Cox4i1 (cytochrome c oxidase subunit 4i1) - Rat Genome Database

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Gene: Cox4i1 (cytochrome c oxidase subunit 4i1) Rattus norvegicus
Analyze
Symbol: Cox4i1
Name: cytochrome c oxidase subunit 4i1
RGD ID: 68374
Description: Predicted to have cytochrome-c oxidase activity. Involved in response to nutrient. Predicted to localize to cytosol; mitochondrial respiratory chain complex IV; and nucleoplasm. Biomarker of protein-energy malnutrition. Human ortholog(s) of this gene implicated in cytochrome-c oxidase deficiency disease. Orthologous to human COX4I1 (cytochrome c oxidase subunit 4I1); PARTICIPATES IN Alzheimer's disease pathway; Huntington's disease pathway; oxidative phosphorylation pathway; INTERACTS WITH 3-methylcholanthrene; 5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: COX IV-1; Cox4; Cox4a; cytochrome c oxidase polypeptide IV; cytochrome c oxidase subunit 4 isoform 1, mitochondrial; cytochrome c oxidase subunit IV; cytochrome c oxidase subunit IV isoform 1; cytochrome c oxidase subunit IVa; cytochrome c oxidase, subunit 4a; cytochrome c oxidase, subunit IV; cytochrome c oxidase, subunit IVa; MGC105470
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21948,721,680 - 48,727,920 (+)NCBI
Rnor_6.0 Ensembl1954,245,950 - 54,252,225 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01954,245,958 - 54,252,198 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01964,965,282 - 64,971,577 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41951,023,960 - 51,030,200 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11951,028,840 - 51,035,081 (+)NCBI
Celera1947,973,554 - 47,979,795 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-dexrazoxane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrophenol  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3-methylcholanthrene  (EXP,ISO)
3-nitropropanoic acid  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
8-bromo-3',5'-cyclic GMP  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alloxan  (EXP)
AM-251  (EXP)
amiodarone  (EXP)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzbromarone  (EXP)
bisphenol A  (EXP)
cadmium atom  (ISO)
calcitriol  (EXP)
capsaicin  (EXP)
CCCP  (ISO)
chloropicrin  (ISO)
chloroquine  (ISO)
clofibrate  (EXP)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (EXP)
cyclosporin A  (ISO)
D-glucose  (ISO)
desferrioxamine B  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (EXP)
disodium selenite  (ISO)
doxorubicin  (ISO)
ebselen  (ISO)
Erythropoietin  (ISO)
ethanol  (EXP)
flutamide  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
glucose  (ISO)
hydrogen peroxide  (ISO)
hydroxytyrosol  (EXP)
L-ethionine  (EXP)
limonene  (EXP)
lipopolysaccharide  (ISO)
LY294002  (ISO)
melatonin  (ISO)
methotrexate  (ISO)
Mitotane  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nitric oxide  (ISO)
omeprazole  (EXP)
ozone  (EXP,ISO)
paracetamol  (ISO)
paraquat  (EXP)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP)
phenylephrine  (EXP)
pirinixic acid  (EXP)
progesterone  (ISO)
pyrogallol  (ISO)
quercetin  (EXP)
resveratrol  (EXP,ISO)
rotenone  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
sodium arsenite  (EXP)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
sodium hydrogensulfite  (EXP)
sodium nitrate  (ISO)
sulfur dioxide  (EXP)
T-2 toxin  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
toluene  (EXP)
triptonide  (ISO)
tungsten  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:2165254   PMID:7601105   PMID:11940593   PMID:12270909   PMID:12477932   PMID:12506326   PMID:12865426   PMID:12910269   PMID:14651853   PMID:15489334   PMID:15565177   PMID:16103131  
PMID:17923681   PMID:18408135   PMID:18614015   PMID:19393246   PMID:19946888   PMID:20833797   PMID:20959514   PMID:21416482   PMID:22396533   PMID:22555453   PMID:22773120   PMID:22783020  
PMID:23376485   PMID:23818984   PMID:24610532   PMID:25002582   PMID:26746385   PMID:26767982   PMID:28161363   PMID:28376086   PMID:29476059   PMID:31505169  


