Cs (citrate synthase) - Rat Genome Database

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Gene: Cs (citrate synthase) Rattus norvegicus
Analyze
Symbol: Cs
Name: citrate synthase
RGD ID: 620330
Description: Exhibits citrate (Si)-synthase activity. Involved in acetyl-CoA metabolic process; carboxylic acid metabolic process; and tricarboxylic acid cycle. Localizes to mitochondrion. Orthologous to human CS (citrate synthase); PARTICIPATES IN citric acid cycle pathway; fumaric aciduria pathway; mitochondrial complex II deficiency pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,2,2-tetramine; 2,4,6-trinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: citrate (Si)-synthase; citrate synthase precursor; citrate synthase, mitochondrial
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27758,074 - 791,421 (+)NCBI
Rnor_6.0 Ensembl72,752,680 - 2,778,963 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.072,752,680 - 2,778,963 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.072,731,092 - 2,757,427 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,626,181 - 1,652,197 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.171,626,180 - 1,652,197 (+)NCBI
Celera7639,242 - 663,715 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrotoluene  (EXP)
3,4-dihydroxybenzoic acid  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-DAMP(1+)  (EXP)
5-methyl-4-oxido-2-pyrazin-4-iumcarboxylic acid  (ISO)
acrolein  (EXP)
aflatoxin B1  (ISO)
AM-251  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atorvastatin calcium  (EXP)
benzo[a]pyrene  (ISO)
benzylpenicillin  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
butan-1-ol  (ISO)
cadmium dichloride  (EXP,ISO)
captan  (ISO)
carbon nanotube  (ISO)
Chicoric acid  (EXP)
chlorogenic acid  (ISO)
cholesterol  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP,ISO)
corticosterone  (EXP)
curcumin  (EXP)
cyclosporin A  (ISO)
Deoxycorticosterone acetate  (EXP)
dexamethasone  (ISO)
dicrotophos  (ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (EXP,ISO)
dopamine  (ISO)
dorsomorphin  (EXP)
doxorubicin  (EXP,ISO)
ebselen  (EXP,ISO)
enzyme inhibitor  (ISO)
erythromycin A  (ISO)
Erythropoietin  (ISO)
ethanol  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folpet  (ISO)
gallic acid  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (EXP)
isoprenaline  (EXP)
josamycin  (ISO)
kaempferol  (ISO)
L-ascorbic acid  (ISO)
methamphetamine  (EXP)
methylmercury chloride  (ISO)
miconazole  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-hexadecanoylsphingosine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nitrites  (EXP)
ochratoxin A  (ISO)
ouabain  (EXP)
ozone  (EXP)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (ISO)
phenobarbital  (ISO)
phlorizin  (ISO)
pirinixic acid  (ISO)
quercetin  (EXP)
resveratrol  (EXP,ISO)
sodium chloride  (EXP)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
sucrose  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tauroursodeoxycholic acid  (ISO)
thapsigargin  (ISO)
thimerosal  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
trovafloxacin  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
zidovudine  (ISO)
zinc atom  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
mitochondrial matrix  (IBA,IEA,ISO,ISS)
mitochondrion  (IDA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:9543345   PMID:10543959   PMID:14651853   PMID:16751257   PMID:18614015   PMID:18729827   PMID:19308875   PMID:20458337   PMID:20833797   PMID:21630459   PMID:22681889   PMID:23376485  
PMID:23602810   PMID:25378300   PMID:26316108   PMID:29476059   PMID:29867124  


Genomics

Comparative Map Data
Cs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27758,074 - 791,421 (+)NCBI
Rnor_6.0 Ensembl72,752,680 - 2,778,963 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.072,752,680 - 2,778,963 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.072,731,092 - 2,757,427 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,626,181 - 1,652,197 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.171,626,180 - 1,652,197 (+)NCBI
Celera7639,242 - 663,715 (+)NCBICelera
Cytogenetic Map7q11NCBI
CS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1256,271,699 - 56,300,391 (-)EnsemblGRCh38hg38GRCh38
GRCh381256,271,699 - 56,300,330 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371256,665,483 - 56,694,114 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361254,951,750 - 54,980,442 (-)NCBINCBI36hg18NCBI36
Celera1256,318,264 - 56,346,961 (-)NCBI
Cytogenetic Map12q13.3NCBI
HuRef1253,704,180 - 53,732,652 (-)NCBIHuRef
CHM1_11256,632,888 - 56,661,575 (-)NCBICHM1_1
Cs
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,173,596 - 128,198,351 (+)NCBIGRCm39mm39
GRCm39 Ensembl10128,173,603 - 128,198,348 (+)Ensembl
GRCm3810128,337,727 - 128,362,482 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,337,734 - 128,362,479 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710127,774,888 - 127,799,535 (+)NCBIGRCm37mm9NCBIm37
MGSCv3610127,740,781 - 127,765,428 (+)NCBImm8
Celera10130,726,084 - 130,750,750 (+)NCBICelera
Cytogenetic Map10D3NCBI
Cs
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554583,881,798 - 3,893,401 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554583,881,798 - 3,913,044 (-)NCBIChiLan1.0ChiLan1.0
CS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11232,867,225 - 32,895,854 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1232,867,225 - 32,895,854 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01232,614,982 - 32,643,719 (+)NCBIMhudiblu_PPA_v0panPan3
CS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110584,000 - 611,351 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl10584,904 - 611,436 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10647,257 - 674,790 (-)NCBI
ROS_Cfam_1.010592,484 - 620,012 (-)NCBI
UMICH_Zoey_3.110569,926 - 597,448 (-)NCBI
UNSW_CanFamBas_1.010812,910 - 840,419 (-)NCBI
UU_Cfam_GSD_1.010937,007 - 964,321 (-)NCBI
Cs
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,165,176 - 58,193,309 (+)NCBI
SpeTri2.0NW_004936646676,926 - 704,988 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,666,510 - 21,700,736 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,669,778 - 21,700,737 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2523,162,491 - 23,186,518 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap5p12-p13NCBI
CS
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11152,224,667 - 52,253,552 (-)NCBI
ChlSab1.1 Ensembl1152,222,724 - 52,253,307 (-)Ensembl

Position Markers
RH128613  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.072,777,788 - 2,778,793NCBIRnor6.0
Rnor_6.0741,978,645 - 41,978,826NCBIRnor6.0
Rnor_5.0742,011,933 - 42,012,114UniSTSRnor5.0
Rnor_5.072,756,252 - 2,757,257UniSTSRnor5.0
RGSC_v3.4737,414,998 - 37,415,179UniSTSRGSC3.4
RGSC_v3.471,651,022 - 1,652,027UniSTSRGSC3.4
Celera7662,540 - 663,545UniSTS
Celera731,611,119 - 31,611,300UniSTS
Cytogenetic Map7q13UniSTS
Cytogenetic Map7q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:85
Count of miRNA genes:75
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000033726
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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000033726   ⟹   ENSRNOP00000034921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl72,752,680 - 2,778,963 (+)Ensembl
RefSeq Acc Id: NM_130755   ⟹   NP_570111
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27763,883 - 790,122 (+)NCBI
Rnor_6.072,752,680 - 2,778,963 (+)NCBI
Rnor_5.072,731,092 - 2,757,427 (+)NCBI
RGSC_v3.471,626,181 - 1,652,197 (+)RGD
Celera7639,242 - 663,715 (+)RGD
Sequence:
RefSeq Acc Id: XM_039078324   ⟹   XP_038934252
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27761,130 - 791,421 (+)NCBI
RefSeq Acc Id: XM_039078325   ⟹   XP_038934253
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27758,074 - 791,421 (+)NCBI
Protein Sequences
Protein RefSeqs NP_570111 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934252 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934253 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAL66372 (Get FASTA)   NCBI Sequence Viewer  
  ABD77259 (Get FASTA)   NCBI Sequence Viewer  
  Q8VHF5 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_570111   ⟸   NM_130755
- Peptide Label: precursor
- UniProtKB: Q8VHF5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000034921   ⟸   ENSRNOT00000033726
RefSeq Acc Id: XP_038934253   ⟸   XM_039078325
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934252   ⟸   XM_039078324
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13694933
Promoter ID:EPDNEW_R5458
Type:initiation region
Name:Cs_1
Description:citrate synthase
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_6.072,752,636 - 2,752,696EPDNEW

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)
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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:620330 AgrOrtholog
Ensembl Genes ENSRNOG00000023520 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034921 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033726 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.230.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.10.580.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Citrate_synth-like_lrg_a-sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Citrate_synth-like_sm_a-sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Citrate_synthase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Citrate_synthase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Citrate_synthase_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Citrate_synthase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:170587 UniProtKB/Swiss-Prot
NCBI Gene 170587 ENTREZGENE
PANTHER PTHR11739 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Citrate_synt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cs PhenoGen
PRINTS CITRTSNTHASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CITRATE_SYNTHASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48256 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs cit_synth_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CISY_RAT UniProtKB/Swiss-Prot
  G3V936_RAT UniProtKB/TrEMBL
  Q0QEL8_RAT UniProtKB/TrEMBL
  Q8VHF5 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Cs  citrate synthase      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cs  citrate synthase      Symbol and Name status set to provisional 70820 PROVISIONAL