Yars2 (tyrosyl-tRNA synthetase 2) - Rat Genome Database

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Gene: Yars2 (tyrosyl-tRNA synthetase 2) Rattus norvegicus
Analyze
Symbol: Yars2
Name: tyrosyl-tRNA synthetase 2
RGD ID: 1311696
Description: Predicted to enable several functions, including L-tyrosine binding activity; protein homodimerization activity; and tyrosine-tRNA ligase activity. Predicted to be involved in mitochondrial tyrosyl-tRNA aminoacylation. Predicted to be located in mitochondrial matrix and nuclear body. Predicted to be active in cytosol and mitochondrion. Human ortholog(s) of this gene implicated in myopathy, lactic acidosis, and sideroblastic anemia 2. Orthologous to human YARS2 (tyrosyl-tRNA synthetase 2); PARTICIPATES IN aminoacyl-tRNA biosynthetic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 4-amino-2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CGI-04; LOC287924; RGD1311696; similar to CGI-04 protein; tyrosine--tRNA ligase; tyrosine--tRNA ligase, mitochondrial; tyrosyl-tRNA synthetase 2 (mitochondrial); tyrosyl-tRNA synthetase 2, mitochondrial; tyrosyl-tRNA synthetase, mitochondrial; tyrRS
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81198,136,530 - 98,142,320 (-)NCBIGRCr8
mRatBN7.21184,632,350 - 84,638,138 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1184,624,369 - 84,638,125 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1193,364,537 - 93,370,276 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01186,025,678 - 86,031,417 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01185,079,277 - 85,085,016 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01188,882,615 - 88,888,377 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1188,882,616 - 88,888,377 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01191,936,942 - 91,942,704 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,609,037 - 86,614,799 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11186,649,633 - 86,655,395 (+)NCBI
Celera1183,377,810 - 83,383,571 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IBA)
mitochondrial matrix  (IEA,ISO)
mitochondrion  (IBA,ISO)
nuclear body  (IEA,ISO)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:15779907   PMID:15840810   PMID:17997975   PMID:18614015   PMID:20598274   PMID:22681889  


Genomics

Comparative Map Data
Yars2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81198,136,530 - 98,142,320 (-)NCBIGRCr8
mRatBN7.21184,632,350 - 84,638,138 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1184,624,369 - 84,638,125 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1193,364,537 - 93,370,276 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01186,025,678 - 86,031,417 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01185,079,277 - 85,085,016 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01188,882,615 - 88,888,377 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1188,882,616 - 88,888,377 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01191,936,942 - 91,942,704 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,609,037 - 86,614,799 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11186,649,633 - 86,655,395 (+)NCBI
Celera1183,377,810 - 83,383,571 (-)NCBICelera
Cytogenetic Map11q23NCBI
YARS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381232,746,544 - 32,755,897 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1232,727,490 - 32,755,897 (-)EnsemblGRCh38hg38GRCh38
GRCh371232,899,478 - 32,908,831 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361232,790,726 - 32,800,141 (-)NCBINCBI36Build 36hg18NCBI36
Celera1212,720,156 - 12,729,572 (-)NCBICelera
Cytogenetic Map12p11.21NCBI
HuRef1232,651,954 - 32,661,361 (-)NCBIHuRef
CHM1_11232,865,980 - 32,875,403 (-)NCBICHM1_1
T2T-CHM13v2.01232,601,526 - 32,632,178 (-)NCBIT2T-CHM13v2.0
Yars2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391616,120,829 - 16,127,504 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1616,120,829 - 16,127,504 (+)EnsemblGRCm39 Ensembl
GRCm381616,302,965 - 16,309,640 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1616,302,965 - 16,309,640 (+)EnsemblGRCm38mm10GRCm38
MGSCv371616,303,075 - 16,309,721 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361616,216,560 - 16,223,206 (+)NCBIMGSCv36mm8
Celera1616,874,023 - 16,880,669 (+)NCBICelera
Cytogenetic Map16A2NCBI
cM Map1610.11NCBI
Yars2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555053,004,146 - 3,010,735 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555053,004,084 - 3,011,003 (+)NCBIChiLan1.0ChiLan1.0
YARS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21063,989,046 - 64,002,439 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11263,987,793 - 63,998,835 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01253,463,086 - 53,493,352 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11256,065,505 - 56,076,026 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1256,065,505 - 56,076,026 (+)Ensemblpanpan1.1panPan2
YARS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12716,139,462 - 16,162,701 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2716,139,499 - 16,161,147 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2730,259,986 - 30,287,139 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02716,320,190 - 16,347,401 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2716,320,205 - 16,343,475 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12716,128,784 - 16,155,906 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02716,161,357 - 16,188,536 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02730,407,857 - 30,435,045 (-)NCBIUU_Cfam_GSD_1.0
Yars2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494576,731,948 - 76,747,507 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366073,565,295 - 3,574,846 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366073,565,333 - 3,590,499 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
YARS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl541,561,626 - 41,584,818 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1541,561,563 - 41,584,534 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
YARS2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11132,181,214 - 32,192,654 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1132,181,397 - 32,192,454 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660692,704,100 - 2,717,210 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Yars2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247783,383,017 - 3,390,036 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247783,382,993 - 3,390,357 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Yars2
22 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:94
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000034902
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat

Markers in Region
RH129946  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map11q23UniSTS
RH131679  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21184,632,091 - 84,632,307 (+)MAPPERmRatBN7.2
Rnor_6.01188,882,357 - 88,882,572NCBIRnor6.0
Rnor_5.01191,936,684 - 91,936,899UniSTSRnor5.0
RGSC_v3.41186,614,842 - 86,615,057UniSTSRGSC3.4
Celera1183,377,552 - 83,377,767UniSTS
Cytogenetic Map11q23UniSTS


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 21 60 106 72 21 72 172 77 96
Low 81 121 75 48 75 36 45 78 38 49 53 24
Below cutoff

Sequence


Ensembl Acc Id: ENSRNOT00000034902   ⟹   ENSRNOP00000037398
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1184,624,369 - 84,638,125 (-)Ensembl
Rnor_6.0 Ensembl1188,882,616 - 88,888,377 (-)Ensembl
RefSeq Acc Id: NM_001009627   ⟹   NP_001009627
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81198,136,530 - 98,142,292 (-)NCBI
mRatBN7.21184,632,350 - 84,638,112 (-)NCBI
Rnor_6.01188,882,615 - 88,888,377 (-)NCBI
Rnor_5.01191,936,942 - 91,942,704 (-)NCBI
RGSC_v3.41186,609,037 - 86,614,799 (+)RGD
Celera1183,377,810 - 83,383,571 (-)RGD
Sequence:
RefSeq Acc Id: XM_039088056   ⟹   XP_038943984
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81198,139,158 - 98,142,320 (-)NCBI
mRatBN7.21184,634,978 - 84,638,138 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001009627 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943984 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88224 (Get FASTA)   NCBI Sequence Viewer  
  EDL77848 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037398.5
GenBank Protein Q5I0L3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001009627   ⟸   NM_001009627
- UniProtKB: Q5I0L3 (UniProtKB/Swiss-Prot),   A6JSQ9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000037398   ⟸   ENSRNOT00000034902
RefSeq Acc Id: XP_038943984   ⟸   XM_039088056
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5I0L3-F1-model_v2 AlphaFold Q5I0L3 1-471 view protein structure

Transcriptome

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

Promoters
RGD ID:13698344
Promoter ID:EPDNEW_R8869
Type:multiple initiation site
Name:Yars2_1
Description:tyrosyl-tRNA synthetase 2
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_6.01188,888,390 - 88,888,450EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311696 AgrOrtholog
BioCyc Gene G2FUF-20550 BioCyc
BioCyc Pathway TRNA-CHARGING-PWY [tRNA charging] BioCyc
BioCyc Pathway Image TRNA-CHARGING-PWY BioCyc
Ensembl Genes ENSRNOG00000025252 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034902.5 UniProtKB/TrEMBL
Gene3D-CATH 3.10.290.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.620 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyrosyl-Transfer RNA Synthetase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7322099 IMAGE-MGC_LOAD
InterPro aa-tRNA-synth_I_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  aa-tRNA-synth_Ic UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rossmann-like_a/b/a_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S4_RNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr-tRNA-ligase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr-tRNA-ligase_bac-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:287924 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108978 IMAGE-MGC_LOAD
NCBI Gene 287924 ENTREZGENE
PANTHER PTHR11766 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYROSINE--TRNA LIGASE, MITOCHONDRIAL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam tRNA-synt_1b UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Yars2 PhenoGen
PRINTS TRNASYNTHTYR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE AA_TRNA_LIGASE_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025252 RatGTEx
Superfamily-SCOP Alpha-L RNA-binding motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotidylyl transferase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2ULB9_RAT UniProtKB/TrEMBL
  A6JSQ9 ENTREZGENE, UniProtKB/TrEMBL
  Q5I0L3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Yars2  tyrosyl-tRNA synthetase 2  Yars2  tyrosyl-tRNA synthetase 2 (mitochondrial)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Yars2  tyrosyl-tRNA synthetase 2 (mitochondrial)  RGD1311696  similar to CGI-04 protein  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1311696  similar to CGI-04 protein  RGD1311696_predicted  similar to CGI-04 protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1311696_predicted  similar to CGI-04 protein (predicted)  LOC287924_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC287924_predicted  similar to CGI-04 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL