Cyb5a (cytochrome b5 type A) - Chinchilla Research Resource Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Cyb5a (cytochrome b5 type A) Rattus norvegicus
Analyze
Symbol: Cyb5a
Name: cytochrome b5 type A
CRRD ID: 620558
Description: Predicted to have electron transfer activity; enzyme binding activity; and heme binding activity. Involved in response to cadmium ion. Localizes to endoplasmic reticulum and endoplasmic reticulum membrane. Biomarker of pyelonephritis. Human ortholog(s) of this gene implicated in methemoglobinemia. Orthologous to human CYB5A (cytochrome b5 type A); INTERACTS WITH (+)-schisandrin B; 1,2,4-trichlorobenzene; 1,2-dimethylhydrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cyb5; cytochrome b-5; cytochrome b5; cytochrome b5 type A (microsomal); MGC108694
Orthologs:
Homo sapiens (human) : CYB5A (cytochrome b5 type A)  HGNC  Alliance
Mus musculus (house mouse) : Cyb5a (cytochrome b5 type A (microsomal))  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : LOC102012144 (cytochrome b5)
Pan paniscus (bonobo/pygmy chimpanzee) : LOC100968898 (cytochrome b5)
Canis lupus familiaris (dog) : CYB5A (cytochrome b5 type A (microsomal))
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : LOC101960314 (cytochrome b5)
Sus scrofa (pig) : CYB5A (cytochrome b5 type A)
Chlorocebus sabaeus (African green monkey) : CYB5A (cytochrome b5 type A)
Heterocephalus glaber (naked mole-rat) : LOC101711375 (cytochrome b5)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01881,694,818 - 81,726,821 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1881,694,808 - 81,726,821 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01880,739,215 - 80,770,883 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41881,415,972 - 81,452,606 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11881,489,421 - 81,526,056 (+)NCBI
Celera1876,829,153 - 76,861,638 (+)NCBICelera
Cytogenetic Map18q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2,4-trichlorobenzene  (EXP)
1,2-dimethylhydrazine  (EXP,ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrabromodibenzodioxine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
2-methylcholine  (ISO)
2-tert-butylhydroquinone  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-nitroquinoline N-oxide  (EXP)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
alfentanil  (ISO)
alpha-hexachlorocyclohexane  (EXP)
ammonium chloride  (EXP)
anthracen-2-amine  (ISO)
aristolochic acid  (EXP)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
calcidiol  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
cetrorelix  (ISO)
chlorzoxazone  (ISO)
cisplatin  (EXP,ISO)
citral  (EXP)
clofibrate  (EXP)
clofibric acid  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cyproconazole  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP)
diethyl maleate  (ISO)
diiodine  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
epoxiconazole  (ISO)
ethanol  (EXP)
ferroheme b  (ISO)
fipronil  (EXP,ISO)
flavonoids  (EXP)
flutamide  (EXP)
genistein  (EXP,ISO)
geranial  (EXP)
geraniol  (EXP)
halothane  (ISO)
heme b  (ISO)
hesperetin  (EXP)
hydrogen peroxide  (ISO)
hydroxylamine  (ISO)
indometacin  (EXP,ISO)
isoniazide  (EXP)
isotretinoin  (ISO)
lamivudine  (ISO)
limonene  (EXP)
lycopene  (ISO)
m-xylene  (EXP)
Malotilate  (ISO)
mercury dibromide  (ISO)
methapyrilene  (EXP)
methoxychlor  (EXP)
methylmercury chloride  (ISO)
metoprolol  (ISO)
N,N-diethyl-m-toluamide  (ISO)
N-Nitrosodi-n-propylamine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
NADP zwitterion  (ISO)
NADP(+)  (ISO)
naphthalene  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (EXP,ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
progesterone  (ISO)
propiconazole  (ISO)
Propiverine  (EXP)
quercetin  (ISO)
rac-lactic acid  (ISO)
Rebamipide  (EXP)
resveratrol  (ISO)
SB 431542  (ISO)
silibinin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium perchlorate  (EXP)
Sudan I  (EXP,ISO)
sunitinib  (ISO)
tangeretin  (EXP)
taurine  (EXP)
testosterone  (ISO)
testosterone enanthate  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
tetracycline  (ISO)
thapsigargin  (ISO)
topotecan  (EXP,ISO)
tributylstannane  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
zidovudine  (EXP,ISO)
zinc atom  (EXP)
zinc(0)  (EXP)
zingerone  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. Banci L, etal., J Biol Inorg Chem 2002 Apr;7(4-5):416-26.
2. Braga Ade F, etal., Acta Cir Bras. 2008 Jul-Aug;23(4):343-7.
3. Choury D, etal., J Clin Invest. 1981 Jan;67(1):149-55.
4. Cowley AB, etal., Biochemistry 2002 Oct 1;41(39):11566-81.
5. Davis CA, etal., Arch Biochem Biophys 2002 Apr 1;400(1):63-75.
6. Fermo E, etal., Blood Cells Mol Dis. 2008 Jul-Aug;41(1):50-5. doi: 10.1016/j.bcmd.2008.02.002. Epub 2008 Mar 17.
7. Furukawa Y, etal., J Am Chem Soc. 2002 Apr 17;124(15):4008-19.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Gupta SK, etal., Am J Gastroenterol. 1999 Jul;94(7):1808-12.
11. Karimov KhIa, etal., Ukr Biokhim Zh. 1998 Jul-Aug;70(4):139-42.
12. Kikuchi M, etal., J Biol Chem. 2004 Jan 2;279(1):421-8. Epub 2003 Oct 15.
13. Kobayashi Y, etal., Blood. 1990 Apr 1;75(7):1408-13.
14. MGD data from the GO Consortium
15. Murugan RS, etal., Free Radic Res. 2008 Oct;42(10):873-84.
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. OMIM Disease Annotation Pipeline
18. Plewka A, etal., Arch Toxicol. 2004 Apr;78(4):194-200. Epub 2003 Nov 1.
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. RGD comprehensive gene curation
22. Tanaka S, etal., J Biochem (Tokyo). 2003 Feb;133(2):247-51.
23. Yoo M Biochem Biophys Res Commun 1997 Jul 30;236(3):641-2.
Additional References at PubMed
PMID:1396600   PMID:2752049   PMID:6840088   PMID:7093287   PMID:8639599   PMID:9363779   PMID:9425037   PMID:9622481   PMID:11294656   PMID:12477932   PMID:12668680   PMID:14563830  
PMID:14651853   PMID:15379561   PMID:15489334   PMID:15680923   PMID:16807901   PMID:18398853   PMID:18398854   PMID:19817686   PMID:19946888   PMID:20511233   PMID:22375059   PMID:23376485  
PMID:29227865   PMID:31006538  


Genomics

Comparative Map Data
Cyb5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01881,694,818 - 81,726,821 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1881,694,808 - 81,726,821 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01880,739,215 - 80,770,883 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41881,415,972 - 81,452,606 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11881,489,421 - 81,526,056 (+)NCBI
Celera1876,829,153 - 76,861,638 (+)NCBICelera
Cytogenetic Map18q12.3NCBI
CYB5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1874,250,846 - 74,291,973 (-)EnsemblGRCh38hg38GRCh38
GRCh381874,250,846 - 74,291,980 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371871,920,527 - 71,959,251 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361870,071,507 - 70,110,201 (-)NCBINCBI36hg18NCBI36
Build 341870,071,507 - 70,110,201NCBI
Celera1868,787,880 - 68,826,566 (-)NCBI
Cytogenetic Map18q22.3NCBI
HuRef1868,652,932 - 68,691,654 (-)NCBIHuRef
CHM1_11871,915,750 - 71,954,471 (-)NCBICHM1_1
Cyb5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391884,869,463 - 84,897,996 (+)NCBI
GRCm381884,851,338 - 84,879,871 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1884,838,704 - 84,879,871 (+)EnsemblGRCm38mm10GRCm38
MGSCv371885,020,806 - 85,049,255 (+)NCBIGRCm37mm9NCBIm37
MGSCv361884,985,607 - 85,014,056 (+)NCBImm8
Celera1885,916,355 - 85,944,796 (+)NCBICelera
Cytogenetic Map18E4NCBI
cM Map1857.53NCBI
LOC102012144
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540257,701,931 - 57,739,163 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540257,701,931 - 57,739,163 (-)NCBIChiLan1.0ChiLan1.0
LOC100968898
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11870,919,329 - 70,957,873 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1870,919,617 - 70,957,732 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01867,638,406 - 67,677,111 (-)NCBIMhudiblu_PPA_v0panPan3
CYB5A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl15,070,865 - 5,106,932 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.115,070,817 - 5,106,668 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
LOC101960314
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366164,176,576 - 4,210,276 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CYB5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1149,737,571 - 149,783,623 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11149,737,584 - 149,773,222 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21165,902,066 - 165,937,612 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CYB5A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl185,599,206 - 5,640,012 (+)Ensembl
ChlSab1.1185,599,198 - 5,636,620 (+)NCBI
LOC101711375
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248066,399,708 - 6,434,667 (+)NCBI

