Mt-nd1 (mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1) - Rat Genome Database

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Gene: Mt-nd1 (mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1) Rattus norvegicus
Analyze
Symbol: Mt-nd1
Name: mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1
RGD ID: 620555
Description: Predicted to enable NADH dehydrogenase (ubiquinone) activity. Predicted to contribute to NADH dehydrogenase activity. Involved in response to drug; response to hydroperoxide; and response to organic cyclic compound. Located in dendrite; mitochondrion; and neuronal cell body. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in several diseases, including MELAS syndrome; neurodegenerative disease (multiple); optic nerve disease (multiple); toxic shock syndrome; and type 2 diabetes mellitus. Orthologous to human MT-ND1 (mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1); INTERACTS WITH acetylsalicylic acid; aconitine; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: mitochondrially encoded NADH dehydrogenase 1; NADH dehydrogenase 1, mitochondrial; NADH dehydrogenase subunit 1; Nd1
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
mRatBN7.2MT2,740 - 3,694 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblMT2,740 - 3,694 (+)Ensembl
Rnor_6.0MT2,740 - 3,694 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblMT2,740 - 3,694 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0MT2,740 - 3,694 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4MT2,740 - 3,694 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic MapMT NCBI


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Black GC, etal., Br J Ophthalmol. 1996 Oct;80(10):915-7.
2. Blokhin A, etal., J Mol Neurosci. 2008 Jul;35(3):283-7. Epub 2008 Jun 20.
3. Brown MD, etal., Hum Genet. 2001 Jul;109(1):33-9.
4. Canter JA, etal., Pharmacogenomics J. 2008 Feb;8(1):71-7. Epub 2007 Aug 7.
5. Da Sylva TR, etal., Arthritis Res Ther. 2005;7(4):R844-51. Epub 2005 Apr 28.
6. Davies JD, etal., J Exp Med 1991 Apr 1;173(4):823-32.
7. Fingert JH, etal., Ophthalmic Genet. 2007 Mar;28(1):1-7.
8. Gadaleta G, etal., J Mol Evol 1989 Jun;28(6):497-516.
9. Gadaleta G, etal., Nucleic Acids Res 1988 Jul 11;16(13):6233.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Guo LJ, etal., Mitochondrion. 2005 Feb;5(1):15-33.
12. Heidari MM, etal., Cell Mol Neurobiol. 2009 Mar;29(2):225-33. Epub 2008 Sep 19.
13. Hofmann S, etal., Mol Cell Biochem. 1997 Sep;174(1-2):209-13.
14. Howell N, etal., Am J Hum Genet. 1991 May;48(5):935-42.
15. Huebinger RM, etal., Shock. 2010 Jan;33(1):19-23.
16. Huoponen K, etal., Am J Hum Genet. 1991 Jun;48(6):1147-53.
17. Ide Y and Sato I, Okajimas Folia Anat Jpn. 2006 Aug;83(2):61-71.
18. Jove M, etal., J Lipid Res. 2004 Jan;45(1):113-23. Epub 2003 Oct 16.
19. KEGG
20. Kim JY, etal., Ann Neurol. 2002 May;51(5):630-4.
21. Kingsbury AE, etal., Ann Neurol. 2001 Aug;50(2):142-9.
22. Kirby DM, etal., J Med Genet. 2004 Oct;41(10):784-9.
23. Kirchner SC, etal., Neurotoxicology. 2000 Aug;21(4):441-5.
24. Kumar M, etal., Mol Vis. 2010 Apr 30;16:782-92.
25. Liang M, etal., Biochem Biophys Res Commun. 2009 Jun 5;383(3):286-92. Epub 2009 Mar 24.
26. Liao WQ, etal., Tohoku J Exp Med. 2008 Aug;215(4):377-84.
27. Liu Y, etal., Biochem Biophys Res Commun. 2008 Mar 28;368(1):18-22. Epub 2008 Jan 14.
28. Lymperopoulos A, etal., J Am Coll Cardiol. 2011 Jan 18;57(3):356-65.
29. Manczak M, etal., Neuromolecular Med. 2004;5(2):147-62.
30. Munakata K, etal., Genomics. 2004 Dec;84(6):1041-50.
31. NCBI rat LocusLink and RefSeq merged data July 26, 2002
32. Pettus EH, etal., J Neurochem. 2000 Jul;75(1):383-92.
33. PubMed Book Article
34. RGD automated data pipeline
35. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
36. RGD automated import pipeline for gene-chemical interactions
37. RGD comprehensive gene curation
38. Suliman HB, etal., Free Radic Biol Med. 2002 Feb 1;32(3):246-56.
39. Swerdlow RH, etal., J Neurol Sci. 2006 Sep 25;247(2):224-30. Epub 2006 Jun 19.
40. Tendi EA, etal., Neurochem Res. 2002 Apr;27(4):319-23.
41. Yamada Y and Nakano K, Brain Res Mol Brain Res. 1999 Nov 10;73(1-2):186-8.
42. Yu P, etal., Chin Med J (Engl). 2004 Jul;117(7):985-9.
43. Zhou X, etal., Invest Ophthalmol Vis Sci. 2012 Jul 9;53(8):4586-94. doi: 10.1167/iovs.11-9109.
Additional References at PubMed
PMID:26298201   PMID:26316108   PMID:31505169  


Genomics

Comparative Map Data
Mt-nd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2MT2,740 - 3,694 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblMT2,740 - 3,694 (+)Ensembl
Rnor_6.0MT2,740 - 3,694 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblMT2,740 - 3,694 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0MT2,740 - 3,694 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4MT2,740 - 3,694 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic MapMT NCBI
MT-ND1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblMT3,307 - 4,262 (+)EnsemblGRCh38hg38GRCh38
GRCh38MT3,307 - 4,262 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37MT3,307 - 4,262 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36MT3,308 - 4,264 (+)NCBINCBI36hg18NCBI36
mt-Nd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39MT2,751 - 3,707 (+)NCBIGRCm39mm39
GRCm39 EnsemblMT2,751 - 3,707 (+)Ensembl
GRCm38MT2,751 - 3,707 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblMT2,751 - 3,707 (+)EnsemblGRCm38mm10GRCm38
MGSCv37MT2,751 - 3,707 (+)NCBIGRCm37mm9NCBIm37
MT-ND1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1MT2,747 - 3,702 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblMT2,747 - 3,703 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaMT2,747 - 3,702 (+)NCBI
MT-ND1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblMT3,922 - 4,876 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1MT3,922 - 4,876 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2MT3,922 - 4,876 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Position Markers
RH136367  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0MT2,338 - 2,532UniSTSRnor5.0
RGSC_v3.4MT2,338 - 2,532UniSTSRGSC3.4
PMC312657P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0MT2,276 - 2,749UniSTSRnor5.0
RGSC_v3.4MT2,276 - 2,749UniSTSRGSC3.4
PMC316374P5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0MT901 - 1,615UniSTSRnor5.0
RGSC_v3.4MT901 - 1,615UniSTSRGSC3.4
PMC31832P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0MT2,239 - 2,376UniSTSRnor5.0
RGSC_v3.4MT2,239 - 2,376UniSTSRGSC3.4

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:65
Interacting mature miRNAs:66
Transcripts:ENSRNOT00000047550
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 41 55 39 3 33 3 66 27 32 3
Medium 8 24 8 16 8 8 8 8 8 9 8 8
Low
Below cutoff

Sequence

Nucleotide Sequences
GenBank Nucleotide AY172581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY769440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673908 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU104717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU104724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU997608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU997609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU997610 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU997611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HM152027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HM152028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX105355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX105356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF011917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ530565 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ939360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ939361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM009112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM009113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM009114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM114603 (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
  KM820832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM820833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM820834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM820835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM820836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM820837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP099715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP100657 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP233827 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP233832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP241960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP244683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000047550   ⟹   ENSRNOP00000049172
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblMT2,740 - 3,694 (+)Ensembl
Rnor_6.0 EnsemblMT2,740 - 3,694 (+)Ensembl
Protein Sequences
Protein RefSeqs YP_665629 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAN77594 (Get FASTA)   NCBI Sequence Viewer  
  AAV31039 (Get FASTA)   NCBI Sequence Viewer  
  ABG11766 (Get FASTA)   NCBI Sequence Viewer  
  ABG11773 (Get FASTA)   NCBI Sequence Viewer  
  ABG11792 (Get FASTA)   NCBI Sequence Viewer  
  ABG11806 (Get FASTA)   NCBI Sequence Viewer  
  ABG11818 (Get FASTA)   NCBI Sequence Viewer  
  ABG11831 (Get FASTA)   NCBI Sequence Viewer  
  ABG11844 (Get FASTA)   NCBI Sequence Viewer  
  ABG11857 (Get FASTA)   NCBI Sequence Viewer  
  ABG11870 (Get FASTA)   NCBI Sequence Viewer  
  ABG11883 (Get FASTA)   NCBI Sequence Viewer  
  ABV22513 (Get FASTA)   NCBI Sequence Viewer  
  ABV22520 (Get FASTA)   NCBI Sequence Viewer  
  ACP50280 (Get FASTA)   NCBI Sequence Viewer  
  ACP50293 (Get FASTA)   NCBI Sequence Viewer  
  ACP50306 (Get FASTA)   NCBI Sequence Viewer  
  ACP50319 (Get FASTA)   NCBI Sequence Viewer  
  ACP50332 (Get FASTA)   NCBI Sequence Viewer  
  ACP50345 (Get FASTA)   NCBI Sequence Viewer  
  ACP50358 (Get FASTA)   NCBI Sequence Viewer  
  ACP50371 (Get FASTA)   NCBI Sequence Viewer  
  ACP50384 (Get FASTA)   NCBI Sequence Viewer  
  ACP50410 (Get FASTA)   NCBI Sequence Viewer  
  ACP50423 (Get FASTA)   NCBI Sequence Viewer  
  ACP50436 (Get FASTA)   NCBI Sequence Viewer  
  ADE05939 (Get FASTA)   NCBI Sequence Viewer  
  ADE05952 (Get FASTA)   NCBI Sequence Viewer  
  ADE05965 (Get FASTA)   NCBI Sequence Viewer  
  ADE05978 (Get FASTA)   NCBI Sequence Viewer  
  ADG85621 (Get FASTA)   NCBI Sequence Viewer  
  ADG85634 (Get FASTA)   NCBI Sequence Viewer  
  AFN06278 (Get FASTA)   NCBI Sequence Viewer  
  AFN06291 (Get FASTA)   NCBI Sequence Viewer  
  AGS12821 (Get FASTA)   NCBI Sequence Viewer  
  AHZ60966 (Get FASTA)   NCBI Sequence Viewer  
  AIU45575 (Get FASTA)   NCBI Sequence Viewer  
  AIU45588 (Get FASTA)   NCBI Sequence Viewer  
  AIU45601 (Get FASTA)   NCBI Sequence Viewer  
  AIU45614 (Get FASTA)   NCBI Sequence Viewer  
  AIU45627 (Get FASTA)   NCBI Sequence Viewer  
  AIU45640 (Get FASTA)   NCBI Sequence Viewer  
  AIU45653 (Get FASTA)   NCBI Sequence Viewer  
  AIU45666 (Get FASTA)   NCBI Sequence Viewer  
  AIU45679 (Get FASTA)   NCBI Sequence Viewer  
  AIU45692 (Get FASTA)   NCBI Sequence Viewer  
  AIU45705 (Get FASTA)   NCBI Sequence Viewer  
  AIY51542 (Get FASTA)   NCBI Sequence Viewer  
  AIZ58322 (Get FASTA)   NCBI Sequence Viewer  
  AIZ58335 (Get FASTA)   NCBI Sequence Viewer  
  AJD83432 (Get FASTA)   NCBI Sequence Viewer  
  AJE26530 (Get FASTA)   NCBI Sequence Viewer  
  AJE61352 (Get FASTA)   NCBI Sequence Viewer  
  AJE61365 (Get FASTA)   NCBI Sequence Viewer  
  AJE61378 (Get FASTA)   NCBI Sequence Viewer  
  AJE61391 (Get FASTA)   NCBI Sequence Viewer  
  AJE61404 (Get FASTA)   NCBI Sequence Viewer  
  AJJ48377 (Get FASTA)   NCBI Sequence Viewer  
  AJJ48749 (Get FASTA)   NCBI Sequence Viewer  
  AJK29981 (Get FASTA)   NCBI Sequence Viewer  
  AJK30557 (Get FASTA)   NCBI Sequence Viewer  
  AJO99993 (Get FASTA)   NCBI Sequence Viewer  
  P03889 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000049172   ⟸   ENSRNOT00000047550

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)
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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
F344/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
FHH/EurMcwi (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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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
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)
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 (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
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)
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)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620555 AgrOrtholog
Ensembl Genes ENSRNOG00000030644 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000049172 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000047550 UniProtKB/Swiss-Prot
InterPro NADH_UbQ_OxRdtase_su1/FPO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NADH_UbQ_OxRdtase_su1_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:26193 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 26193 ENTREZGENE
PANTHER PTHR11432 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam NADHdh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Mt-nd1 PhenoGen
PROSITE COMPLEX1_ND1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  COMPLEX1_ND1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt NU1M_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q8HID1 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary H9KVF8 UniProtKB/TrEMBL
  O63197 UniProtKB/Swiss-Prot
  Q37653 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-03-17 Mt-nd1  mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1  Mt-nd1  mitochondrially encoded NADH dehydrogenase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-08-29 Mt-nd1  mitochondrially encoded NADH dehydrogenase 1  mt-Nd1  NADH dehydrogenase 1, mitochondrial  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-11 mt-Nd1  NADH dehydrogenase 1, mitochondrial      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 mt-Nd1  NADH dehydrogenase 1, mitochondrial      Symbol and Name status set to provisional 70820 PROVISIONAL