Mt-nd5 (mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5) - Rat Genome Database
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Gene: Mt-nd5 (mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5) Rattus norvegicus
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Symbol: Mt-nd5
Name: mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5
RGD ID: 620560
Description: Predicted to have NADH dehydrogenase activity. Involved in response to hydrogen peroxide; response to hypoxia; and response to organonitrogen compound. Localizes to neuron projection. Biomarker of hepatocellular carcinoma. Human ortholog(s) of this gene implicated in Leber hereditary optic neuropathy; Leigh disease; and MELAS syndrome. Orthologous to human MT-ND5 (mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5); INTERACTS WITH 2,6-dinitrotoluene; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: mitochondrially encoded NADH dehydrogenase 5; NADH dehydrogenase 5, mitochondrial; NADH dehydrogenase subunit 5; Nd5
RGD Orthologs
Human
Mouse
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0 EnsemblMT11,736 - 13,565 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0MT11,736 - 13,565 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0MT11,736 - 13,565 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4MT11,736 - 13,565 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic MapMT NCBI


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Brautbar A, etal., Mol Genet Metab. 2008 Aug;94(4):485-90. Epub 2008 May 20.
2. Brown MD, etal., Genetics. 1992 Jan;130(1):163-73.
3. Cai W, etal., J Genet Genomics. 2008 Nov;35(11):649-55.
4. Choi BO, etal., Exp Mol Med. 2008 Jun 30;40(3):354-60.
5. Corral M, etal., Exp Cell Res. 1989 Sep;184(1):158-66.
6. Gadaleta G, etal., J Mol Evol 1989 Jun;28(6):497-516.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Janssen YM, etal., Environ Health Perspect. 1998 Oct;106 Suppl 5:1191-5.
9. Ji YC, etal., Yi Chuan. 2011 Apr;33(4):322-8.
10. KEGG
11. Liu XL, etal., Ophthalmology. 2011 May;118(5):978-85. Epub 2010 Dec 4.
12. Malfatti E, etal., Brain. 2007 Jul;130(Pt 7):1894-904. Epub 2007 May 29.
13. Mayorov V, etal., Ann Neurol. 2005 Nov;58(5):807-11.
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. Piruat JI and Lopez-Barneo J, J Biol Chem. 2005 Dec 30;280(52):42676-84. Epub 2005 Oct 28.
16. Polosa PL and Attardi G, J Biol Chem. 1991 May 25;266(15):10011-7.
17. Pulkes T, etal., Ann Neurol. 1999 Dec;46(6):916-9.
18. RGD automated data pipeline
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. Valentino ML, etal., J Med Genet. 2006 Jul;43(7):e38.
23. Zhao D, etal., J Hum Genet. 2011 Aug 18. doi: 10.1038/jhg.2011.96.
Additional References at PubMed
PMID:22414913   PMID:26316108  


Genomics

Comparative Map Data
Mt-nd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0 EnsemblMT11,736 - 13,565 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0MT11,736 - 13,565 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0MT11,736 - 13,565 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4MT11,736 - 13,565 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic MapMT NCBI
MT-ND5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblMT12,337 - 14,148 (+)EnsemblGRCh38hg38GRCh38
GRCh38MT12,337 - 14,148 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37MT12,337 - 14,148 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36MT12,338 - 14,149 (+)NCBINCBI36hg18NCBI36
mt-Nd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39MT11,742 - 13,565 (+)NCBIGRCm39mm39
GRCm38MT11,742 - 13,565 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblMT11,742 - 13,565 (+)EnsemblGRCm38mm10GRCm38
MGSCv37MT11,742 - 13,565 (+)NCBIGRCm37mm9NCBIm37
MT-ND5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblMT11,778 - 13,598 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1MT11,778 - 13,598 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
MT-ND5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblMT12,935 - 14,755 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1MT12,935 - 14,755 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2MT12,935 - 14,755 (+)NCBISscrofa10.2Sscrofa10.2susScr3

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:34
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000048767
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 3 42 25 23 4 23 3 66 27 31 3
Medium 1 32 18 15 18 8 8 8 8 10 8 8
Low
Below cutoff

Sequence

Nucleotide Sequences
GenBank Nucleotide AJ428514 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  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
  DQ673909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ673910 (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
  DQ673917 (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
  FJ919768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ919769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU997608 (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
  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
  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
  KM820831 (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
  KM820837 (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
  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: ENSRNOT00000048767   ⟹   ENSRNOP00000044573
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblMT11,736 - 13,565 (+)Ensembl
Protein Sequences
Protein RefSeqs YP_665639 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAN77604 (Get FASTA)   NCBI Sequence Viewer  
  AAV31049 (Get FASTA)   NCBI Sequence Viewer  
  ABG11771 (Get FASTA)   NCBI Sequence Viewer  
  ABG11797 (Get FASTA)   NCBI Sequence Viewer  
  ABG11811 (Get FASTA)   NCBI Sequence Viewer  
  ABG11836 (Get FASTA)   NCBI Sequence Viewer  
  ABG11849 (Get FASTA)   NCBI Sequence Viewer  
  ABG11862 (Get FASTA)   NCBI Sequence Viewer  
  ABG11875 (Get FASTA)   NCBI Sequence Viewer  
  ABG11901 (Get FASTA)   NCBI Sequence Viewer  
  ACP50316 (Get FASTA)   NCBI Sequence Viewer  
  ACP50329 (Get FASTA)   NCBI Sequence Viewer  
  ACP50342 (Get FASTA)   NCBI Sequence Viewer  
  ACP50355 (Get FASTA)   NCBI Sequence Viewer  
  ACP50368 (Get FASTA)   NCBI Sequence Viewer  
  ACP50381 (Get FASTA)   NCBI Sequence Viewer  
  ACP50394 (Get FASTA)   NCBI Sequence Viewer  
  ACP50407 (Get FASTA)   NCBI Sequence Viewer  
  ACP50420 (Get FASTA)   NCBI Sequence Viewer  
  ADE05962 (Get FASTA)   NCBI Sequence Viewer  
  ADE05975 (Get FASTA)   NCBI Sequence Viewer  
  ADE05988 (Get FASTA)   NCBI Sequence Viewer  
  AFN06288 (Get FASTA)   NCBI Sequence Viewer  
  AFN06301 (Get FASTA)   NCBI Sequence Viewer  
  AGS12831 (Get FASTA)   NCBI Sequence Viewer  
  AIU45585 (Get FASTA)   NCBI Sequence Viewer  
  AIU45598 (Get FASTA)   NCBI Sequence Viewer  
  AIU45611 (Get FASTA)   NCBI Sequence Viewer  
  AIU45624 (Get FASTA)   NCBI Sequence Viewer  
  AIU45637 (Get FASTA)   NCBI Sequence Viewer  
  AIU45650 (Get FASTA)   NCBI Sequence Viewer  
  AIU45663 (Get FASTA)   NCBI Sequence Viewer  
  AIU45676 (Get FASTA)   NCBI Sequence Viewer  
  AIU45689 (Get FASTA)   NCBI Sequence Viewer  
  AIU45702 (Get FASTA)   NCBI Sequence Viewer  
  AIU45715 (Get FASTA)   NCBI Sequence Viewer  
  AIY51552 (Get FASTA)   NCBI Sequence Viewer  
  AIZ58332 (Get FASTA)   NCBI Sequence Viewer  
  AIZ58345 (Get FASTA)   NCBI Sequence Viewer  
  AJE26540 (Get FASTA)   NCBI Sequence Viewer  
  AJE61349 (Get FASTA)   NCBI Sequence Viewer  
  AJE61375 (Get FASTA)   NCBI Sequence Viewer  
  AJE61388 (Get FASTA)   NCBI Sequence Viewer  
  AJE61401 (Get FASTA)   NCBI Sequence Viewer  
  AJE61414 (Get FASTA)   NCBI Sequence Viewer  
  AJJ48759 (Get FASTA)   NCBI Sequence Viewer  
  AJK29991 (Get FASTA)   NCBI Sequence Viewer  
  AJK30567 (Get FASTA)   NCBI Sequence Viewer  
  CAD21569 (Get FASTA)   NCBI Sequence Viewer  
  P11661 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000044573   ⟸   ENSRNOT00000048767
Protein Domains
NADH5_C   Proton_antipo_M   Proton_antipo_N

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 (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)
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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
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620560 AgrOrtholog
Ensembl Genes ENSRNOG00000029971 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000044573 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000048767 UniProtKB/Swiss-Prot
InterPro NADH_DH_su5_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NADHpl_OxRdtase_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ND/Mrp_mem UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Proton_antipo_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:26202 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 26202 ENTREZGENE
Pfam NADH5_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Proton_antipo_M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Proton_antipo_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Mt-nd5 PhenoGen
TIGRFAMs NDH_I_L UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt NU5M_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q8SEZ0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-03-17 Mt-nd5  mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5  Mt-nd5  mitochondrially encoded NADH dehydrogenase 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-08-29 Mt-nd5  mitochondrially encoded NADH dehydrogenase 5  mt-Nd5  NADH dehydrogenase 5, mitochondrial  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-11 mt-Nd5  NADH dehydrogenase 5, mitochondrial      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 mt-Nd5  NADH dehydrogenase 5, mitochondrial      Symbol and Name status set to provisional 70820 PROVISIONAL