Vars2 (valyl-tRNA synthetase 2, mitochondrial) - Rat Genome Database
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Gene: Vars2 (valyl-tRNA synthetase 2, mitochondrial) Rattus norvegicus
Analyze
Symbol: Vars2
Name: valyl-tRNA synthetase 2, mitochondrial
RGD ID: 1303122
Description: Predicted to have valine-tRNA ligase activity. Predicted to be involved in valyl-tRNA aminoacylation. Predicted to localize to cytosol. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 20. Orthologous to human VARS2 (valyl-tRNA synthetase 2, mitochondrial); PARTICIPATES IN aminoacyl-tRNA biosynthetic pathway; valine, leucine and isoleucine biosynthetic pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: KIAA1885; valine--tRNA ligase; valine--tRNA ligase, mitochondrial; valRS; valyl-tRNA synthetase 2, mitochondrial (putative); valyl-tRNA synthetase 2-like; valyl-tRNA synthetase, mitochondrial; valyl-tRNA synthetase-like; Vars2l; Varsl
Orthologs:
Homo sapiens (human) : VARS2 (valyl-tRNA synthetase 2, mitochondrial)  HGNC  Alliance
Mus musculus (house mouse) : Vars2 (valyl-tRNA synthetase 2, mitochondrial)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Vars2 (valyl-tRNA synthetase 2, mitochondrial)
Pan paniscus (bonobo/pygmy chimpanzee) : VARS2 (valyl-tRNA synthetase 2, mitochondrial)
Canis lupus familiaris (dog) : VARS2 (valyl-tRNA synthetase 2, mitochondrial)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Vars2 (valyl-tRNA synthetase 2, mitochondrial)
Sus scrofa (pig) : VARS2 (valyl-tRNA synthetase 2, mitochondrial)
Chlorocebus sabaeus (African green monkey) : VARS2 (valyl-tRNA synthetase 2, mitochondrial)
Heterocephalus glaber (naked mole-rat) : Vars2 (valyl-tRNA synthetase 2, mitochondrial)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0203,588,462 - 3,599,514 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,588,497 - 3,599,514 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,685,445 - 5,696,499 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,228,063 - 3,238,909 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,228,289 - 3,239,136 (+)NCBI
Celera20502,836 - 513,682 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IBA)
mitochondrion  (IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:18614015  


Genomics

Comparative Map Data
Vars2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0203,588,462 - 3,599,514 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,588,497 - 3,599,514 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,685,445 - 5,696,499 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,228,063 - 3,238,909 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,228,289 - 3,239,136 (+)NCBI
Celera20502,836 - 513,682 (+)NCBICelera
Cytogenetic Map20p12NCBI
VARS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl630,914,205 - 30,926,459 (+)EnsemblGRCh38hg38GRCh38
GRCh38630,914,238 - 30,926,459 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37630,881,982 - 30,894,236 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36630,989,961 - 31,002,212 (+)NCBINCBI36hg18NCBI36
Build 34630,989,960 - 31,002,212NCBI
Celera632,480,085 - 32,492,348 (+)NCBI
Cytogenetic Map6p21.33NCBI
HuRef630,682,069 - 30,694,336 (+)NCBIHuRef
CHM1_1630,884,171 - 30,896,411 (+)NCBICHM1_1
Vars2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,966,526 - 35,978,531 (-)NCBI
GRCm381735,655,634 - 35,667,639 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,655,634 - 35,667,592 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,792,579 - 35,804,537 (-)NCBIGRCm37mm9NCBIm37
MGSCv361734,743,659 - 34,754,865 (-)NCBImm8
MGSCv361735,264,443 - 35,275,645 (-)NCBImm8
Cytogenetic Map17B1NCBI
Vars2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955583848,481 - 866,424 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955583848,166 - 862,360 (+)NCBIChiLan1.0ChiLan1.0
VARS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1631,527,503 - 31,539,814 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl631,527,372 - 31,539,814 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0630,659,346 - 30,671,678 (+)NCBIMhudiblu_PPA_v0panPan3
