Csad (cysteine sulfinic acid decarboxylase) - Rat Genome Database

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Gene: Csad (cysteine sulfinic acid decarboxylase) Rattus norvegicus
Analyze
Symbol: Csad
Name: cysteine sulfinic acid decarboxylase
RGD ID: 621030
Description: Enables sulfinoalanine decarboxylase activity. Involved in L-cysteine catabolic process to hypotaurine and L-cysteine catabolic process to taurine. Located in cytoplasm. Orthologous to human CSAD (cysteine sulfinic acid decarboxylase); PARTICIPATES IN taurine and hypotaurine metabolic pathway; transsulfuration pathway of homocysteine metabolism; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 3,3',5-triiodo-L-thyronine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: aspartate 1-decarboxylase; cysteine-sulfinate decarboxylase; sulfinoalanine decarboxylase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27133,308,571 - 133,337,914 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7133,308,574 - 133,337,615 (-)Ensembl
Rnor_6.07143,781,520 - 143,810,880 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7143,781,702 - 143,793,970 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07141,579,061 - 141,608,043 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47140,917,995 - 140,944,405 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17140,994,262 - 141,036,798 (-)NCBI
Celera7129,743,152 - 129,755,012 (-)NCBICelera
Cytogenetic Map7q36NCBI
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
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chlorohydrocarbon  (EXP)
clobetasol  (ISO)
clofibrate  (ISO)
cocaine  (EXP)
coumarin  (EXP)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dioxygen  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
finasteride  (EXP)
folic acid  (ISO)
furan  (EXP,ISO)
gentamycin  (EXP)
glycidol  (EXP)
indometacin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linezolid  (EXP)
lipopolysaccharide  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
naphthalenes  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
perfluorooctanoic acid  (ISO)
permethrin  (EXP,ISO)
phenformin  (EXP)
phenobarbital  (EXP,ISO)
pirinixic acid  (EXP,ISO)
pravastatin  (EXP,ISO)
propiconazole  (ISO)
Propiverine  (EXP)
quercetin  (ISO)
quinolin-8-ol  (ISO)
rac-lactic acid  (ISO)
ritodrine  (ISO)
sodium arsenite  (EXP)
succimer  (ISO)
tamoxifen  (ISO)
tauroursodeoxycholic acid  (EXP)
Tesaglitazar  (EXP)
testosterone  (EXP,ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vincristine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IDA)
cytosol  (TAS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:15489334   PMID:17634260   PMID:24639894  


