Pdss2 (decaprenyl diphosphate synthase subunit 2) - Rat Genome Database

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Gene: Pdss2 (decaprenyl diphosphate synthase subunit 2) Rattus norvegicus
Analyze
Symbol: Pdss2
Name: decaprenyl diphosphate synthase subunit 2
RGD ID: 1359372
Description: Is predicted to contribute to trans-hexaprenyltranstransferase activity and trans-octaprenyltranstransferase activity. Predicted to be involved in several processes, including cerebellum development; isoprenoid biosynthetic process; and ubiquinone biosynthetic process. Predicted to localize to cytosol and transferase complex. Human ortholog(s) of this gene implicated in primary coenzyme Q10 deficiency 3. Orthologous to human PDSS2 (decaprenyl diphosphate synthase subunit 2); PARTICIPATES IN terpenoid biosynthetic pathway; INTERACTS WITH acetamide; bisphenol A; diuron.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: all trans-polyprenyl-diphosphate synthase PDSS2; all-trans-decaprenyl-diphosphate synthase subunit 2; decaprenyl pyrophosphate synthase subunit 2; decaprenyl pyrophosphate synthetase subunit 2; decaprenyl-diphosphate synthase subunit 2; LOC365592; prenyl (decaprenyl) diphosphate synthase, subunit 2; prenyl (solanesyl) diphosphate synthase, subunit 2; similar to CG10585-PA; solanesyl-diphosphate synthase subunit 2
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
mRatBN7.22046,709,631 - 46,938,704 (+)NCBI
Rnor_6.0 Ensembl2047,966,583 - 48,192,743 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02047,966,513 - 48,192,747 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02049,627,299 - 49,699,472 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.02049,750,928 - 49,851,503 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42047,128,350 - 47,359,830 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12047,157,046 - 47,388,523 (+)NCBI
Celera2053,049,724 - 53,270,077 (-)NCBICelera
Cytogenetic Map20q13NCBI
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
cytosol  (IEA,ISO)
mitochondrion  (IEA)
transferase complex  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:5098070   PMID:15489334   PMID:16262699   PMID:18614015  


Genomics

Comparative Map Data
Pdss2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22046,709,631 - 46,938,704 (+)NCBI
Rnor_6.0 Ensembl2047,966,583 - 48,192,743 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02047,966,513 - 48,192,747 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02049,627,299 - 49,699,472 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.02049,750,928 - 49,851,503 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42047,128,350 - 47,359,830 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12047,157,046 - 47,388,523 (+)NCBI
Celera2053,049,724 - 53,270,077 (-)NCBICelera
Cytogenetic Map20q13NCBI
PDSS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6107,152,562 - 107,459,564 (-)EnsemblGRCh38hg38GRCh38
GRCh386107,152,557 - 107,459,681 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376107,473,766 - 107,780,768 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366107,580,456 - 107,887,448 (-)NCBINCBI36hg18NCBI36
Build 346107,580,455 - 107,887,448NCBI
Celera6108,222,204 - 108,529,221 (-)NCBI
Cytogenetic Map6q21NCBI
HuRef6105,044,813 - 105,351,570 (-)NCBIHuRef
CHM1_16107,736,502 - 108,043,494 (-)NCBICHM1_1
Pdss2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391043,095,396 - 43,340,878 (+)NCBIGRCm39mm39
GRCm39 Ensembl1043,097,482 - 43,340,878 (+)Ensembl
GRCm381043,218,248 - 43,464,882 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1043,221,486 - 43,464,882 (+)EnsemblGRCm38mm10GRCm38
MGSCv371042,941,292 - 43,184,688 (+)NCBIGRCm37mm9NCBIm37
MGSCv361042,909,901 - 43,153,297 (+)NCBImm8
Celera1044,087,907 - 44,331,621 (+)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1022.91NCBI
Pdss2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541132,422,513 - 32,714,062 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541132,426,604 - 32,714,337 (-)NCBIChiLan1.0ChiLan1.0
PDSS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16108,831,154 - 109,137,354 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6108,833,223 - 109,137,055 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06104,963,942 - 105,272,807 (-)NCBIMhudiblu_PPA_v0panPan3
PDSS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11264,371,548 - 64,620,652 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1264,338,950 - 64,620,367 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1264,157,690 - 64,407,542 (-)NCBI
ROS_Cfam_1.01265,214,682 - 65,465,310 (-)NCBI
UMICH_Zoey_3.11264,574,421 - 64,823,617 (-)NCBI
UNSW_CanFamBas_1.01264,417,912 - 64,668,719 (-)NCBI
UU_Cfam_GSD_1.01264,692,925 - 64,942,617 (-)NCBI
Pdss2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494699,254,277 - 99,538,434 (-)NCBI
SpeTri2.0NW_0049365643,529,140 - 3,813,449 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDSS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl173,235,097 - 73,510,573 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1173,234,950 - 73,510,533 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2182,739,757 - 82,746,514 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDSS2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11366,405,014 - 66,704,559 (+)NCBI
ChlSab1.1 Ensembl1366,405,521 - 66,704,696 (+)Ensembl
Vero_WHO_p1.0NW_02366604038,729,663 - 39,030,971 (+)NCBI
Pdss2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478014,803,750 - 15,130,156 (+)NCBI

Position Markers
RH131620  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22046,938,437 - 46,938,625 (+)MAPPER
Rnor_6.02048,192,481 - 48,192,668NCBIRnor6.0
Rnor_5.02049,851,237 - 49,851,424UniSTSRnor5.0
RGSC_v3.42047,359,564 - 47,359,751UniSTSRGSC3.4
Celera2053,049,803 - 53,049,990UniSTS
RH 3.4 Map334.8UniSTS
Cytogenetic Map20q13UniSTS
RH138146  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22046,723,034 - 46,723,235 (+)MAPPER
Rnor_6.02047,979,915 - 47,980,115NCBIRnor6.0
Rnor_5.02049,640,631 - 49,640,831UniSTSRnor5.0
RGSC_v3.42047,141,675 - 47,141,875UniSTSRGSC3.4
Celera2053,256,552 - 53,256,752UniSTS
RH 3.4 Map20493.24UniSTS
Cytogenetic Map20q13UniSTS
BE117161  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22046,713,479 - 46,713,681 (+)MAPPER
Rnor_6.02047,970,363 - 47,970,564NCBIRnor6.0
Rnor_5.02049,631,079 - 49,631,280UniSTSRnor5.0
RGSC_v3.42047,132,123 - 47,132,324UniSTSRGSC3.4
Celera2053,266,103 - 53,266,304UniSTS
RH 3.4 Map20494.35UniSTS
Cytogenetic Map20q13UniSTS
RH69187  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera2053,129,355 - 53,130,333UniSTS
Cytogenetic Map20q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:58
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000067169
Prediction methods: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 38 39 31 4 31 8 11 70 31 31 11 8
Low 5 18 10 15 10 4 4 10
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067169   ⟹   ENSRNOP00000059060
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2047,966,583 - 48,192,743 (+)Ensembl
RefSeq Acc Id: NM_001014249   ⟹   NP_001014271
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,709,706 - 46,938,704 (+)NCBI
Rnor_6.02047,966,583 - 48,192,747 (+)NCBI
Rnor_5.02049,627,299 - 49,699,472 (+)NCBI
Rnor_5.02049,750,928 - 49,851,503 (+)NCBI
RGSC_v3.42047,128,350 - 47,359,830 (+)RGD
Celera2053,049,724 - 53,270,077 (-)RGD
Sequence:
RefSeq Acc Id: XM_008773004   ⟹   XP_008771226
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02047,966,513 - 48,170,452 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098908   ⟹   XP_038954836
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,709,638 - 46,913,953 (+)NCBI
RefSeq Acc Id: XM_039098909   ⟹   XP_038954837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,709,639 - 46,937,578 (+)NCBI
RefSeq Acc Id: XR_001842423
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,709,637 - 46,938,030 (+)NCBI
Rnor_6.02047,966,513 - 48,192,026 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005497300
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,709,631 - 46,938,030 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001014271 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954836 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954837 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85898 (Get FASTA)   NCBI Sequence Viewer  
  Q5U2R1 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001014271   ⟸   NM_001014249
- UniProtKB: Q5U2R1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008771226   ⟸   XM_008773004
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000059060   ⟸   ENSRNOT00000067169
RefSeq Acc Id: XP_038954836   ⟸   XM_039098908
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954837   ⟸   XM_039098909
- Peptide Label: isoform X2

Transcriptome

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

Promoters
RGD ID:13701673
Promoter ID:EPDNEW_R12197
Type:initiation region
Name:Pdss2_1
Description:decaprenyl diphosphate synthase subunit 2
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_6.02047,966,534 - 47,966,594EPDNEW

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)
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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
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)
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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
SBN/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: SBN/Ygl sequenced by MCW
SBN/Ygl (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/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
SHRSP/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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
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:1359372 AgrOrtholog
Ensembl Genes ENSRNOG00000042962 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000059060 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000067169 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.600.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7193369 IMAGE-MGC_LOAD
InterPro Isoprenoid_synthase_dom_sf UniProtKB/Swiss-Prot
  Polyprenyl_synt UniProtKB/Swiss-Prot
KEGG Report rno:365592 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94721 IMAGE-MGC_LOAD
NCBI Gene 365592 ENTREZGENE
Pfam polyprenyl_synt UniProtKB/Swiss-Prot
PhenoGen Pdss2 PhenoGen
Superfamily-SCOP SSF48576 UniProtKB/Swiss-Prot
UniProt DLP1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-01-03 Pdss2  decaprenyl diphosphate synthase subunit 2  Pdss2  prenyl (decaprenyl) diphosphate synthase, subunit 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-06 Pdss2  prenyl (decaprenyl) diphosphate synthase, subunit 2  Pdss2  prenyl (solanesyl) diphosphate synthase, subunit 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Pdss2  prenyl (solanesyl) diphosphate synthase, subunit 2  LOC365592  similar to CG10585-PA  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED