh38hg38GRCh38
GRCh38297,646,062 - 97,648,383 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37298,262,521 - 98,264,657 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36297,628,953 - 97,631,089 (+)NCBINCBI36hg18NCBI36
Build 34297,721,038 - 97,723,174NCBI
Celera292,466,522 - 92,468,658 (+)NCBI
Cytogenetic Map2q11.2ENTREZGENE
HuRef292,028,218 - 92,030,354 (+)NCBIHuRef
CHM1_1298,266,878 - 98,269,014 (+)NCBICHM1_1
Cox5b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39136,730,568 - 36,732,469 (+)NCBI
GRCm38136,691,487 - 36,693,388 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl136,691,449 - 36,693,681 (+)EnsemblGRCm38mm10GRCm38
MGSCv37136,748,332 - 36,750,233 (+)NCBIGRCm37mm9NCBIm37
MGSCv36136,636,084 - 36,637,931 (+)NCBImm8
Celera136,478,001 - 36,479,902 (+)NCBICelera
Cytogenetic Map1BNCBI
LOC102024993
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554704,321,555 - 4,324,824 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554704,321,555 - 4,323,449 (+)NCBIChiLan1.0ChiLan1.0
LOC100972878
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A98,544,980 - 98,547,502 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A98,544,980 - 98,547,502 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A101,675,232 - 101,677,417 (-)NCBIMhudiblu_PPA_v0panPan3
COX5B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1044,979,654 - 44,991,703 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11044,979,654 - 44,991,620 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
LOC101965209
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936744921,888 - 923,803 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COX5B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl356,629,270 - 56,632,120 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1356,630,297 - 56,632,107 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2359,376,451 - 59,378,263 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COX5B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1141,331,853 - 1,334,144 (+)NCBI
LOC101714602
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247492,837,030 - 2,838,880 (+)NCBI

Position Markers
PMC195978P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0943,259,401 - 43,259,661NCBIRnor6.0
Rnor_5.0942,911,909 - 42,912,169UniSTSRnor5.0
RGSC_v3.4935,625,173 - 35,625,433UniSTSRGSC3.4
Celera936,688,053 - 36,688,313UniSTS
Cytogenetic Map9q21UniSTS
Cox5b  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera2029,401,613 - 29,401,809UniSTS
Celera936,689,013 - 36,690,028UniSTS
Cytogenetic Map9q21UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91555490147249201Rat
724543Cm20Cardiac mass QTL 203.9heart mass (VT:0007028)calculated heart weight (CMO:0000073)91952048945029794Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)92575432054885226Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92748603663264281Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92748603666757620Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:53
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000022487
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 6 27 1
Medium 2 22 57 41 19 41 8 10 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07067402 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01059404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC083179 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D10951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D10952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218282 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X14208 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000022487   ⟹   ENSRNOP00000022487
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl943,259,709 - 43,262,040 (+)Ensembl
RefSeq Acc Id: NM_053586   ⟹   NP_446038
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0943,259,706 - 43,262,039 (+)NCBI
Rnor_5.0942,912,214 - 42,914,547 (+)NCBI
RGSC_v3.4935,625,478 - 35,627,304 (+)RGD
Celera936,688,358 - 36,690,184 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446038   ⟸   NM_053586
- Peptide Label: precursor
- UniProtKB: P12075 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022487   ⟸   ENSRNOT00000022487

Transcriptome

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

Promoters
RGD ID:13696608
Promoter ID:EPDNEW_R7133
Type:initiation region
Name:Cox5b_1
Description:cytochrome c oxidase subunit 5B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0943,259,706 - 43,259,766EPDNEW

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)
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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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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
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
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)
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
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)
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
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)
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:620608 AgrOrtholog
Ensembl Genes ENSRNOG00000016660 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000022487 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022487 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.11.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7300877 IMAGE-MGC_LOAD
InterPro Cyt_c_oxidase_su5b UniProtKB/Swiss-Prot
  Cyt_c_oxidase_su5b_sf UniProtKB/Swiss-Prot
  Cyt_c_oxidase_su5b_Zn_BS UniProtKB/Swiss-Prot
KEGG Report rno:94194 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105368 IMAGE-MGC_LOAD
NCBI Gene 94194 ENTREZGENE
PANTHER PTHR10122 UniProtKB/Swiss-Prot
Pfam COX5B UniProtKB/Swiss-Prot
PhenoGen Cox5b PhenoGen
PROSITE COX5B_1 UniProtKB/Swiss-Prot
  COX5B_2 UniProtKB/Swiss-Prot
UniGene Rn.6686 ENTREZGENE
UniProt COX5B_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Cox5b  cytochrome c oxidase subunit 5B  Cox5b  cytochrome c oxidase subunit Vb  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Cox5b  cytochrome c oxidase subunit Vb      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cox5b  cytochrome c oxidase subunit Vb      Symbol and Name status set to provisional 70820 PROVISIONAL