Cad (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) - Rat Genome Database

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Gene: Cad (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) Rattus norvegicus
Analyze
Symbol: Cad
Name: carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase
RGD ID: 1588606
Description: Exhibits several functions, including aspartate carbamoyltransferase activity; carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity; and dihydroorotase activity. Involved in several processes, including alpha-amino acid metabolic process; animal organ development; and pyrimidine-containing compound biosynthetic process. Localizes to several cellular components, including cytosol; neuronal cell body; and terminal bouton. Used to study hepatocellular carcinoma. Biomarker of hepatocellular carcinoma. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 50. Orthologous to human CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase); PARTICIPATES IN 2-hydroxyglutaric aciduria pathway; beta-ureidopropionase deficiency pathway; Canavan disease pathway; INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; 4-amino-2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: INFERRED
Also known as: Cad_mapped; Carbamyl phosphatate synthetase; carbamyl phosphatate synthetase 2; carbamyl phosphatate synthetase 2 (mapped)
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
mRatBN7.2625,292,133 - 25,315,176 (-)NCBI
Rnor_6.0 Ensembl626,657,780 - 26,680,284 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0626,657,507 - 26,680,459 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0636,472,498 - 36,495,450 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4625,272,416 - 25,296,266 (-)NCBIRGSC3.4rn4RGSC3.4
Celera624,783,039 - 24,805,943 (-)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
1. Aoki T, etal., J Biol Chem. 1982 Jan 10;257(1):432-8.
2. Blade C, etal., Arch Int Physiol Biochim. 1988 Dec;96(5):201-9.
3. Bond JS Biochim Biophys Acta. 1976 Nov 18;451(1):238-49.
4. Bush A, etal., Genes Dev. 1998 Dec 15;12(24):3797-802.
5. CALVA E and COHEN PP, Cancer Res. 1959 Jul;19(6, Part 1):679-83.
6. CALVA E, etal., Cancer Res. 1959 Jan;19(1):101-3.
7. Cammer W and Downing M, J Histochem Cytochem. 1991 May;39(5):695-700.
8. Chernova OB, etal., Trends Biochem Sci 1995 Oct;20(10):431-4.
9. Evans DR and Guy HI, J Biol Chem. 2004 Aug 6;279(32):33035-8. Epub 2004 Apr 19.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Gorlich M and Heise E, Nature. 1967 Mar 4;213(5079):934-5.
12. Graves LM, etal., Nature. 2000 Jan 20;403(6767):328-32.
13. Karsai T, etal., Anticancer Res. 1985 Jul-Aug;5(4):441-4.
14. Kunjara S, etal., Biochem Med Metab Biol. 1992 Dec;48(3):263-74.
15. Minana MD, etal., J Neurochem. 1984 Dec;43(6):1556-60.
16. Mori M and Tatibana M, Eur J Biochem. 1978 May 16;86(2):381-8.
17. Mori M, etal., Biochemistry. 1975 Jun 17;14(12):2622-30.
18. Nagasaki T Nippon Sanka Fujinka Gakkai Zasshi. 1985 Jan;37(1):24-30.
19. NORDMANN Y, etal., Nature. 1964 Feb 8;201:616-7.
20. Otto E, etal., J Biol Chem. 1989 Feb 25;264(6):3390-6.
21. Patnaik SK and Patnaik R, Biochem Int. 1990;20(4):641-7.
22. Pipeline to import KEGG annotations from KEGG into RGD
23. Pipeline to import SMPDB annotations from SMPDB into RGD
24. Reardon MA and Weber G, Biochem J. 1987 Jun 1;244(2):345-50.
25. Reardon MA, etal., Biochem Biophys Res Commun. 1987 Aug 31;147(1):494-500.
26. RGD automated data pipeline
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Schroeder PE, etal., Drug Metab Dispos. 2008 Sep;36(9):1780-5. Epub 2008 May 30.
30. Szondy Z and Newsholme EA, Biochem J. 1989 Aug 1;261(3):979-83.
31. Thibodeau PS and Thayer SA, Endocrinology. 1967 Mar;80(3):505-9.
32. Zhou P, etal., Cancer Res. 1996 Jan 1;56(1):36-9.
Additional References at PubMed
PMID:9525610   PMID:15326225   PMID:15890648   PMID:19946888   PMID:20458337   PMID:24332717   PMID:24746616   PMID:25763846   PMID:30361391  


