Iars1 (isoleucyl-tRNA synthetase 1) - Rat Genome Database

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Gene: Iars1 (isoleucyl-tRNA synthetase 1) Rattus norvegicus
Analyze
Symbol: Iars1
Name: isoleucyl-tRNA synthetase 1
RGD ID: 621022
Description: Predicted to enable GTPase binding activity and isoleucine-tRNA ligase activity. Predicted to be involved in isoleucyl-tRNA aminoacylation. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of aminoacyl-tRNA synthetase multienzyme complex. Orthologous to human IARS1 (isoleucyl-tRNA synthetase 1); PARTICIPATES IN aminoacyl-tRNA biosynthetic pathway; valine, leucine and isoleucine biosynthetic pathway; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Iars; Iarsl; isoleucine tRNA synthetase; isoleucine--tRNA ligase, cytoplasmic; isoleucine--tRNA ligase, cytoplasmic-like; isoleucine-tRNA synthetase; isoleucine-tRNA synthetase-like; isoleucyl tRNA synthetase; isoleucyl-tRNA synthetase; isoleucyl-tRNA synthetase, cytoplasmic; LOC103690033; LOC306804
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
mRatBN7.21714,940,919 - 14,987,277 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1714,940,924 - 14,987,237 (-)Ensembl
Rnor_6.01715,356,016 - 15,402,680 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1715,355,529 - 15,402,649 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01717,414,466 - 17,461,119 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01716,604,188 - 16,614,960 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41720,895,852 - 20,942,180 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11720,895,861 - 20,937,378 (-)NCBI
Celera1714,672,657 - 14,718,804 (-)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-nitropyrene  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
acetylsalicylic acid  (ISO)
aconitine  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
amphetamine  (EXP)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
chloroacetaldehyde  (ISO)
chromium(6+)  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (ISO)
Cuprizon  (EXP)
cyclosporin A  (EXP,ISO)
diarsenic trioxide  (ISO)
dioxygen  (ISO)
elemental selenium  (ISO)
enzyme inhibitor  (ISO)
fenofibrate  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
ibuprofen  (EXP,ISO)
ifosfamide  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
lead diacetate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
menadione  (ISO)
mercury dichloride  (EXP)
metformin  (EXP)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
methylparaben  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
nefazodone  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
perfluorononanoic acid  (ISO)
quercetin  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8052601   PMID:12060739   PMID:12477932   PMID:16210410   PMID:19131329   PMID:19289464   PMID:19946888   PMID:20458337   PMID:22424946   PMID:24337748  


Genomics

Comparative Map Data
Iars1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21714,940,919 - 14,987,277 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1714,940,924 - 14,987,237 (-)Ensembl
Rnor_6.01715,356,016 - 15,402,680 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1715,355,529 - 15,402,649 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01717,414,466 - 17,461,119 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01716,604,188 - 16,614,960 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41720,895,852 - 20,942,180 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11720,895,861 - 20,937,378 (-)NCBI
Celera1714,672,657 - 14,718,804 (-)NCBICelera
Cytogenetic Map17p14NCBI
IARS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl992,210,207 - 92,293,854 (-)EnsemblGRCh38hg38GRCh38
GRCh38992,210,207 - 92,293,697 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37994,972,489 - 95,055,979 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36994,012,446 - 94,095,859 (-)NCBINCBI36hg18NCBI36
