Ndufs6-ps1 (NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Ndufs6-ps1 (NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Ndufs6-ps1
Name: NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1
RGD ID: 3156
Description: Predicted to be involved in mitochondrial electron transport, NADH to ubiquinone. Predicted to act upstream of or within several processes, including DNA damage response, signal transduction by p53 class mediator; mesenchymal stem cell proliferation; and mitochondrial respiratory chain complex I assembly. Predicted to be part of respiratory chain complex I. Predicted to be active in mitochondrial inner membrane. Biomarker of arteriosclerosis. Human ortholog(s) of this gene implicated in cervical cancer and nuclear type mitochondrial complex I deficiency 9. Orthologous to human NDUFS6 (NADH:ubiquinone oxidoreductase subunit S6); PARTICIPATES IN Alzheimer's disease pathway; Huntington's disease pathway; oxidative phosphorylation pathway; .
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: CI-13kD-A; complex I-13kD-A; Ip13dis; NADH dehydrogenase (ubiquinone) Fe-S protein 6; NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial; NADH dehydrogenase Fe-S protein 6; NADH ubiquinone oxidoreductase; NADH-ubiquinone oxidoreductase 13 kDa-A subunit; NADH:ubiquinone oxidoreductase subunit S6; Ndub13; Ndufs6; RATIp13dis
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Related Functional Gene: Ndufs6  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8228,936,402 - 28,936,955 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl228,936,414 - 28,936,969 (+)EnsemblGRCr8
mRatBN7.2227,201,706 - 27,202,241 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl227,201,713 - 27,202,258 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx234,242,225 - 34,242,760 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0232,342,323 - 32,342,858 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0227,158,647 - 27,159,182 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd229,048,252 - 29,048,803 (+)NCBIDahl_SR_JrHsd
Lyon_Normotensive229,067,589 - 29,068,140 (+)NCBILyon_Normotensive
Lyon_Hypertensive228,984,580 - 28,985,133 (+)NCBILyon_Hypertensive
F344_StmMcwi228,884,953 - 28,885,505 (+)NCBIF344_StmMcwi
Rnor_6.0226,471,173 - 26,471,587 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl226,471,173 - 26,471,584 (+)Ensemblrn6Rnor6.0
Rnor_5.0245,600,795 - 45,601,209 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4226,295,710 - 26,296,123 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera223,262,351 - 23,262,764 (+)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Proteomic analysis of rat aorta during atherosclerosis induced by high cholesterol diet and injection of vitamin D3. Almofti MR, etal., Clin Exp Pharmacol Physiol. 2006 Apr;33(4):305-9.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
12. Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha. Scotto L, etal., Mol Cancer. 2008 Jun 17;7:58.
13. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
14. Genomic sequence, structural organization and evolutionary conservation of the 13.2-kDa subunit of rat NADH:ubiquinone oxidoreductase. Watson JD, etal., Gene 1995 Jun 9;158(2):275-80.
Additional References at PubMed
PMID:12611891   PMID:18614015   PMID:22474353   PMID:23320803   PMID:27626371   PMID:28844695   PMID:29476059  


Genomics

Variants

.
Variants in Ndufs6-ps1
5 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:23
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000024327
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21332504158325041Rat
7387318Stl32Serum triglyceride level QTL 323.20.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)22411781369117813Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)220695736231474293Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2142977529Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
9590080Insglur4Insulin/glucose ratio QTL 428.70.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)2615276751152767Rat
1579916Bp270Blood pressure QTL 2700.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21605188361051883Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22203804467038044Rat
731166Mamtr2Mammary tumor resistance QTL 20.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358154623581Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)227148328145807373Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22888999173889991Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21436870759368707Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328159440891Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358144538110Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24265106205135428Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)227148557159440760Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)27605533104774005Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328159440891Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22865266683465677Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)2573632550736325Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)227148557159440760Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)228652666139067443Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21822713763227137Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22865266673652666Rat

Markers in Region
D2Uwm34  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2227,205,023 - 27,205,223 (+)MAPPERmRatBN7.2
Rnor_6.0226,474,486 - 26,474,685NCBIRnor6.0
Rnor_5.0245,604,108 - 45,604,307UniSTSRnor5.0
RGSC_v3.4226,299,021 - 26,299,220UniSTSRGSC3.4
RGSC_v3.4226,299,020 - 26,299,220RGDRGSC3.4
Celera223,265,652 - 23,265,855UniSTS
Cytogenetic Map2q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
3 10 19 23 34 33 25 6 25 1 91 35 17 21 27 8

Sequence


Ensembl Acc Id: ENSRNOT00000024327
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl228,936,414 - 28,936,969 (+)Ensembl
mRatBN7.2 Ensembl227,201,713 - 27,202,258 (+)Ensembl
Rnor_6.0 Ensembl226,471,173 - 26,471,584 (+)Ensembl
RefSeq Acc Id: NM_019223   ⟹   NP_062096
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2227,201,706 - 27,202,241 (+)NCBI
Rnor_6.0226,471,173 - 26,471,587 (+)NCBI
Rnor_5.0245,600,795 - 45,601,209 (+)NCBI
RGSC_v3.4226,295,710 - 26,296,123 (+)RGD
Celera223,262,351 - 23,262,764 (+)RGD
Sequence:
RefSeq Acc Id: XM_039101943   ⟹   XP_038957871
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2227,201,713 - 27,202,126 (+)NCBI
Protein Sequences
GenBank Protein AAA79310 (Get FASTA)   NCBI Sequence Viewer  
  P52504 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_062096   ⟸   NM_019223
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_038957871   ⟸   XM_039101943
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P52504-F1-model_v2 AlphaFold P52504 1-116 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3156 AgrOrtholog
BioCyc Gene G2FUF-54787 BioCyc
BioCyc Pathway PWY-3781 [aerobic respiration I (cytochrome c)] BioCyc
BioCyc Pathway Image PWY-3781 BioCyc
Ensembl Genes ENSRNOG00000018068 Ensembl, ENTREZGENE
Gene3D-CATH q5lls5 like domains UniProtKB/Swiss-Prot
InterPro NDUFS6 UniProtKB/Swiss-Prot
  Znf_CHCC UniProtKB/Swiss-Prot
NCBI Gene 29478 ENTREZGENE
PANTHER NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 6, MITOCHONDRIAL UniProtKB/Swiss-Prot
  NADH-UBIQUINONE OXIDOREDUCTASE 13 KD-A SUBUNIT UniProtKB/Swiss-Prot
Pfam zf-CHCC UniProtKB/Swiss-Prot
PhenoGen Ndufs6-ps1 PhenoGen
PIRSF CI-13KD-A UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000018068 RatGTEx
TIGR TC205648
UniProt A0ABK0L3Q3_RAT UniProtKB/TrEMBL
  NDUS6_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-08-07 Ndufs6-ps1  NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1  Ndufs6-ps1  NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1  Type changed (type changed from [protein-coding] to [pseudo]) 629549 APPROVED
2023-08-07 Ndufs6-ps1  NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1  Ndufs6=ps1  NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1  Symbol changed 629549 APPROVED
2023-08-07 Ndufs6=ps1  NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1  Ndufs6  NADH:ubiquinone oxidoreductase subunit S6  Name and Symbol changed 629549 APPROVED
2016-07-05 Ndufs6  NADH:ubiquinone oxidoreductase subunit S6  Ndufs6  NADH dehydrogenase (ubiquinone) Fe-S protein 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Ndufs6  NADH dehydrogenase (ubiquinone) Fe-S protein 6    NADH dehydrogenase (ubiquinone) Fe-S protein 6  Symbol and Name updated 629477 APPROVED
2003-03-06 Ndufs6  NADH dehydrogenase (ubiquinone) Fe-S protein 6  Ndub13  NADH ubiquinone oxidoreductase  Data merged from RGD:3154 628472 PROVISIONAL
2002-06-10 Ndub13  NADH ubiquinone oxidoreductase      Symbol and Name status set to approved 70586 APPROVED
2002-06-10 Ndufs6  NADH dehydrogenase Fe-S protein 6       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein 13.2 kDa in size 69900