Genomics

Comparative Map Data
Cox4i1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21948,721,680 - 48,727,920 (+)NCBI
Rnor_6.0 Ensembl1954,245,950 - 54,252,225 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01954,245,958 - 54,252,198 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01964,965,282 - 64,971,577 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41951,023,960 - 51,030,200 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11951,028,840 - 51,035,081 (+)NCBI
Celera1947,973,554 - 47,979,795 (+)NCBICelera
Cytogenetic Map19q12NCBI
COX4I1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1685,798,633 - 85,807,054 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1685,798,633 - 85,807,068 (+)EnsemblGRCh38hg38GRCh38
GRCh381685,799,695 - 85,807,068 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371685,833,301 - 85,840,674 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361684,390,697 - 84,398,109 (+)NCBINCBI36hg18NCBI36
Build 341684,390,696 - 84,398,109NCBI
Celera1670,136,278 - 70,143,686 (+)NCBI
Cytogenetic Map16q24.1NCBI
HuRef1671,574,688 - 71,582,119 (+)NCBIHuRef
CHM1_11687,244,717 - 87,252,149 (+)NCBICHM1_1
Cox4i1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398121,394,964 - 121,400,948 (+)NCBIGRCm39mm39
GRCm39 Ensembl8121,394,961 - 121,400,946 (+)Ensembl
GRCm388120,668,225 - 120,674,209 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8120,668,222 - 120,674,207 (+)EnsemblGRCm38mm10GRCm38
MGSCv378123,192,190 - 123,198,109 (+)NCBIGRCm37mm9NCBIm37
MGSCv368123,554,281 - 123,572,260 (+)NCBImm8
Celera8124,884,148 - 124,890,066 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map869.99NCBI
LOC102020379
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955541884,988 - 890,890 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955541885,824 - 890,824 (+)NCBIChiLan1.0ChiLan1.0
LOC100969890
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11685,805,595 - 85,812,851 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1685,805,611 - 85,812,851 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01666,467,259 - 66,474,652 (+)NCBIMhudiblu_PPA_v0panPan3
COX4I1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1566,883,730 - 66,891,734 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl566,883,732 - 66,891,500 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha566,899,917 - 66,907,747 (-)NCBI
ROS_Cfam_1.0567,112,369 - 67,120,207 (-)NCBI
UMICH_Zoey_3.1567,133,830 - 67,141,650 (-)NCBI
UNSW_CanFamBas_1.0566,967,910 - 66,975,726 (-)NCBI
UU_Cfam_GSD_1.0567,382,851 - 67,390,678 (-)NCBI
LOC101971634
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934926,937,176 - 26,943,452 (-)NCBI
SpeTri2.0NW_0049366412,690,723 - 2,695,230 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COX4I1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl63,131,019 - 3,240,221 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.163,131,017 - 3,137,619 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.263,453,560 - 3,458,877 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103233412
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1571,207,509 - 71,214,976 (+)NCBI
ChlSab1.1 Ensembl571,206,941 - 71,215,034 (+)Ensembl
LOC101705610
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247462,187,443 - 2,193,874 (+)NCBI

Position Markers
RH127425  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01954,250,957 - 54,252,044NCBIRnor6.0
Rnor_5.01964,970,334 - 64,971,421UniSTSRnor5.0
RGSC_v3.41951,028,959 - 51,030,046UniSTSRGSC3.4
Celera389,339,647 - 89,339,855UniSTS
Celera1947,978,554 - 47,979,641UniSTS
RH 3.4 Map81190.8UniSTS
Cytogenetic Map19q12UniSTS
RH125550  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01954,250,443 - 54,250,553NCBIRnor6.0
Rnor_6.0393,832,685 - 93,832,794NCBIRnor6.0
Rnor_5.01964,969,820 - 64,969,930UniSTSRnor5.0
RGSC_v3.41951,028,445 - 51,028,555UniSTSRGSC3.4
RGSC_v3.4389,170,772 - 89,170,882UniSTSRGSC3.4
Celera1947,978,040 - 47,978,150UniSTS
Celera389,339,868 - 89,339,978UniSTS
Cytogenetic Map3q32UniSTS
Cytogenetic Map19q12UniSTS
Cox4a  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01954,251,003 - 54,252,111NCBIRnor6.0
Rnor_5.01964,970,380 - 64,971,488UniSTSRnor5.0
RGSC_v3.41951,029,005 - 51,030,113UniSTSRGSC3.4
Celera1947,978,600 - 47,979,708UniSTS
Cytogenetic Map19q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir338rno-miR-338-3pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Western blotFunctional MTI19020050