Build 34992,052,179 - 92,135,522NCBI
Celera965,408,928 - 65,492,347 (-)NCBI
Cytogenetic Map9q22.31NCBI
HuRef964,650,352 - 64,733,811 (-)NCBIHuRef
CHM1_1995,118,853 - 95,202,471 (-)NCBICHM1_1
Iars
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391349,835,606 - 49,887,743 (+)NCBIGRCm39mm39
GRCm39 Ensembl1349,835,576 - 49,887,743 (+)Ensembl
GRCm381349,682,130 - 49,734,267 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1349,682,100 - 49,734,267 (+)EnsemblGRCm38mm10GRCm38
MGSCv371349,777,499 - 49,829,636 (+)NCBIGRCm37mm9NCBIm37
MGSCv361349,694,081 - 49,746,194 (+)NCBImm8
Celera1350,772,786 - 50,823,970 (+)NCBICelera
Cytogenetic Map13A5NCBI
Iars1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555155,498,231 - 5,557,629 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555155,506,064 - 5,558,075 (+)NCBIChiLan1.0ChiLan1.0
IARS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1991,406,008 - 91,489,167 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl991,406,008 - 91,489,167 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0963,332,030 - 63,415,567 (-)NCBIMhudiblu_PPA_v0panPan3
IARS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1199,045,023 - 99,113,865 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl199,045,102 - 99,113,620 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha199,438,844 - 99,507,644 (+)NCBI
ROS_Cfam_1.0199,662,000 - 99,730,810 (+)NCBI
UMICH_Zoey_3.1199,274,953 - 99,343,693 (+)NCBI
UNSW_CanFamBas_1.0199,010,147 - 99,079,155 (+)NCBI
UU_Cfam_GSD_1.0199,766,929 - 99,835,896 (+)NCBI
Iars1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049447,672,824 - 7,732,017 (-)NCBI
SpeTri2.0NW_0049364871,889,428 - 1,948,447 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IARS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl341,945,843 - 42,052,920 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1341,945,846 - 42,022,610 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2342,962,905 - 43,014,138 (-)NCBISscrofa10.2Sscrofa10.2susScr3
IARS1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112102,745,155 - 102,819,638 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl12102,744,569 - 102,819,603 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603891,017,103 - 91,091,888 (-)NCBIVero_WHO_p1.0
Iars1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248684,062,938 - 4,168,712 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH141803  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21714,990,604 - 14,990,815 (+)MAPPERmRatBN7.2
Rnor_6.01715,406,019 - 15,406,229NCBIRnor6.0
Rnor_6.01714,565,982 - 14,566,192NCBIRnor6.0
Rnor_5.01717,464,469 - 17,464,679UniSTSRnor5.0
Rnor_5.01716,618,303 - 16,618,513UniSTSRnor5.0
RGSC_v3.41720,945,568 - 20,945,778UniSTSRGSC3.4
Celera1714,722,192 - 14,722,402UniSTS
RH 3.4 Map17157.3UniSTS
Cytogenetic Map17p14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17429913021293263Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1581553Pur14Proteinuria QTL 145.30.0001total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17797996816317111Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat
1549900Iddm20Insulin dependent diabetes mellitus QTL 203.7pancreas integrity trait (VT:0010560)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)171398677321975515Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:300
Count of miRNA genes:183
Interacting mature miRNAs:201
Transcripts:ENSRNOT00000019862
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 3 27 42 29 18 29 1 3 74 28 33 11 1
Low 16 15 12 1 12 7 8 7 8 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019862   ⟹   ENSRNOP00000019862
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1714,940,924 - 14,987,237 (-)Ensembl
Rnor_6.0 Ensembl1715,356,016 - 15,402,631 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078166   ⟹   ENSRNOP00000071046
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1714,940,924 - 14,987,237 (-)Ensembl
Rnor_6.0 Ensembl1714,541,949 - 14,557,792 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086344   ⟹   ENSRNOP00000069534
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1714,940,926 - 14,987,237 (-)Ensembl
Rnor_6.0 Ensembl1715,355,529 - 15,398,988 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093637   ⟹   ENSRNOP00000076307
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1714,940,926 - 14,987,237 (-)Ensembl
Rnor_6.0 Ensembl1715,356,019 - 15,402,649 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101044   ⟹   ENSRNOP00000085677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1714,941,664 - 14,987,237 (-)Ensembl
RefSeq Acc Id: NM_001100572   ⟹   NP_001094042
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21714,940,919 - 14,987,217 (-)NCBI
Rnor_6.01715,356,016 - 15,402,631 (-)NCBI
Rnor_5.01717,414,466 - 17,461,119 (-)NCBI
RGSC_v3.41720,895,852 - 20,942,180 (-)RGD
Celera1714,672,657 - 14,718,804 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253706   ⟹   XP_006253768
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21714,941,414 - 14,987,277 (-)NCBI
Rnor_6.01715,356,023 - 15,402,680 (-)NCBI
Rnor_5.01717,414,466 - 17,461,119 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771533   ⟹   XP_008769755
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21714,941,414 - 14,987,254 (-)NCBI
Rnor_6.01715,356,023 - 15,402,679 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001094042 (Get FASTA)   NCBI Sequence Viewer  
  XP_006253768 (Get FASTA)   NCBI Sequence Viewer  
  XP_008769755 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91369 (Get FASTA)   NCBI Sequence Viewer  
  EDL98104 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001094042   ⟸   NM_001100572
- UniProtKB: F1LS86 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253768   ⟸   XM_006253706
- Peptide Label: isoform X1
- UniProtKB: F1LS86 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769755   ⟸   XM_008771533
- Peptide Label: isoform X1
- UniProtKB: F1LS86 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000076307   ⟸   ENSRNOT00000093637
RefSeq Acc Id: ENSRNOP00000019862   ⟸   ENSRNOT00000019862
RefSeq Acc Id: ENSRNOP00000069534   ⟸   ENSRNOT00000086344
RefSeq Acc Id: ENSRNOP00000071046   ⟸   ENSRNOT00000078166
RefSeq Acc Id: ENSRNOP00000085677   ⟸   ENSRNOT00000101044
Protein Domains
Anticodon_1   tRNA-synt_1

Transcriptome

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

Promoters
RGD ID:13700350
Promoter ID:EPDNEW_R10872
Type:initiation region
Name:Iars_1
Description:isoleucyl-tRNA synthetase
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_6.01715,402,648 - 15,402,708EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
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)
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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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)
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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
F344/Stm (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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/FarMcwi (2019)
Visual CSV TAB Printer
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)
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2019)
Visual CSV TAB Printer
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)
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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)
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 (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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)
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/RijCrl (2020)
Visual CSV TAB Printer
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)
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
WKY/N (2020)
Visual CSV TAB Printer
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)
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
WKY/NCrl (2019)
Visual CSV TAB Printer
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)
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
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 17414977 17414978 G A snv SDLEF7/Barth (UDEL), BDIX/NemOda (KyushuU), Crl:SD (UDEL), LE/OrlBarth (UDEL)
17 17415001 17415002 G T snv BDIX.Cg-Tal/NemOda (KyushuU), F344/NSlc (KyushuU), Crl:SD (UDEL), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL)
17 17416406 17416407 G T snv LE/Stm (KyushuU)
17 17416432 17416433 C T snv LE/Stm (KyushuU)
17 17428187 17428188 C A snv SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), F344/Stm (KyushuU), BDIX/NemOda (KyushuU)
17 17428224 17428225 G T snv F344/Stm (KyushuU), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), BDIX/NemOda (KyushuU)
17 17429090 17429091 C A snv LE/OrlBarth (UDEL), Crl:SD (UDEL)
17 17429109 17429110 C A snv LE/OrlBarth (UDEL), Crl:SD (UDEL)
17 17434701 17434702 C T snv LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL)
17 17434713 17434714 A T snv LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL)
17 17434733 17434734 G T snv SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL)
17 17434742 17434743 T C snv LE/OrlBarth (UDEL), Crl:SD (UDEL), F344/NSlc (KyushuU), SDLEF7/Barth (UDEL)
17 17434773 17434774 C T snv Crl:SD (UDEL), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL)
17 17438848 17438849 C T snv SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL)
17 17438875 17438876 G T snv Crl:SD (UDEL), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL)
17 17438937 17438938 C T snv LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), Crl:SD (UDEL)
17 17438947 17438948 C T snv F344/NSlc (KyushuU), Crl:SD (UDEL), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL)
17 17438976 17438977 C T snv NIG-III/Hok (KyushuU), F344/NSlc (KyushuU), SDLEF7/Barth (UDEL), Crl:SD (UDEL), LE/OrlBarth (UDEL)
17 17438980 17438981 G A snv Crl:SD (UDEL), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), NIG-III/Hok (KyushuU), F344/NSlc (KyushuU)
17 17440155 17440156 T G snv LE/OrlBarth (UDEL), Crl:SD (UDEL)
17 17443610 17443611 G A snv Crl:SD (UDEL), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL)
17 17443614 17443615 G T snv F344/NSlc (KyushuU), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU), Crl:SD (UDEL)
17 17445687 17445688 C T snv Crl:SD (UDEL), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL)
17 17445693 17445694 G T snv LE/OrlBarth (UDEL), Crl:SD (UDEL), SDLEF7/Barth (UDEL)
17 17445737 17445738 C T snv LE/OrlBarth (UDEL)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 14942861 14942862 G T snv ACI/EurMcwi (2019), ACI/N (2020), WN/N (2020), WAG/RijCrl (2020), SR/JrHsd (2020), MWF/Hsd (2019), MR/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), FXLE18/Stm (2020), FXLE16/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), DA/OlaHsd (2019), F344/NCrl (2019)
17 14942887 14942888 C T snv MWF/Hsd (2019), WN/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), FXLE16/Stm (2020), F344/Stm (2019), F344/NCrl (2019), ACI/N (2020), ACI/EurMcwi (2019), WAG/RijCrl (2020), SR/JrHsd (2020), MR/N (2020)
17 14942894 14942895 G T snv ACI/EurMcwi (2019), ACI/N (2020), F344/NCrl (2019), F344/Stm (2019), FXLE16/Stm (2020), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), MR/N (2020), MWF/Hsd (2019), SR/JrHsd (2020), WAG/RijCrl (2020), WN/N (2020)
17 14961157 14961158 C T snv WN/N (2020), LEXF10A/StmMcwi (2020), LEXF1C/Stm (2019), LEXF1A/Stm (2019)
17 14961169 14961170 A T snv LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF10A/StmMcwi (2020)
17 14961189 14961190 G T snv ACI/N (2020), WN/N (2020), LEXF10A/StmMcwi (2020), LEXF1C/Stm (2019), LEXF1A/Stm (2019)
17 14961198 14961199 T C snv LEXF1C/Stm (2019), LEXF1A/Stm (2019), ACI/N (2020), WN/N (2020), LEXF10A/StmMcwi (2020)
17 14961229 14961230 C T snv LEXF10A/StmMcwi (2020), LEXF1A/Stm (2019), WN/N (2020), LEXF1C/Stm (2019), ACI/N (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 15356527 15356528 G A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), GH/OmrMcwi (MCW)
17 15356551 15356552 G T snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW)
17 15357956 15357957 G T snv MWF/Hsd (2019), SR/JrHsd (2020), WAG/RijCrl (2020), WN/N (2020), MR/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), FXLE18/Stm (2020), FXLE16/Stm (2020), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), DA/OlaHsd (2019), ACI/N (2020), ACI/EurMcwi (2019), CDR, SR/JrHsd (MCW)
17 15357982 15357983 C T snv F344/NCrl (2019), F344/Stm (2019), FXLE16/Stm (2020), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), MR/N (2020), MWF/Hsd (2019), SR/JrHsd (2020), WAG/RijCrl (2020), WN/N (2020), CDR, ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019)
17 15357989 15357990 G T snv CDR, WN/N (2020), ACI/N (2020), F344/NCrl (2019), F344/Stm (2019), FXLE16/Stm (2020), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), MR/N (2020), MWF/Hsd (2019), SR/JrHsd (2020), WAG/RijCrl (2020), ACI/EurMcwi (2019)
17 15362398 15362399 A T snv CDR, COP/CrCrl (MCW & UW)
17 15364739 15364740 C T snv COP/CrCrl (MCW & UW)
17 15364748 15364749 C T snv COP/CrCrl (MCW & UW)
17 15365967 15365968 C G snv CDR, LE/Stm (RGD)
17 15365997 15365998 G C snv CDR
17 15366000 15366001 G A snv CDR
17 15366009 15366010 G T snv CDR
17 15366023 15366024 G A snv CDR
17 15366029 15366030 G A snv CDR
17 15366030 15366031 C G snv CDR
17 15368880 15368881 C T snv PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WN/N (2020), MWF/Hsd (2019), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF3/Stm (2020), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), LEW/Crl (2019), FXLE18/Stm (2020), FXLE16/Stm (2020), FHH/EurMcwi (2019), F344/N (2020), F344/Stm (2019), F344/NCrl (2019), F344/DuCrl (2019), DA/OlaHsd (2019), ACI/N (2020), ACI/EurMcwi (2019), CDR
17 15368892 15368893 A G snv LEXF1A/Stm (2019), F344/NCrl (2019), LEXF3/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WN/N (2020), F344/DuCrl (2019), DA/OlaHsd (2019), ACI/N (2020), ACI/EurMcwi (2019), COP/CrCrl (MCW & UW), CDR, LEXF11/Stm (2020), LEW/Crl (2019), FXLE18/Stm (2020), FXLE16/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), LEXF1C/Stm (2019)
17 15368903 15368904 C G snv CDR, COP/CrCrl (MCW & UW), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WN/N (2020)
17 15368911 15368912 C T snv SS/JrHsdMcwi (2019), SR/JrHsd (2020), WN/N (2020), PVG/Seac (2019), MWF/Hsd (2019), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF3/Stm (2020), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), LEW/Crl (2019), FXLE18/Stm (2020), FXLE16/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), DA/OlaHsd (2019), ACI/N (2020), ACI/EurMcwi (2019), COP/CrCrl (MCW & UW), CDR
17 15368913 15368914 G A snv SS/JrHsdMcwi (2019), CDR, SR/JrHsd (2020), PVG/Seac (2019), MWF/Hsd (2019), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF3/Stm (2020), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), LEW/Crl (2019), FXLE18/Stm (2020), FXLE16/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), DA/OlaHsd (2019), ACI/N (2020), ACI/EurMcwi (2019), COP/CrCrl (MCW & UW), WN/N (2020)
17 15368940 15368941 G C snv LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF3/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WN/N (2020), CDR, ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020)
17 15369737 15369738 C A snv CDR, ACI/EurMcwi (MCW), WN/N (2020), WAG/RijCrl (2020), SS/JrHsdMcwi (2019), SR/JrHsd (2020), PVG/Seac (2019), MWF/Hsd (2019), MR/N (2020), M520/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF2B/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), LEW/Crl (2019), FXLE18/Stm (2020), FXLE16/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019)
17 15369774 15369775 G T snv LEXF1A/Stm (2019), WN/N (2020), F344/NCrl (2019), F344/DuCrl (2019), ACI/N (2020), ACI/EurMcwi (2019), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), WAG/RijCrl (2020), SR/JrHsd (2020), PVG/Seac (2019), MR/N (2020), M520/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), FXLE18/Stm (2020)
17 15370640 15370641 C A snv ACI/N (2020), FHH/EurMcwi (2019), WAG/RijCrl (2020), LEXF4/Stm (2020), LEXF10A/StmMcwi (2020), LEXF3/Stm (2020)
17 15370659 15370660 C A snv SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), ACI/N (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/Stm (2019), FHH/EurMcwi (2019), LEXF11/Stm (2020), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/N (2020), MWF/Hsd (2019)
17 15376251 15376252 C T snv SBN/Ygl (MCW), ACI/N (2020), F344/DuCrl (2019), F344/N (2020), FXLE16/Stm (2020), WN/N (2020), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF4/Stm (2020), LEXF10A/StmMcwi (2020), M520/N (2020), FXLE18/Stm (2020)
17 15376263 15376264 A T snv M520/N (2020), WN/N (2020), LEXF10A/StmMcwi (2020), LEXF4/Stm (2020), LEXF1A/Stm (2019), LEXF11/Stm (2020), FXLE18/Stm (2020), FXLE16/Stm (2020), F344/N (2020), F344/DuCrl (2019), ACI/N (2020), SBN/Ygl (MCW), COP/CrCrl (MCW & UW)
17 15376283 15376284 G T snv F344/DuCrl (2019), F344/N (2020), FXLE16/Stm (2020), FXLE18/Stm (2020), LEXF11/Stm (2020), ACI/N (2020), LEXF4/Stm (2020), LEXF10A/StmMcwi (2020), M520/N (2020), WAG/RijCrl (2020), WN/N (2020), LEXF1A/Stm (2019)
17 15376292 15376293 T C snv LEXF1A/Stm (2019), LEXF4/Stm (2020), LEXF10A/StmMcwi (2020), M520/N (2020), WAG/RijCrl (2020), WN/N (2020), ACI/EurMcwi (MCW), LEXF11/Stm (2020), FXLE18/Stm (2020), FXLE16/Stm (2020), F344/N (2020), F344/DuCrl (2019), ACI/N (2020), ACI/N (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW)
17 15376323 15376324 C T snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), ACI/N (2020), F344/DuCrl (2019), F344/N (2020), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF4/Stm (2020), LEXF10A/StmMcwi (2020), M520/N (2020), WAG/RijCrl (2020), WN/N (2020)
17 15380398 15380399 C T snv CDR, WN/N (2020), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), ACI/EurMcwi (MCW)
17 15380425 15380426 G T snv SBH/Ygl (MCW), SS/JrHsdMcwi (MCW), SBN/Ygl (RGD), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WN/N (2020), CDR, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW)
17 15380447 15380448 C A snv WAG/RijCrl (2020), SS/JrHsdMcwi (2019), WN/N (2020), SR/JrHsd (2020), PVG/Seac (2019), MWF/Hsd (2019), MR/N (2020), M520/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF2B/Stm (2019), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), LEW/Crl (2019), FXLE18/Stm (2020), FXLE16/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), DA/OlaHsd (2019), ACI/N (2020), ACI/EurMcwi (2019), SBN/Ygl (RGD), SS/JrHsdMcwi (MCW), CDR
17 15380452 15380453 T A snv WN/N (2020), CDR, SS/JrHsdMcwi (2019), SR/JrHsd (2020), PVG/Seac (2019), MWF/Hsd (2019), MR/N (2020), M520/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF2B/Stm (2019), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), LEW/Crl (2019), FXLE18/Stm (2020), FXLE16/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), DA/OlaHsd (2019), ACI/N (2020), ACI/EurMcwi (2019), WAG/RijCrl (2020)
17 15380453 15380454 C G snv CDR, ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WN/N (2020)
17 15380454 15380455 T G snv LEXF1A/Stm (2019), LEXF11/Stm (2020), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WN/N (2020), CDR, ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF1C/Stm (2019)
17 15380487 15380488 C T snv LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WN/N (2020), CDR, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019)
17 15380497 15380498 C T snv CDR, WN/N (2020), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), ACI/EurMcwi (MCW)
17 15380526 15380527 C T snv LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WN/N (2020), CDR, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020)
17 15380530 15380531 G A snv CDR, WN/N (2020), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), ACI/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 20916128 20916129 T C snv ACI/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621022 AgrOrtholog
  RGD:9226700 AgrOrtholog
Ensembl Genes ENSRNOG00000014616 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000052977 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019862 UniProtKB/TrEMBL
  ENSRNOP00000069534 UniProtKB/TrEMBL
  ENSRNOP00000071046 UniProtKB/TrEMBL
  ENSRNOP00000076307 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019862 UniProtKB/TrEMBL
  ENSRNOT00000078166 UniProtKB/TrEMBL
  ENSRNOT00000086344 UniProtKB/TrEMBL
  ENSRNOT00000093637 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.620 UniProtKB/TrEMBL
  3.90.740.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7319346 IMAGE-MGC_LOAD
InterPro aa-tRNA-synth_I_CS UniProtKB/TrEMBL
  aa-tRNA-synth_Ia UniProtKB/TrEMBL
  Anticodon_Ile_ABEc UniProtKB/TrEMBL
  Ile-tRNA-ligase UniProtKB/TrEMBL
  Ile-tRNA-ligase_type2 UniProtKB/TrEMBL
  Rossmann-like_a/b/a_fold UniProtKB/TrEMBL
  tRNAsynth_1a_anticodon-bd UniProtKB/TrEMBL
  V/L/I-tRNA-synth_anticodon-bd UniProtKB/TrEMBL
  Val/Leu/Ile-tRNA-synth_edit UniProtKB/TrEMBL
KEGG Report rno:306804 UniProtKB/TrEMBL
MGC_CLONE MGC:109429 IMAGE-MGC_LOAD
NCBI Gene 306804 ENTREZGENE
Pfam Anticodon_1 UniProtKB/TrEMBL
  tRNA-synt_1 UniProtKB/TrEMBL
PhenoGen Iars1 PhenoGen
PRINTS TRNASYNTHILE UniProtKB/TrEMBL
PROSITE AA_TRNA_LIGASE_I UniProtKB/TrEMBL
Superfamily-SCOP tRNAsyn_1a_bind UniProtKB/TrEMBL
  ValRS_IleRS_edit UniProtKB/TrEMBL
TIGRFAMs ileS UniProtKB/TrEMBL
UniProt A0A0G2JVL8_RAT UniProtKB/TrEMBL
  A0A0G2JZH2_RAT UniProtKB/TrEMBL
  F1LS86 ENTREZGENE, UniProtKB/TrEMBL
  Q5BJR3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Iars1  isoleucyl-tRNA synthetase 1  LOC103690033  isoleucine--tRNA ligase, cytoplasmic-like  Data Merged 737654 PROVISIONAL
2019-08-08 Iars1  isoleucyl-tRNA synthetase 1  Iars  isoleucyl-tRNA synthetase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103690033  isoleucine--tRNA ligase, cytoplasmic-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-11-06 Iars  isoleucyl-tRNA synthetase  Iars  isoleucine-tRNA synthetase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-23 Iars  isoleucine-tRNA synthetase  Iarsl  isoleucine-tRNA synthetase-like  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2008-09-23 Iarsl  isoleucine-tRNA synthetase-like  Iars  isoleucine-tRNA synthetase  Data Merged 737654 APPROVED
2008-05-05 Iars  isoleucine-tRNA synthetase  Iars_predicted  isoleucine-tRNA synthetase (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-05 Iarsl  isoleucine-tRNA synthetase-like  Iars  isoleucine-tRNA synthetase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Iars  isoleucine-tRNA synthetase      Symbol and Name status set to approved 1299863 APPROVED
2005-01-12 Iars_predicted  isoleucine-tRNA synthetase (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Iars  isoleucine-tRNA synthetase      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the vascular smooth muscle cells 631940
gene_process maybe involved in determining distinctive epithelioid phenotype of smooth muscle cells 631940
gene_regulation over-expressed after injury 631940