Genomics

Comparative Map Data
Cad
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2625,292,133 - 25,315,176 (-)NCBI
Rnor_6.0 Ensembl626,657,780 - 26,680,284 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0626,657,507 - 26,680,459 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0636,472,498 - 36,495,450 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4625,272,416 - 25,296,266 (-)NCBIRGSC3.4rn4RGSC3.4
Celera624,783,039 - 24,805,943 (-)NCBICelera
Cytogenetic Map6q14NCBI
CAD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl227,217,369 - 27,243,943 (+)EnsemblGRCh38hg38GRCh38
GRCh38227,217,369 - 27,243,943 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37227,440,237 - 27,466,811 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36227,293,762 - 27,320,158 (+)NCBINCBI36hg18NCBI36
Build 34227,351,908 - 27,378,305NCBI
Celera227,286,585 - 27,312,981 (+)NCBI
Cytogenetic Map2p23.3NCBI
HuRef227,181,964 - 27,208,360 (+)NCBIHuRef
CHM1_1227,370,163 - 27,396,565 (+)NCBICHM1_1
Cad
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39531,211,964 - 31,235,823 (+)NCBIGRCm39mm39
GRCm39 Ensembl531,212,124 - 31,235,823 (+)Ensembl
GRCm38531,054,620 - 31,078,479 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl531,054,780 - 31,078,479 (+)EnsemblGRCm38mm10GRCm38
MGSCv37531,357,184 - 31,380,852 (+)NCBIGRCm37mm9NCBIm37
MGSCv36531,331,392 - 31,355,060 (+)NCBImm8
Celera528,526,834 - 28,551,927 (+)NCBICelera
Cytogenetic Map5B1NCBI
Cad
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554699,203,434 - 9,227,865 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554699,203,433 - 9,227,526 (+)NCBIChiLan1.0ChiLan1.0
CAD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A27,306,488 - 27,332,804 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A27,306,527 - 27,332,804 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A27,218,699 - 27,245,156 (+)NCBIMhudiblu_PPA_v0panPan3
CAD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11721,198,839 - 21,221,897 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1721,197,826 - 21,221,635 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1721,090,639 - 21,113,701 (+)NCBI
ROS_Cfam_1.01721,519,811 - 21,542,872 (+)NCBI
UMICH_Zoey_3.11721,206,567 - 21,229,628 (+)NCBI
UNSW_CanFamBas_1.01721,217,636 - 21,240,698 (+)NCBI
UU_Cfam_GSD_1.01721,264,518 - 21,287,583 (+)NCBI
Cad
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629265,506,657 - 65,529,337 (+)NCBI
SpeTri2.0NW_0049364935,308,268 - 5,332,934 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3111,887,020 - 111,914,495 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13111,887,017 - 111,914,511 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CAD
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11480,371,154 - 80,399,193 (-)NCBI
ChlSab1.1 Ensembl1480,371,096 - 80,398,914 (-)Ensembl
Cad
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247389,318,213 - 9,340,765 (+)NCBI

Position Markers
MARC4015-4016  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2625,293,392 - 25,293,827 (+)MAPPER
Rnor_6.0626,658,767 - 26,659,201NCBIRnor6.0
Rnor_5.0636,473,758 - 36,474,192UniSTSRnor5.0
RGSC_v3.4625,273,677 - 25,274,111UniSTSRGSC3.4
Celera624,784,303 - 24,784,737UniSTS
Cytogenetic Map6q14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6135623029Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6135623029Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6135623029Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6135623029Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6135623029Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6112039328706721Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295834367603Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:188
Count of miRNA genes:128
Interacting mature miRNAs:136
Transcripts:ENSRNOT00000039709
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 2 26 38 22 19 22 1 1 60 22 34 11 1
Low 1 17 19 19 19 7 10 14 13 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039709   ⟹   ENSRNOP00000030030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl626,657,780 - 26,680,284 (-)Ensembl
RefSeq Acc Id: NM_001105710   ⟹   NP_001099180
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,292,133 - 25,315,078 (-)NCBI
Rnor_6.0626,657,507 - 26,680,459 (-)NCBI
Rnor_5.0636,472,498 - 36,495,450 (-)NCBI
RGSC_v3.4625,272,416 - 25,296,266 (-)RGD
Celera624,783,039 - 24,805,943 (-)RGD
Sequence:
RefSeq Acc Id: XM_039111774   ⟹   XP_038967702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,292,134 - 25,315,176 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099180   ⟸   NM_001105710
- Sequence:
RefSeq Acc Id: ENSRNOP00000030030   ⟸   ENSRNOT00000039709
RefSeq Acc Id: XP_038967702   ⟸   XM_039111774
- Peptide Label: isoform X1
Transcriptome

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


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)
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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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
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
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 25291448 25291449 G T snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588606 AgrOrtholog
Ensembl Genes ENSRNOG00000026474 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000030030 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039709 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.1030.10 UniProtKB/TrEMBL
  3.30.1490.20 UniProtKB/TrEMBL
  3.40.50.1370 UniProtKB/TrEMBL
  3.40.50.1380 UniProtKB/TrEMBL
  3.40.50.880 UniProtKB/TrEMBL
  3.50.30.20 UniProtKB/TrEMBL
InterPro Amidohydro-rel UniProtKB/TrEMBL
  Asp/Orn_carbamoyltranf_P-bd UniProtKB/TrEMBL
  Asp/Orn_carbamoylTrfase UniProtKB/TrEMBL
  Asp/Orn_carbamoylTrfase_sf UniProtKB/TrEMBL
  Asp_carbamoyltransf_Asp/Orn-bd UniProtKB/TrEMBL
  Asp_carbamoyltransf_euk UniProtKB/TrEMBL
  ATP-grasp UniProtKB/TrEMBL
  ATP_grasp_subdomain_1 UniProtKB/TrEMBL
  CarbamoylP_synth_lsu UniProtKB/TrEMBL
  CarbamoylP_synth_lsu_ATP-bd UniProtKB/TrEMBL
  CarbamoylP_synth_lsu_Gln-dep UniProtKB/TrEMBL
  CarbamoylP_synth_lsu_oligo UniProtKB/TrEMBL
  CarbamoylP_synth_lsu_oligo_sf UniProtKB/TrEMBL
  CarbamoylP_synth_ssu UniProtKB/TrEMBL
  CarbamoylP_synth_ssu_N UniProtKB/TrEMBL
  CarbP_synth_ssu_N_sf UniProtKB/TrEMBL
  Class_I_gatase-like UniProtKB/TrEMBL
  CPSase_GATase1 UniProtKB/TrEMBL
  Dihydroorotase_CS UniProtKB/TrEMBL
  GATASE_1 UniProtKB/TrEMBL
  Metal-dep_hydrolase_composite UniProtKB/TrEMBL
  Metal_Hydrolase UniProtKB/TrEMBL
  MGS UniProtKB/TrEMBL
  MGS-like_dom_sf UniProtKB/TrEMBL
  PreATP-grasp-like UniProtKB/TrEMBL
NCBI Gene 24240 ENTREZGENE
Pfam Amidohydro_1 UniProtKB/TrEMBL
  CPSase_L_D2 UniProtKB/TrEMBL
  CPSase_L_D3 UniProtKB/TrEMBL
  CPSase_sm_chain UniProtKB/TrEMBL
  GATase UniProtKB/TrEMBL
  MGS UniProtKB/TrEMBL
  OTCace UniProtKB/TrEMBL
  OTCace_N UniProtKB/TrEMBL
PhenoGen Cad PhenoGen
PRINTS AOTCASE UniProtKB/TrEMBL
  CPSASE UniProtKB/TrEMBL
PROSITE ATP_GRASP UniProtKB/TrEMBL
  CARBAMOYLTRANSFERASE UniProtKB/TrEMBL
  CPSASE_1 UniProtKB/TrEMBL
  CPSASE_2 UniProtKB/TrEMBL
  DIHYDROOROTASE_1 UniProtKB/TrEMBL
  DIHYDROOROTASE_2 UniProtKB/TrEMBL
  GATASE_TYPE_1 UniProtKB/TrEMBL
  MGS UniProtKB/TrEMBL
SMART CPSase_L_D3 UniProtKB/TrEMBL
  CPSase_sm_chain UniProtKB/TrEMBL
  MGS UniProtKB/TrEMBL
Superfamily-SCOP Asp/Orn_carbamoyltranf UniProtKB/TrEMBL
  CarbamoylP_synth_lsu_oligo UniProtKB/TrEMBL
  CP_synthsmall UniProtKB/TrEMBL
  Metalo_hydrolase UniProtKB/TrEMBL
  MGS-like_dom UniProtKB/TrEMBL
  PreATP-grasp-like UniProtKB/TrEMBL
  SSF51556 UniProtKB/TrEMBL
  SSF52317 UniProtKB/TrEMBL
TIGRFAMs asp_carb_tr UniProtKB/TrEMBL
  CPSaseII_lrg UniProtKB/TrEMBL
  CPSaseIIsmall UniProtKB/TrEMBL
UniProt D4A8A0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-03 Cad  carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase  Cad  carbamyl phosphatate synthetase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-13   carbamyl phosphatate synthetase 2  Cad  carbamyl phosphatate synthetase 2 (mapped)  Name updated 737654 APPROVED
2007-04-10 Cad  carbamyl phosphatate synthetase 2 (mapped)  Cad_mapped  carbamyl phosphatate synthetase 2 (mapped)  Data Merged 737654 APPROVED
2006-11-19 Cad  carbamyl phosphatate synthetase 2 (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Cad_mapped  carbamyl phosphatate synthetase 2 (mapped)  Cad  carbamyl phosphatate synthetase 2  Symbol and Name updated 1556543 APPROVED
2003-04-09 Cad  carbamyl phosphatate synthetase 2    Carbamyl phosphatate synthetase  Name updated 629478 APPROVED
2002-06-10 Cad  Carbamyl phosphatate synthetase      Symbol and Name status set to approved 70586 APPROVED