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:43
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000024033
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 8 27 3 6 9 1
Medium 1 22 57 41 19 41 8 8 68 26 40 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024033   ⟹   ENSRNOP00000024033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1954,245,950 - 54,252,225 (+)Ensembl
RefSeq Acc Id: NM_017202   ⟹   NP_058898
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21948,721,680 - 48,727,920 (+)NCBI
Rnor_6.01954,245,958 - 54,252,198 (+)NCBI
Rnor_5.01964,965,282 - 64,971,577 (+)NCBI
RGSC_v3.41951,023,960 - 51,030,200 (+)RGD
Celera1947,973,554 - 47,979,795 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058898   ⟸   NM_017202
- Peptide Label: precursor
- UniProtKB: P10888 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024033   ⟸   ENSRNOT00000024033

Transcriptome

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

Promoters
RGD ID:13701197
Promoter ID:EPDNEW_R11720
Type:initiation region
Name:Cox4i1_1
Description:cytochrome c oxidase subunit 4i1
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_6.01954,245,981 - 54,246,041EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 64966457 64966458 C T snv ZFDM (KyushuU)
19 64969815 64969816 A G snv Crl:SD (UDEL), IS/Kyo (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), LEC/Tj (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU), SDLEF7/Barth (UDEL), BN/SsNSlc (KyushuU)
19 64969905 64969906 C T snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), BN/SsNSlc (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), KFRS3B/Kyo (KyushuU), ZFDM (KyushuU)
19 64970364 64970365 G A snv NIG-III/Hok (KyushuU), HWY/Slc (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), SDLEF7/Barth (UDEL), IS-Tlk/Kyo (KyushuU), F344/DuCrlCrlj (KyushuU), LEC/Tj (KyushuU)
19 64971399 64971400 G A snv SS/JrHsdMcwi (MCW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), IS/Kyo (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), BN/SsNSlc (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), ZFDM (KyushuU), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 54247080 54247081 C T snv ACI/EurMcwi (MCW), MNS/Gib (RGD), LN/MavRrrc (RGD), MR/N (MCW), CDS, CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW)
19 54250438 54250439 A G snv SHR/NHsd (RGD), SBN/Ygl (MCW), LEW/Crl (RGD), ACI/EurMcwi (MCW), SR/JrHsd (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW)
19 54250528 54250529 C T snv SR/JrHsd (MCW), SBN/Ygl (MCW), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), CDS, SBH/Ygl (MCW), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), CDR, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW)
19 54250987 54250988 G A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), CDS, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), CDR
19 54252022 54252023 G A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), CDR, CDS, ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), MR/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), LEW/Crl (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 51025082 51025083 C T snv MR/N (KNAW)
19 51030024 51030025 G A snv GH/OmrMcwi (MCW), BN/NHsdMcwi (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), M520/N (KNAW), MR/N (KNAW), WN/N (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), COP/CrCrl (MCW & UW), SHRSP/Gcrc (MDC), ACI/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68374 AgrOrtholog
Ensembl Genes ENSRNOG00000017817 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000024033 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000024033 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.442.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7317602 IMAGE-MGC_LOAD
InterPro Cyt_c_oxidase_su4 UniProtKB/Swiss-Prot
  Cyt_c_oxidase_su4_fam UniProtKB/Swiss-Prot
  Cyt_c_oxidase_su4_sf UniProtKB/Swiss-Prot
KEGG Report rno:29445 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105470 IMAGE-MGC_LOAD
NCBI Gene 29445 ENTREZGENE
PANTHER PTHR10707 UniProtKB/Swiss-Prot
Pfam COX4 UniProtKB/Swiss-Prot
PhenoGen Cox4i1 PhenoGen
PRINTS CYTCOXIDASE4 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF81406 UniProtKB/Swiss-Prot
UniProt COX41_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Cox4i1  cytochrome c oxidase subunit 4i1  Cox4i1  cytochrome c oxidase subunit IV isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Cox4i1  cytochrome c oxidase subunit IV isoform 1  Cox4a  cytochrome c oxidase, subunit 4a  Symbol and Name updated 1299863 APPROVED
2002-06-10 Cox4a  cytochrome c oxidase, subunit 4a      Name updated 70584 APPROVED
2001-12-12 Cox4a  cytochrome c oxidase, subunit IVa      Symbol and Name updated to reflect Human and Mouse nomenclature 69665 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in all tissues 632600
gene_transcript 5' region contains multiple transcription start sites mapped to within an approximately 50 bp region and a GC-rich promoter lacking typical CCAAT or TATAA sequences 632600