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 enable valine-tRNA ligase activity. Predicted to be involved in valyl-tRNA aminoacylation. Predicted to be located in mitochondrion. Predicted to be active in 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 (Ensembl: pseudogene)
RefSeq Status: VALIDATED
Previously 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
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
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,077,132 - 3,087,994 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,077,132 - 3,087,994 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx203,128,469 - 3,139,341 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0203,133,442 - 3,144,314 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0203,159,764 - 3,170,643 (+)NCBIRnor_WKY
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Information Derived from GenBank Report RGD, Sept. 2003
Additional References at PubMed
PMID:18614015  


Genomics

Comparative Map Data
Vars2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,077,132 - 3,087,994 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,077,132 - 3,087,994 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx203,128,469 - 3,139,341 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0203,133,442 - 3,144,314 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0203,159,764 - 3,170,643 (+)NCBIRnor_WKY
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38630,914,238 - 30,926,459 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl630,914,205 - 30,926,459 (+)EnsemblGRCh38hg38GRCh38
GRCh37630,882,015 - 30,894,236 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36630,989,961 - 31,002,212 (+)NCBINCBI36Build 36hg18NCBI36
Build 34630,989,960 - 31,002,212NCBI
Celera632,480,085 - 32,492,348 (+)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef630,682,069 - 30,694,336 (+)NCBIHuRef
CHM1_1630,884,168 - 30,896,411 (+)NCBICHM1_1
T2T-CHM13v2.0630,778,904 - 30,791,138 (+)NCBIT2T-CHM13v2.0
Vars2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,966,526 - 35,978,531 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,966,526 - 35,978,484 (-)EnsemblGRCm39 Ensembl
GRCm381735,655,634 - 35,667,639 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,655,634 - 35,667,592 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,792,579 - 35,804,537 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,743,659 - 34,754,865 (-)NCBIMGSCv36mm8
MGSCv361735,264,443 - 35,275,645 (-)NCBIMGSCv36mm8
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_v0Mhudiblu_PPA_v0panPan3
VARS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.112681,638 - 694,154 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl12680,484 - 693,913 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha12819,638 - 832,091 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.012826,116 - 838,552 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl12826,144 - 839,748 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.112685,417 - 697,855 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.012753,862 - 766,305 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.012821,750 - 834,201 (+)NCBIUU_Cfam_GSD_1.0
Vars2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494634,187,526 - 34,200,138 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936837552,839 - 565,530 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936837552,837 - 565,348 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VARS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,404,824 - 23,416,439 (+)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11741,537,842 - 41,550,063 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1741,534,552 - 41,549,439 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604430,615,225 - 30,627,428 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vars2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475424,856,939 - 24,870,932 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475424,856,704 - 24,870,932 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vars2
144 total Variants
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.


QTLs in Region (mRatBN7.2)
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)2013624629Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat


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
mRatBN7.2 Ensembl203,077,132 - 3,087,994 (+)Ensembl
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
mRatBN7.2203,077,132 - 3,087,994 (+)NCBI
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:
Protein Sequences
Protein RefSeqs NP_998728 (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: ENSRNOP00000046565   ⟸   ENSRNOT00000048103

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG21-F1-model_v2 AlphaFold Q6MG21 1-1065 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303122 AgrOrtholog
BioCyc Gene G2FUF-4764 BioCyc
BioCyc Pathway TRNA-CHARGING-PWY [tRNA charging] BioCyc
Ensembl Genes ENSRNOG00000000833 Ensembl
Gene3D-CATH 3.40.50.620 UniProtKB/Swiss-Prot
  3.90.740.10 UniProtKB/Swiss-Prot
InterPro aa-tRNA-synth_I_CS UniProtKB/Swiss-Prot
  aa-tRNA-synth_Ia UniProtKB/Swiss-Prot
  Anticodon_Ia_Val UniProtKB/Swiss-Prot
  M/V/L/I-tRNA-synth_anticd-bd UniProtKB/Swiss-Prot
  Rossmann-like_a/b/a_fold UniProtKB/Swiss-Prot
  tRNAsynth_Ia_anticodon-bd UniProtKB/Swiss-Prot
  Val/Leu/Ile-tRNA-synth_edit UniProtKB/Swiss-Prot
  Valyl-tRNA_ligase UniProtKB/Swiss-Prot
KEGG Report rno:309596 UniProtKB/Swiss-Prot
NCBI Gene 309596 ENTREZGENE
PANTHER PTHR11946 UniProtKB/Swiss-Prot
Pfam Anticodon_1 UniProtKB/Swiss-Prot
  tRNA-synt_1 UniProtKB/Swiss-Prot
PhenoGen Vars2 PhenoGen
PRINTS TRNASYNTHVAL UniProtKB/Swiss-Prot
PROSITE AA_TRNA_LIGASE_I UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47323 UniProtKB/Swiss-Prot
  SSF50677 UniProtKB/Swiss-Prot
TIGRFAMs valS UniProtKB/Swiss-Prot
UniProt 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