Mt-cyb (mitochondrially encoded cytochrome b) - Rat Genome Database

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Gene: Mt-cyb (mitochondrially encoded cytochrome b) Rattus norvegicus
Analyze
Symbol: Mt-cyb
Name: mitochondrially encoded cytochrome b
RGD ID: 620081
Description: Predicted to enable ubiquinol-cytochrome-c reductase activity. Involved in several processes, including electron transport coupled proton transport; response to cobalamin; and response to glucagon. Located in mitochondrial inner membrane. Is integral component of mitochondrial inner membrane. Part of protein-containing complex. Biomarker of thyrotoxicosis; type 2 diabetes mellitus; and visual epilepsy. Human ortholog(s) of this gene implicated in ovarian carcinoma and urinary bladder cancer. Orthologous to human MT-CYB (mitochondrially encoded cytochrome b); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; aflatoxin B1; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cytb; cytochrome b; cytochrome b, mitochondrial; Mt-cytb
RGD Orthologs
Human
Mouse
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2MT14,136 - 15,278 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblMT14,136 - 15,278 (+)Ensembl
Rnor_6.0MT14,136 - 15,278 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblMT14,136 - 15,278 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0MT14,136 - 15,278 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4MT14,136 - 15,278 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic MapMT NCBI


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
1. Acharya MM and Katyare SS, Exp Neurol. 2005 Mar;192(1):79-88.
2. Cai C, etal., J Huazhong Univ Sci Technolog Med Sci. 2008 Apr;28(2):207-10. Epub 2008 May 15.
3. Costa LE, etal., Am J Physiol. 1993 Jun;264(6 Pt 1):C1395-400.
4. Dasgupta S, etal., Cancer Res. 2008 Feb 1;68(3):700-6.
5. Gadaleta G, etal., J Mol Evol 1989 Jun;28(6):497-516.
6. Gaikwad AS, etal., Biochim Biophys Acta. 1990 Jun 26;1017(3):242-50.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gellerfors P, etal., Eur J Biochem. 1981 Apr;115(2):275-8.
9. Gupte S, etal., Proc Natl Acad Sci U S A. 1984 May;81(9):2606-10.
10. Katyare SS and Rajan RR, Comp Biochem Physiol C Pharmacol Toxicol Endocrinol. 1995 Nov;112(3):353-7.
11. KEGG
12. Kimura S, etal., Biochem Biophys Res Commun. 1984 Feb 29;119(1):212-9.
13. Klohn PC, etal., FEBS Lett. 1996 Jul 8;389(3):233-7.
14. Koyama H, etal., Biochem Biophys Res Commun. 1998 Feb 24;243(3):858-61.
15. Leeds FS and Brass EP, J Biol Chem. 1994 Feb 11;269(6):3947-51.
16. Levenson CW, etal., Biol Trace Elem Res. 1999 Nov;70(2):149-64.
17. Liu VW, etal., Cancer Res. 2001 Aug 15;61(16):5998-6001.
18. Lund BO, etal., Biochem Pharmacol. 1993 May 25;45(10):2017-24.
19. MGD data from the GO Consortium
20. Miccadei S and Floridi A, Chem Biol Interact. 1993 Dec;89(2-3):159-67.
21. Morimoto T, etal., Clin Sci (Lond). 1988 May;74(5):485-9.
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. Nishio Y, etal., Ann N Y Acad Sci. 2004 Apr;1011:78-85.
24. Padma P and Setty OH, Indian J Biochem Biophys. 1997 Jun;34(3):296-301.
25. Price BD and Brand MD, Biochem J. 1982 Aug 15;206(2):419-21.
26. RGD automated data pipeline
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Sajan MP, etal., Toxicol Lett. 1995 Oct;80(1-3):55-60.
30. Salazar I, etal., Toxicol Appl Pharmacol. 2004 Jul 1;198(1):1-10.
31. Satav JG and Katyare SS, Mol Cell Endocrinol. 1982 Oct;28(2):173-89.
32. Serizawa K, etal., Biochem Genet 2000 Feb;38(1-2):27-40.
33. Serradas P, etal., Endocrinology. 1995 Dec;136(12):5623-31.
34. Suzuki H, etal., Mol Phylogenet Evol 2000 Apr;15(1):15-24.
35. Tavakoli H and Mela L, Infect Immun. 1982 Nov;38(2):536-41.
36. Thayer WS and Rubin E, J Biol Chem. 1981 Jun 25;256(12):6090-7.
37. Tsuji E, etal., Biochem Biophys Res Commun 1996 Dec 4;229(1):134-8.
38. Van Itallie CM, etal., Am J Physiol. 1993 Sep;265(3 Pt 1):C712-9.
39. Vlessis AA, etal., J Neurochem. 1990 Apr;54(4):1412-8.
40. Wang XM, etal., Burns Incl Therm Inj. 1986 Oct;12(7):461-4.
41. Williams JN Jr, etal., J Nutr. 1966 Dec;90(4):400-4.
Additional References at PubMed
PMID:25318588   PMID:26316108  


Genomics

Comparative Map Data
Mt-cyb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2MT14,136 - 15,278 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblMT14,136 - 15,278 (+)Ensembl
Rnor_6.0MT14,136 - 15,278 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblMT14,136 - 15,278 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0MT14,136 - 15,278 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4MT14,136 - 15,278 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic MapMT NCBI
MT-CYB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblMT14,747 - 15,887 (+)EnsemblGRCh38hg38GRCh38
GRCh38MT14,747 - 15,887 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37MT14,747 - 15,887 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36MT14,748 - 15,882 (+)NCBINCBI36hg18NCBI36
mt-Cytb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39MT14,145 - 15,288 (+)NCBIGRCm39mm39
GRCm39 EnsemblMT14,145 - 15,288 (+)Ensembl
GRCm38MT14,145 - 15,288 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblMT14,145 - 15,288 (+)EnsemblGRCm38mm10GRCm38
MGSCv37MT14,145 - 15,288 (+)NCBIGRCm37mm9NCBIm37
MT-CYB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1MT14,183 - 15,322 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblMT14,183 - 15,322 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaMT14,183 - 15,322 (+)NCBI
CYTB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblMT15,342 - 16,481 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1MT15,342 - 16,481 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2MT15,342 - 16,481 (+)NCBISscrofa10.2Sscrofa10.2susScr3

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:56
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000042098
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 9 48 63 39 5 33 1 4 66 31 33 3 1
Medium 1 16 8 14 8 7 7 8 4 8 8 7
Low
Below cutoff

Sequence

Nucleotide Sequences
GenBank Nucleotide AY172581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ439839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ439842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ439843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ439844 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ842269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ842270 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ842271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ842272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ842273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ842277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ842278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ842279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU592980 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HM031677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HM031678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HM031679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HM031680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HM031681 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HQ157799 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ939360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ939361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM009112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM009113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM114604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM114605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM114606 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM114607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM114608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM577635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM657952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM657953 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY356105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY356130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY356138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY356141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000042098   ⟹   ENSRNOP00000047954
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblMT14,136 - 15,278 (+)Ensembl
Rnor_6.0 EnsemblMT14,136 - 15,278 (+)Ensembl
Protein Sequences
Protein RefSeqs YP_665641 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAN77606 (Get FASTA)   NCBI Sequence Viewer  
  ABD83985 (Get FASTA)   NCBI Sequence Viewer  
  ABD83988 (Get FASTA)   NCBI Sequence Viewer  
  ABD83989 (Get FASTA)   NCBI Sequence Viewer  
  ABD83990 (Get FASTA)   NCBI Sequence Viewer  
  ACP50370 (Get FASTA)   NCBI Sequence Viewer  
  ACY82371 (Get FASTA)   NCBI Sequence Viewer  
  ACY82372 (Get FASTA)   NCBI Sequence Viewer  
  ACY82373 (Get FASTA)   NCBI Sequence Viewer  
  ACY82374 (Get FASTA)   NCBI Sequence Viewer  
  ACY82375 (Get FASTA)   NCBI Sequence Viewer  
  ACY82379 (Get FASTA)   NCBI Sequence Viewer  
  ACY82380 (Get FASTA)   NCBI Sequence Viewer  
  ACY82381 (Get FASTA)   NCBI Sequence Viewer  
  ADF97314 (Get FASTA)   NCBI Sequence Viewer  
  ADF97315 (Get FASTA)   NCBI Sequence Viewer  
  ADF97316 (Get FASTA)   NCBI Sequence Viewer  
  ADF97317 (Get FASTA)   NCBI Sequence Viewer  
  ADF97319 (Get FASTA)   NCBI Sequence Viewer  
  ADF97321 (Get FASTA)   NCBI Sequence Viewer  
  ADF97327 (Get FASTA)   NCBI Sequence Viewer  
  ADF97329 (Get FASTA)   NCBI Sequence Viewer  
  ADF97333 (Get FASTA)   NCBI Sequence Viewer  
  ADF97335 (Get FASTA)   NCBI Sequence Viewer  
  ADF97338 (Get FASTA)   NCBI Sequence Viewer  
  ADO17043 (Get FASTA)   NCBI Sequence Viewer  
  AEB66386 (Get FASTA)   NCBI Sequence Viewer  
  AEB66387 (Get FASTA)   NCBI Sequence Viewer  
  AEB66388 (Get FASTA)   NCBI Sequence Viewer  
  AEB66389 (Get FASTA)   NCBI Sequence Viewer  
  AEB66390 (Get FASTA)   NCBI Sequence Viewer  
  AIU45587 (Get FASTA)   NCBI Sequence Viewer  
  AIU45600 (Get FASTA)   NCBI Sequence Viewer  
  AIU45613 (Get FASTA)   NCBI Sequence Viewer  
  AIU45626 (Get FASTA)   NCBI Sequence Viewer  
  AIU45665 (Get FASTA)   NCBI Sequence Viewer  
  AIU45678 (Get FASTA)   NCBI Sequence Viewer  
  AIU45691 (Get FASTA)   NCBI Sequence Viewer  
  AIU45704 (Get FASTA)   NCBI Sequence Viewer  
  AIU45717 (Get FASTA)   NCBI Sequence Viewer  
  AIY51554 (Get FASTA)   NCBI Sequence Viewer  
  AIZ58334 (Get FASTA)   NCBI Sequence Viewer  
  AIZ58347 (Get FASTA)   NCBI Sequence Viewer  
  ARS45303 (Get FASTA)   NCBI Sequence Viewer  
  ARS45328 (Get FASTA)   NCBI Sequence Viewer  
  ARS45336 (Get FASTA)   NCBI Sequence Viewer  
  ARS45339 (Get FASTA)   NCBI Sequence Viewer  
  P00159 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000047954   ⟸   ENSRNOT00000042098
Protein Domains
CYTB_CTER   CYTB_NTER

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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)
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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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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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/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620081 AgrOrtholog
Ensembl Genes ENSRNOG00000031766 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000047954 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000042098 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.810.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cyt_b/b6_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_b/b6_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_b/b6_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cytb/b6-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cytochrome_b UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Di-haem_cyt_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:26192 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 26192 ENTREZGENE
Pfam Cytochrom_B_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cytochrome_B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Mt-cyb PhenoGen
PIRSF COB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CYTB_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CYTB_NTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF81342 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81648 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CYB_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q8HIC4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-19 Mt-cyb  mitochondrially encoded cytochrome b  Mt-cytb  mitochondrially encoded cytochrome b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-02-12 Mt-cytb  mitochondrially encoded cytochrome b  Mt-cyb  mitochondrially encoded cytochrome b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-08-29 Mt-cyb  mitochondrially encoded cytochrome b  mt-Cytb  cytochrome b, mitochondrial  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-11 mt-Cytb  cytochrome b, mitochondrial      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 mt-Cytb  cytochrome b, mitochondrial      Symbol and Name status set to provisional 70820 PROVISIONAL