Position Markers
RH140952  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01813,903,992 - 13,904,208NCBIRnor6.0
Rnor_5.01813,686,964 - 13,687,180UniSTSRnor5.0
RGSC_v3.41814,598,173 - 14,598,389UniSTSRGSC3.4
Celera1814,157,870 - 14,158,086UniSTS
Cytogenetic Map18q12.3UniSTS
Cytogenetic Map18p12UniSTS
RH 3.4 Map18167.4UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
CRRD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181569587287080053Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181569587287080053Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)182028575887080053Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260373687074531Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182596102681761656Rat
2303120Mamtr8Mammary tumor resistance QTL 80.001mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)183267035287080053Rat
631518Bw11Body weight QTL 112.8body mass (VT:0001259)body weight (CMO:0000012)183822191983221919Rat
61367Iddm4Insulin dependent diabetes mellitus QTL 42.330.0074blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)184037576985375769Rat
6893683Bw110Body weight QTL 1102.70.002body mass (VT:0001259)body weight (CMO:0000012)184500219488201929Rat
1598826Anxrr20Anxiety related response QTL 203.04body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)184631947688201929Rat
9589041Epfw12Epididymal fat weight QTL 1217.080.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)184913092088201929Rat
8694432Bw165Body weight QTL 1653.810.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)184913092088201929Rat
8694366Abfw8Abdominal fat weight QTL 86.380.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)184913092088201929Rat
2303571Bw92Body weight QTL 923body mass (VT:0001259)body weight (CMO:0000012)185137581688201929Rat
2303584Gluco55Glucose level QTL 552blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185137581688201929Rat
738008Hcar14Hepatocarcinoma resistance QTL 144.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion number (CMO:0001462)185303349487080053Rat
1558649Bw58Body weight QTL 583.40.0005body mass (VT:0001259)body weight (CMO:0000012)185744867888201929Rat
6893359Bw103Body weight QTL 1031.20.12body mass (VT:0001259)body weight (CMO:0000012)185744867888201929Rat
6893368Bw107Body weight QTL 1070.30.5body mass (VT:0001259)body weight (CMO:0000012)185744867888201929Rat
1298072Cia26Collagen induced arthritis QTL 263.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)185819630088201929Rat
6903356Bp354Blood pressure QTL 3544.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)186198564888201929Rat
724542Kidm2Kidney mass QTL 22.6kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)186300981288201929Rat
634333Pia19Pristane induced arthritis QTL 193.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)187715130183366399Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:197
Count of miRNA genes:141
Interacting mature miRNAs:149
Transcripts:ENSRNOT00000020446, ENSRNOT00000064490
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 25 23 17
Medium 3 43 40 24 19 24 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020446   ⟹   ENSRNOP00000020446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1881,694,808 - 81,726,821 (+)Ensembl
RefSeq Acc Id: NM_022245   ⟹   NP_071581
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01881,694,818 - 81,726,821 (+)NCBI
Rnor_5.01880,739,215 - 80,770,883 (+)NCBI
RGSC_v3.41881,415,972 - 81,452,606 (+)RGD
Celera1876,829,153 - 76,861,638 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_071581   ⟸   NM_022245
- UniProtKB: P00173 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000020446   ⟸   ENSRNOT00000020446
Protein Domains
Cytochrome b5 heme-binding

Transcriptome

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

Promoters
RGD ID:13700895
Promoter ID:EPDNEW_R11419
Type:initiation region
Name:Cyb5a_1
Description:cytochrome b5 type A
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_6.01881,694,809 - 81,694,869EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
18 81713792 81713793 C T snv MR/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
18 81434946 81434947 C T snv MR/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620558 AgrOrtholog
Ensembl Genes ENSRNOG00000015205 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000020446 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000020446 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.10.120.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7322141 IMAGE-MGC_LOAD
InterPro Cyt_B5-like_heme/steroid-bd UniProtKB/Swiss-Prot
  Cyt_B5-like_heme/steroid_sf UniProtKB/Swiss-Prot
  Cyt_B5_heme-BS UniProtKB/Swiss-Prot
KEGG Report rno:64001 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108694 IMAGE-MGC_LOAD
NCBI Gene 64001 ENTREZGENE
Pfam Cyt-b5 UniProtKB/Swiss-Prot
PharmGKB CYB5A RGD
PhenoGen Cyb5a PhenoGen
PRINTS CYTOCHROMEB5 UniProtKB/Swiss-Prot
PROSITE CYTOCHROME_B5_1 UniProtKB/Swiss-Prot
  CYTOCHROME_B5_2 UniProtKB/Swiss-Prot
SMART Cyt-b5 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF55856 UniProtKB/Swiss-Prot
UniGene Rn.1055 ENTREZGENE
UniProt CYB5_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O35768 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-13 Cyb5a  cytochrome b5 type A  Cyb5a  cytochrome b5 type A (microsomal)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Cyb5a  cytochrome b5 type A (microsomal)  Cyb5  cytochrome b-5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Cyb5  cytochrome b-5    cytochrome b5  Name updated 1299863 APPROVED
2002-08-07 Cyb5  cytochrome b5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains both heme and FAD prosthetic groups 632262