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

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Gene: Ndufs6-ps1 (NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Ndufs6-ps1 (Ensembl: Ndufs6)
Name: NADH:ubiquinone oxidoreductase subunit S6, pseudogene 1 (Ensembl:NADH:ubiquinone oxidoreductase subunit S6)
RGD ID: 3156
Description: Predicted to be part of mitochondrial respiratory chain complex I. 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: pseudogene)
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 Genes
More Info homologs ...
Related Functional Gene: Ndufs6  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2227,201,706 - 27,202,241 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl227,201,713 - 27,202,258 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx234,242,225 - 34,242,760 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0232,342,323 - 32,342,858 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0227,158,647 - 27,159,182 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0226,471,173 - 26,471,587 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl226,471,173 - 26,471,584 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0245,600,795 - 45,601,209 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4226,295,710 - 26,296,123 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera223,262,351 - 23,262,764 (+)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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
4 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22699957143154682Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat

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
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
Medium 2 2 2 2 2 2 1 2 2 1
Low 4 2 4 4 4 2 4
Below cutoff 8 18 11 3 11 3 4 4 9 7 2 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024327
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
Protein RefSeqs NP_062096 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957871 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA79310 (Get FASTA)   NCBI Sequence Viewer  
  P52504 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
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
Ensembl Genes ENSRNOG00000018068 Ensembl, ENTREZGENE
Gene3D-CATH q5lls5 like domains UniProtKB/Swiss-Prot
InterPro NDUFS6 UniProtKB/Swiss-Prot
  Znf_CHCC UniProtKB/Swiss-Prot
KEGG Report rno:29478 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 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