Genomics

Comparative Map Data
Csad
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27133,308,571 - 133,337,914 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7133,308,574 - 133,337,615 (-)Ensembl
Rnor_6.07143,781,520 - 143,810,880 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7143,781,702 - 143,793,970 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07141,579,061 - 141,608,043 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47140,917,995 - 140,944,405 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17140,994,262 - 141,036,798 (-)NCBI
Celera7129,743,152 - 129,755,012 (-)NCBICelera
Cytogenetic Map7q36NCBI
CSAD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1253,157,663 - 53,180,925 (-)EnsemblGRCh38hg38GRCh38
GRCh381253,157,663 - 53,181,663 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371253,551,447 - 53,574,709 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361251,837,714 - 51,860,647 (-)NCBINCBI36hg18NCBI36
Build 341251,837,714 - 51,860,647NCBI
Celera1253,200,050 - 53,223,033 (-)NCBI
Cytogenetic Map12q13.13NCBI
HuRef1250,594,015 - 50,617,263 (-)NCBIHuRef
CHM1_11253,517,875 - 53,541,124 (-)NCBICHM1_1
Csad
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,085,432 - 102,113,487 (-)NCBIGRCm39mm39
GRCm39 Ensembl15102,085,434 - 102,113,159 (-)Ensembl
GRCm3815102,176,997 - 102,205,052 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,176,999 - 102,204,724 (-)EnsemblGRCm38mm10GRCm38
MGSCv3715102,007,429 - 102,019,474 (-)NCBIGRCm37mm9NCBIm37
MGSCv3615102,005,032 - 102,017,077 (-)NCBImm8
Celera15104,331,920 - 104,345,992 (-)NCBICelera
Cytogenetic Map15F2NCBI
Csad
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955458423,085 - 433,429 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955458423,156 - 449,763 (-)NCBIChiLan1.0ChiLan1.0
CSAD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11236,354,360 - 36,379,738 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1236,354,437 - 36,379,738 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01235,572,064 - 35,598,077 (+)NCBIMhudiblu_PPA_v0panPan3
CSAD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1272,005,482 - 2,036,703 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl272,005,355 - 2,036,228 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2744,212,975 - 44,245,324 (-)NCBI
ROS_Cfam_1.0272,008,554 - 2,041,174 (+)NCBI
UMICH_Zoey_3.1272,027,628 - 2,058,651 (+)NCBI
UNSW_CanFamBas_1.0272,011,598 - 2,043,893 (+)NCBI
UU_Cfam_GSD_1.02744,613,914 - 44,645,943 (-)NCBI
Csad
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494562,689,751 - 62,717,369 (+)NCBI
SpeTri2.0NW_00493651210,447,457 - 10,475,231 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSAD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl518,379,340 - 18,410,212 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1518,379,340 - 18,410,446 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2518,793,689 - 18,805,868 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CSAD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11149,256,629 - 49,288,367 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1149,256,628 - 49,288,112 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037196,772,440 - 196,805,680 (+)NCBIVero_WHO_p1.0
Csad
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249041,190,393 - 1,228,337 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
AI576585  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27133,309,191 - 133,309,408 (+)MAPPERmRatBN7.2
Rnor_6.07143,782,141 - 143,782,357NCBIRnor6.0
Rnor_5.07141,579,682 - 141,579,898UniSTSRnor5.0
RGSC_v3.47140,918,446 - 140,918,662UniSTSRGSC3.4
Celera7129,743,603 - 129,743,819UniSTS
RH 3.4 Map71062.1UniSTS
Cytogenetic Map7q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:373
Count of miRNA genes:209
Interacting mature miRNAs:229
Transcripts:ENSRNOT00000016205
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


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 1 26 51 35 14 35 1 1 74 35 34 11 1
Low 2 17 6 6 5 6 7 10 7 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001134454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_021750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242438 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765782 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005486716 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC110347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH008061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ132615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ132661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC081804 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU786150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU906909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M64755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U74492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X94152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000016205   ⟹   ENSRNOP00000016205
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,309,011 - 133,337,615 (-)Ensembl
Rnor_6.0 Ensembl7143,781,781 - 143,793,970 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079678   ⟹   ENSRNOP00000073508
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,308,574 - 133,336,981 (-)Ensembl
Rnor_6.0 Ensembl7143,781,702 - 143,793,774 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102299   ⟹   ENSRNOP00000087863
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,308,574 - 133,323,786 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110884   ⟹   ENSRNOP00000093937
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,308,574 - 133,336,981 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113521   ⟹   ENSRNOP00000080923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,309,346 - 133,337,615 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117956   ⟹   ENSRNOP00000085105
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,308,574 - 133,336,981 (-)Ensembl
RefSeq Acc Id: NM_021750   ⟹   NP_068518
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,336,981 (-)NCBI
Rnor_6.07143,781,747 - 143,793,970 (-)NCBI
Rnor_5.07141,579,061 - 141,608,043 (-)NCBI
RGSC_v3.47140,917,995 - 140,944,405 (-)RGD
Celera7129,743,209 - 129,755,012 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242438   ⟹   XP_006242500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,337,911 (-)NCBI
Rnor_6.07143,781,520 - 143,810,880 (-)NCBI
Rnor_5.07141,579,061 - 141,608,043 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242439   ⟹   XP_006242501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,337,196 (-)NCBI
Rnor_6.07143,781,520 - 143,810,087 (-)NCBI
Rnor_5.07141,579,061 - 141,608,043 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242440   ⟹   XP_006242502
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,337,910 (-)NCBI
Rnor_6.07143,781,520 - 143,810,880 (-)NCBI
Rnor_5.07141,579,061 - 141,608,043 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039079834   ⟹   XP_038935762
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,336,708 (-)NCBI
RefSeq Acc Id: XM_039079835   ⟹   XP_038935763
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,337,132 (-)NCBI
RefSeq Acc Id: XM_039079836   ⟹   XP_038935764
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,322,342 (-)NCBI
RefSeq Acc Id: XM_039079837   ⟹   XP_038935765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,321,088 (-)NCBI
RefSeq Acc Id: XM_039079838   ⟹   XP_038935766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,337,914 (-)NCBI
RefSeq Acc Id: XM_039079839   ⟹   XP_038935767
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,336,708 (-)NCBI
RefSeq Acc Id: XR_005486716
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,308,571 - 133,321,088 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_068518   ⟸   NM_021750
- UniProtKB: Q64611 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242500   ⟸   XM_006242438
- Peptide Label: isoform X1
- UniProtKB: Q64611 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242502   ⟸   XM_006242440
- Peptide Label: isoform X1
- UniProtKB: Q64611 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242501   ⟸   XM_006242439
- Peptide Label: isoform X1
- UniProtKB: Q64611 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016205   ⟸   ENSRNOT00000016205
RefSeq Acc Id: ENSRNOP00000073508   ⟸   ENSRNOT00000079678
RefSeq Acc Id: XP_038935766   ⟸   XM_039079838
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038935763   ⟸   XM_039079835
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935767   ⟸   XM_039079839
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038935762   ⟸   XM_039079834
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935764   ⟸   XM_039079836
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935765   ⟸   XM_039079837
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000087863   ⟸   ENSRNOT00000102299
RefSeq Acc Id: ENSRNOP00000080923   ⟸   ENSRNOT00000113521
RefSeq Acc Id: ENSRNOP00000093937   ⟸   ENSRNOT00000110884
RefSeq Acc Id: ENSRNOP00000085105   ⟸   ENSRNOT00000117956

Transcriptome

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

Promoters
RGD ID:13695692
Promoter ID:EPDNEW_R6217
Type:initiation region
Name:Csad_1
Description:cysteine sulfinic acid decarboxylase
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_6.07143,794,012 - 143,794,072EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (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)
ACI/EurMcwi (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
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
COP/CrCrl (MCW & UW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NRrrc (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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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)
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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)
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)
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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/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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)
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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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:621030 AgrOrtholog
Ensembl Genes ENSRNOG00000011573 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016205 UniProtKB/Swiss-Prot
  ENSRNOP00000073508 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016205 UniProtKB/Swiss-Prot
  ENSRNOT00000079678 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7106840 IMAGE-MGC_LOAD
InterPro PyrdxlP-dep_de-COase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_small UniProtKB/TrEMBL
  Pyridoxal-P_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60356 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93461 IMAGE-MGC_LOAD
NCBI Gene 60356 ENTREZGENE
Pfam Pyridoxal_deC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Csad PhenoGen
PROSITE DDC_GAD_HDC_YDC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53383 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K5P7_RAT UniProtKB/TrEMBL
  B3VPA7_RAT UniProtKB/TrEMBL
  B5LSW7_RAT UniProtKB/TrEMBL
  CSAD_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q9R1F5_RAT UniProtKB/TrEMBL
UniProt Secondary Q546T1 UniProtKB/Swiss-Prot
  Q64577 UniProtKB/Swiss-Prot
  Q9R1F6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Csad  cysteine sulfinic acid decarboxylase    cysteine-sulfinate decarboxylase  Name updated 1299863 APPROVED
2002-08-07 Csad  cysteine-sulfinate decarboxylase      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation expression and activity are inhibited by triiodothyronine and estrogen 632596