Pdss1 (decaprenyl diphosphate synthase subunit 1) - Rat Genome Database
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Gene: Pdss1 (decaprenyl diphosphate synthase subunit 1) Rattus norvegicus
Analyze
Symbol: Pdss1
Name: decaprenyl diphosphate synthase subunit 1
RGD ID: 2319976
Description: Is predicted to contribute to trans-hexaprenyltranstransferase activity and trans-octaprenyltranstransferase activity. Predicted to be involved in isoprenoid biosynthetic process and ubiquinone biosynthetic process. Predicted to localize to transferase complex. Human ortholog(s) of this gene implicated in primary coenzyme Q10 deficiency 2. Orthologous to human PDSS1 (decaprenyl diphosphate synthase subunit 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; glyphosate; 1,2-dimethylhydrazine (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Also known as: all trans-polyprenyl-diphosphate synthase PDSS1; COenzyme Q (ubiquinone) biosynthesis family member (coq-1)-like; decaprenyl-diphosphate synthase subunit 1; LOC100364990; prenyl (decaprenyl) diphosphate synthase, subunit 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21785,059,953 - 85,098,739 (+)NCBI
Rnor_6.0 Ensembl1790,033,539 - 90,071,408 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01790,033,432 - 90,072,506 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01791,698,837 - 91,736,565 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1783,796,677 - 83,835,554 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
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

References

Additional References at PubMed
PMID:12477932   PMID:16262699   PMID:18614015  


Genomics

Comparative Map Data
Pdss1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21785,059,953 - 85,098,739 (+)NCBI
Rnor_6.0 Ensembl1790,033,539 - 90,071,408 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01790,033,432 - 90,072,506 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01791,698,837 - 91,736,565 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1783,796,677 - 83,835,554 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
PDSS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1026,697,701 - 26,746,798 (+)EnsemblGRCh38hg38GRCh38
GRCh381026,697,424 - 26,747,246 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371026,986,630 - 27,035,727 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361027,026,601 - 27,075,733 (+)NCBINCBI36hg18NCBI36
Build 341027,026,600 - 27,075,730NCBI
Celera1026,698,509 - 26,744,104 (+)NCBI
Cytogenetic Map10p12.1NCBI
HuRef1026,646,251 - 26,696,013 (+)NCBIHuRef
CHM1_11026,986,979 - 27,033,181 (+)NCBICHM1_1
Pdss1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39222,784,393 - 22,830,273 (+)NCBIGRCm39mm39
GRCm39 Ensembl222,785,534 - 22,830,278 (+)Ensembl
GRCm38222,894,382 - 22,940,266 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl222,895,522 - 22,940,266 (+)EnsemblGRCm38mm10GRCm38
MGSCv37222,751,042 - 22,795,781 (+)NCBIGRCm37mm9NCBIm37
MGSCv36222,747,279 - 22,767,173 (+)NCBImm8
Celera222,626,848 - 22,671,620 (+)NCBICelera
Cytogenetic Map2A3NCBI
Pdss1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554292,783,847 - 2,818,206 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554292,783,847 - 2,818,204 (-)NCBIChiLan1.0ChiLan1.0
PDSS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11027,178,645 - 27,227,866 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1027,178,933 - 27,227,542 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01026,811,243 - 26,863,594 (+)NCBIMhudiblu_PPA_v0panPan3
PDSS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl27,059,683 - 7,101,163 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.127,059,455 - 7,103,178 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pdss1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364842,062,330 - 2,091,231 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDSS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1049,068,942 - 49,120,367 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11049,069,258 - 49,120,393 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21054,434,768 - 54,485,500 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDSS1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1926,322,083 - 26,379,493 (+)NCBI
ChlSab1.1 Ensembl926,323,478 - 26,377,415 (+)Ensembl
Pdss1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247962,431,383 - 2,466,044 (-)NCBI

Position Markers
BI277286  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1783,833,803 - 83,833,981UniSTS
RH 3.4 Map17836.6UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175347518090690466Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175387148890843779Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175399194790843779Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176751265790843779Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:213
Count of miRNA genes:142
Interacting mature miRNAs:152
Transcripts:ENSRNOT00000071978
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
Medium 3 31 28 18 19 18 5 7 70 22 33 8 5
Low 12 29 23 23 3 4 4 13 8 3 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071978   ⟹   ENSRNOP00000065114
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1790,033,539 - 90,071,408 (-)Ensembl
RefSeq Acc Id: XM_002725307   ⟹   XP_002725353
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1783,796,677 - 83,835,552 (-)NCBI
Sequence:
RefSeq Acc Id: XM_003751734   ⟹   XP_003751782
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21785,059,969 - 85,098,734 (+)NCBI
Rnor_6.01790,033,432 - 90,072,504 (-)NCBI
Rnor_5.01791,698,837 - 91,736,565 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771923   ⟹   XP_008770145
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01790,033,432 - 90,072,506 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008774049   ⟹   XP_008772271
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1783,796,677 - 83,835,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017587762   ⟹   XP_017443251
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1783,796,677 - 83,834,469 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039096342   ⟹   XP_038952270
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21785,060,396 - 85,098,734 (+)NCBI
RefSeq Acc Id: XM_039096343   ⟹   XP_038952271
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21785,060,396 - 85,098,734 (+)NCBI
RefSeq Acc Id: XM_039096344   ⟹   XP_038952272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21785,060,427 - 85,098,734 (+)NCBI
RefSeq Acc Id: XM_039096345   ⟹   XP_038952273
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21785,059,953 - 85,078,863 (+)NCBI
RefSeq Acc Id: XR_005495576
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21785,059,964 - 85,098,739 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_002725353   ⟸   XM_002725307
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_003751782   ⟸   XM_003751734
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008772271   ⟸   XM_008774049
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008770145   ⟸   XM_008771923
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017443251   ⟸   XM_017587762
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000065114   ⟸   ENSRNOT00000071978
RefSeq Acc Id: XP_038952273   ⟸   XM_039096345
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038952270   ⟸   XM_039096342
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038952271   ⟸   XM_039096343
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038952272   ⟸   XM_039096344
- Peptide Label: isoform X3

Transcriptome

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

Promoters
RGD ID:13700619
Promoter ID:EPDNEW_R11141
Type:initiation region
Name:Pdss1_1
Description:decaprenyl diphosphate synthase subunit 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01790,071,403 - 90,071,463EPDNEW

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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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)
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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 91736304 91736305 T A snv FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), ZF (KyushuU), LE/OrlBarth (UDEL), MNS/Gib (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 90071464 90071465 T A snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), MNS/Gib (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2319976 AgrOrtholog
Ensembl Genes ENSRNOG00000048849 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065114 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071978 UniProtKB/TrEMBL
Gene3D-CATH 1.10.600.10 UniProtKB/TrEMBL
InterPro Polyprenyl_synt UniProtKB/TrEMBL
  Polyprenyl_synt_CS UniProtKB/TrEMBL
  Terpenoid_synth UniProtKB/TrEMBL
NCBI Gene 100364990 ENTREZGENE
Pfam polyprenyl_synt UniProtKB/TrEMBL
PhenoGen Pdss1 PhenoGen
PROSITE POLYPRENYL_SYNTHASE_1 UniProtKB/TrEMBL
  POLYPRENYL_SYNTHASE_2 UniProtKB/TrEMBL
Superfamily-SCOP Terpenoid_synth UniProtKB/TrEMBL
UniProt M0R6Q9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-01-03 Pdss1  decaprenyl diphosphate synthase subunit 1  Pdss1  prenyl (decaprenyl) diphosphate synthase, subunit 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-07 Pdss1  prenyl (decaprenyl) diphosphate synthase, subunit 1  LOC100364990  COenzyme Q (ubiquinone) biosynthesis family member (coq-1)-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100364990  COenzyme Q (ubiquinone) biosynthesis family member (coq-1)-like      Symbol and Name status set to provisional 70820 PROVISIONAL