VARS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl12680,484 - 693,913 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.112681,638 - 694,154 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Vars2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936837552,837 - 565,348 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VARS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,398,445 - 23,418,295 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1723,404,400 - 23,416,442 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,126,633 - 27,138,695 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VARS2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1741,534,552 - 41,549,439 (-)Ensembl
ChlSab1.11741,537,842 - 41,550,063 (-)NCBI
Vars2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,856,704 - 24,870,932 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2020187706567419Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2031518156896013Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2031518156896013Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:81
Count of miRNA genes:69
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000048103
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 30 20 17 3 17 66 25 32 3
Low 13 37 24 16 24 8 11 8 10 9 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048103   ⟹   ENSRNOP00000046565
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,588,497 - 3,598,904 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,598,171 - 3,599,514 (+)Ensembl
RefSeq Acc Id: NM_213563   ⟹   NP_998728
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0203,588,513 - 3,599,359 (+)NCBI
Rnor_5.0205,685,445 - 5,696,499 (+)NCBI
RGSC_v3.4203,228,063 - 3,238,909 (+)RGD
Celera20502,836 - 513,682 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255932   ⟹   XP_006255994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0203,588,462 - 3,599,514 (+)NCBI
Rnor_5.0205,685,445 - 5,696,499 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255933   ⟹   XP_006255995
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0203,588,921 - 3,599,514 (+)NCBI
Rnor_5.0205,685,445 - 5,696,499 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255934   ⟹   XP_006255996
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0203,588,462 - 3,599,514 (+)NCBI
Rnor_5.0205,685,445 - 5,696,499 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_998728 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255994 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255995 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255996 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAE84026 (Get FASTA)   NCBI Sequence Viewer  
  Q6MG21 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_998728   ⟸   NM_213563
- Peptide Label: precursor
- UniProtKB: Q6MG21 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006255996   ⟸   XM_006255934
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006255994   ⟸   XM_006255932
- Peptide Label: isoform X1
- UniProtKB: A0A0H2UHY0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255995   ⟸   XM_006255933
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000046565   ⟸   ENSRNOT00000048103
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:13701307
Promoter ID:EPDNEW_R11831
Type:initiation region
Name:Vars2_1
Description:valyl-tRNA synthetase 2, mitochondrial
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_6.0203,588,536 - 3,588,596EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5686815 5686816 T A snv SBH/Ygl (MCW), ZF (KyushuU), SBN/Ygl (MCW), MHS/Gib (KNAW), MR/N (KNAW), WAG/Rij (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), FHL/EurMcwi (KNAW), MNS/Gib (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), LEC/Tj (KyushuU), KFRS3B/Kyo (KyushuU), FHL/EurMcwi (MCW)
20 5688925 5688926 G A snv SBH/Ygl (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), MHS/Gib (KNAW), MR/N (KNAW), WAG/Rij (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), FHL/EurMcwi (KNAW), MNS/Gib (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), LEC/Tj (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU)
20 5690814 5690815 G A snv LE/Stm (SOLiD) (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (KyushuU), LN/MavRrrc (KNAW), LH/MavRrrc (KNAW), BUF/N (KNAW), M520/N (KNAW)
20 5695067 5695068 A T snv SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), F344/NRrrc (Illumina) (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), LE/OrlBarth (UDEL), Crl:SD (UDEL), F344/DuCrlCrlj (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), SR/JrHsd (KNAW), LL/MavRrrc (KNAW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW), F344/Jcl (KyushuU), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 3589830 3589831 T A snv BBDP/Wor (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), WAG/Rij (RGD), SBN/Ygl (RGD), SBH/Ygl (RGD), MNS/Gib (RGD), MHS/Gib (RGD), WKY/NHsd (RGD), FHL/EurMcwi (RGD), WKY/N (MCW), MR/N (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW)
20 3591940 3591941 G A snv SBH/Ygl (MCW), WKY/N (MCW), SBH/Ygl (RGD), WKY/Gcrc (RGD), SBN/Ygl (MCW), FHL/EurMcwi (MCW), SBN/Ygl (RGD), MNS/Gib (RGD), FHL/EurMcwi (RGD)
20 3593829 3593830 G A snv LN/MavRrrc (RGD), LH/MavRrrc (RGD), LE/Stm (RGD), M520/N (MCW), Buf/N (MCW)
20 3598082 3598083 A T snv F344/NRrrc (MCW), COP/CrCrl (MCW & UW), ACI/N (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (RGD), LL/MavRrrc (RGD), SS/Jr (RGD), ACI/EurMcwi (RGD), FHH/EurMcwi (MCW), SR/JrHsd (RGD), SS/JrHsdMcwi (RGD), ACI/EurMcwi (MCW), F344/NCrl (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 3229380 3229381 T A snv FHL/EurMcwi (ICL), WKY/NHsd (ICL), WAG/Rij (ICL), MHS/Gib (ICL), WKY/Gcrc (ICL), SBN/Ygl (ICL), SBH/Ygl (ICL), BBDP/WorN (ICL), WKY/N (KNAW), LCR/1Mco (UMich), HCR/1Mco (UMich), MNS/Gib (ICL), FHL/EurMcwi (MCW), HCR/2Mco (UMich), WKY/NCrl (ICL), MR/N (KNAW)
20 3231490 3231491 G A snv WKY/NHsd (ICL), WKY/NCrl (ICL), WKY/N (KNAW), LCR/1Mco (UMich), BBDP/WorN (ICL), HCR/2Mco (UMich), WKY/Gcrc (ICL), SBN/Ygl (ICL), SBH/Ygl (ICL), MNS/Gib (ICL), MHS/Gib (ICL), FHL/EurMcwi (MCW), FHL/EurMcwi (ICL)
20 3233379 3233380 G A snv LCR/2Mco (UMich), BUF/N (KNAW), M520/N (KNAW), LN/MavRrrc (ICL), LE/Stm (KNAW), LH/MavRrrc (ICL), HCR/1Mco (UMich), LE/Stm (ICL), LCR/1Mco (UMich)
20 3237632 3237633 A T snv F344/NHsd (ICAHN), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), SS/JrHsdMcwi (ICL), SS/Jr (ICL), SR/JrHsd (ICL), LL/MavRrrc (ICL), FHH/EurMcwi (ICL), F344/NCrl (ICL), ACI/EurMcwi (ICL), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), F344/NRrrc (KNAW), ACI/N (KNAW), DA/BklArbNsi (ICAHN), FHH/EurMcwi (MDC), SS/JrHsdMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303122 AgrOrtholog
Ensembl Genes ENSRNOG00000000833 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046565 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048103 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.620 UniProtKB/TrEMBL
  3.90.740.10 UniProtKB/TrEMBL
InterPro aa-tRNA-synth_I_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  aa-tRNA-synth_Ia UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Anticodon_Ia_Val UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  M/V/L/I-tRNA-synth_anticd-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rossmann-like_a/b/a_fold UniProtKB/TrEMBL
  tRNAsynth_Ia_anticodon-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Val/Leu/Ile-tRNA-synth_edit UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Valyl-tRNA_ligase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:309596 UniProtKB/Swiss-Prot
NCBI Gene 309596 ENTREZGENE
Pfam Anticodon_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  tRNA-synt_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vars2 PhenoGen
PRINTS TRNASYNTHVAL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE AA_TRNA_LIGASE_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47323 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50677 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs valS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.43153 ENTREZGENE
UniProt A0A0H2UHY0 ENTREZGENE, UniProtKB/TrEMBL
  Q6MG21 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-11-07 Vars2  valyl-tRNA synthetase 2, mitochondrial  Vars2  valyl-tRNA synthetase 2, mitochondrial (putative)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Vars2  valyl-tRNA synthetase 2, mitochondrial (putative)  Varsl  valyl-tRNA synthetase-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Varsl  valyl-tRNA synthetase-like  Vars2l  valyl-tRNA synthetase 2-like  Symbol and Name updated 1299863 APPROVED
2006-03-30 Vars2l  valyl-tRNA synthetase 2-like      Symbol and Name status set to approved 1299863 APPROVED
2005-02-14 Vars2l  valyl-tRNA synthetase 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL