Lars2 (leucyl-tRNA synthetase 2, mitochondrial) - Rat Genome Database

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Gene: Lars2 (leucyl-tRNA synthetase 2, mitochondrial) Rattus norvegicus
Analyze
Symbol: Lars2
Name: leucyl-tRNA synthetase 2, mitochondrial
RGD ID: 1308429
Description: Predicted to enable leucine-tRNA ligase activity. Predicted to be involved in leucyl-tRNA aminoacylation and mitochondrial translation. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in Perrault syndrome. Orthologous to human LARS2 (leucyl-tRNA synthetase 2, mitochondrial); PARTICIPATES IN aminoacyl-tRNA biosynthetic pathway; valine, leucine and isoleucine biosynthetic pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: leucine--tRNA ligase, mitochondrial; leucyl-tRNA synthetase 2; leucyl-tRNA synthetase, mitochondrial; LOC363172; probable leucine--tRNA ligase, mitochondrial; probable leucyl-tRNA synthetase, mitochondrial
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
GRCr88131,887,728 - 131,983,866 (+)NCBIGRCr8
mRatBN7.28123,010,271 - 123,106,395 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,010,293 - 123,106,395 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,599,822 - 128,694,986 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,798,766 - 126,893,950 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08124,628,137 - 124,723,305 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,441,277 - 132,537,176 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,441,285 - 132,536,369 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,593,987 - 131,689,876 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,136,948 - 128,232,441 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,156,801 - 128,252,130 (+)NCBI
Celera8122,121,425 - 122,216,021 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10684970   PMID:14651853   PMID:18614015   PMID:26537577  


Genomics

Comparative Map Data
Lars2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88131,887,728 - 131,983,866 (+)NCBIGRCr8
mRatBN7.28123,010,271 - 123,106,395 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,010,293 - 123,106,395 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,599,822 - 128,694,986 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,798,766 - 126,893,950 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08124,628,137 - 124,723,305 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,441,277 - 132,537,176 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,441,285 - 132,536,369 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,593,987 - 131,689,876 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,136,948 - 128,232,441 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,156,801 - 128,252,130 (+)NCBI
Celera8122,121,425 - 122,216,021 (+)NCBICelera
Cytogenetic Map8q32NCBI
LARS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38345,388,576 - 45,549,407 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl345,388,561 - 45,554,726 (+)EnsemblGRCh38hg38GRCh38
GRCh37345,430,068 - 45,590,899 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,405,079 - 45,565,332 (+)NCBINCBI36Build 36hg18NCBI36
Build 34345,405,078 - 45,565,332NCBI
Celera345,368,449 - 45,528,754 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef345,473,932 - 45,634,902 (+)NCBIHuRef
CHM1_1345,380,072 - 45,540,452 (+)NCBICHM1_1
T2T-CHM13v2.0345,404,942 - 45,565,766 (+)NCBIT2T-CHM13v2.0
Lars2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399123,196,001 - 123,291,731 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9123,195,992 - 123,291,731 (+)EnsemblGRCm39 Ensembl
GRCm389123,366,927 - 123,462,675 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,366,927 - 123,462,666 (+)EnsemblGRCm38mm10GRCm38
MGSCv379123,276,058 - 123,371,782 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369123,215,638 - 123,311,362 (+)NCBIMGSCv36mm8
Celera9123,819,514 - 123,915,073 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map973.92NCBI
Lars2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542026,343,649 - 26,441,736 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542026,342,129 - 26,446,959 (-)NCBIChiLan1.0ChiLan1.0
LARS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2245,353,155 - 45,513,037 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1345,357,921 - 45,517,809 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0345,296,129 - 45,455,836 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1346,405,636 - 46,564,994 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl346,405,636 - 46,564,994 (+)Ensemblpanpan1.1panPan2
LARS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12042,891,823 - 43,080,987 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2042,892,801 - 43,081,197 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2042,808,439 - 42,996,879 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02043,376,360 - 43,565,565 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2043,376,366 - 43,565,639 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12042,616,558 - 42,805,467 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02043,024,169 - 43,213,262 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02043,299,029 - 43,487,924 (-)NCBIUU_Cfam_GSD_1.0
Lars2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118198,001,624 - 198,139,721 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936695350,975 - 492,011 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936695353,965 - 492,014 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LARS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1328,524,796 - 28,692,327 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11328,524,778 - 28,692,327 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21331,530,356 - 31,641,132 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LARS2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1226,861,105 - 7,021,325 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl226,861,006 - 7,020,009 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041160,147,025 - 160,307,861 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lars2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473075,228,316 - 75,335,052 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473075,228,638 - 75,335,045 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lars2
547 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:176
Count of miRNA genes:140
Interacting mature miRNAs:153
Transcripts:ENSRNOT00000068233
Prediction methods:Microtar, 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
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

Markers in Region
D8Rat192  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28123,047,278 - 123,047,447 (+)MAPPERmRatBN7.2
Rnor_6.08132,478,292 - 132,478,460NCBIRnor6.0
Rnor_5.08131,630,992 - 131,631,160UniSTSRnor5.0
RGSC_v3.48128,174,399 - 128,174,568RGDRGSC3.4
RGSC_v3.48128,174,400 - 128,174,568UniSTSRGSC3.4
RGSC_v3.18128,194,136 - 128,194,305RGD
Celera8122,157,980 - 122,158,148UniSTS
Cytogenetic Map8q32UniSTS
BE110407  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28123,105,908 - 123,106,025 (+)MAPPERmRatBN7.2
Rnor_6.08132,536,684 - 132,536,800NCBIRnor6.0
Rnor_5.08131,689,384 - 131,689,500UniSTSRnor5.0
RGSC_v3.48128,232,792 - 128,232,908UniSTSRGSC3.4
Celera8122,216,372 - 122,216,488UniSTS
RH 3.4 Map81277.79UniSTS
Cytogenetic Map8q32UniSTS


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 38 43 27 18 27 6 9 70 34 34 9 6
Low 2 5 14 14 1 14 2 2 4 1 7 2 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068233   ⟹   ENSRNOP00000058878
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,010,301 - 123,105,558 (+)Ensembl
Rnor_6.0 Ensembl8132,441,314 - 132,536,333 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087488   ⟹   ENSRNOP00000074967
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,010,293 - 123,105,695 (+)Ensembl
Rnor_6.0 Ensembl8132,441,285 - 132,536,369 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096718   ⟹   ENSRNOP00000078962
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,054,924 - 123,105,558 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101297   ⟹   ENSRNOP00000082486
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,010,302 - 123,106,395 (+)Ensembl
RefSeq Acc Id: NM_001413842   ⟹   NP_001400771
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,887,756 - 131,983,866 (+)NCBI
mRatBN7.28123,010,302 - 123,106,395 (+)NCBI
RefSeq Acc Id: XM_008766727   ⟹   XP_008764949
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,887,732 - 131,983,866 (+)NCBI
mRatBN7.28123,010,271 - 123,105,558 (+)NCBI
Rnor_6.08132,441,277 - 132,536,333 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063265860   ⟹   XP_063121930
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,887,728 - 131,973,038 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_008764949   ⟸   XM_008766727
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K9E5 (UniProtKB/TrEMBL),   A0A8I6G2M3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074967   ⟸   ENSRNOT00000087488
RefSeq Acc Id: ENSRNOP00000058878   ⟸   ENSRNOT00000068233
RefSeq Acc Id: ENSRNOP00000078962   ⟸   ENSRNOT00000096718
RefSeq Acc Id: ENSRNOP00000082486   ⟸   ENSRNOT00000101297
RefSeq Acc Id: NP_001400771   ⟸   NM_001413842
- UniProtKB: A0A8I5ZU78 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121930   ⟸   XM_063265860
- Peptide Label: isoform X2
Protein Domains
Aminoacyl-tRNA synthetase class Ia   Leucyl-tRNA synthetase editing   Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K9E5-F1-model_v2 AlphaFold A0A0G2K9E5 1-902 view protein structure

Transcriptome

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

Promoters
RGD ID:13696408
Promoter ID:EPDNEW_R6933
Type:multiple initiation site
Name:Lars2_1
Description:leucyl-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_6.08132,441,315 - 132,441,375EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308429 AgrOrtholog
BioCyc Gene G2FUF-28615 BioCyc
BioCyc Pathway TRNA-CHARGING-PWY [tRNA charging] BioCyc
BioCyc Pathway Image TRNA-CHARGING-PWY BioCyc
Ensembl Genes ENSRNOG00000004760 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068233.2 UniProtKB/TrEMBL
  ENSRNOT00000087488.2 UniProtKB/TrEMBL
  ENSRNOT00000096718.1 UniProtKB/TrEMBL
  ENSRNOT00000101297 ENTREZGENE
  ENSRNOT00000101297.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.620 UniProtKB/TrEMBL
InterPro aa-tRNA-synth_I_CS UniProtKB/TrEMBL
  aa-tRNA-synth_Ia UniProtKB/TrEMBL
  Leu-tRNA-synth_Ia_bac/mito UniProtKB/TrEMBL
  Leu_tRNA-synth_edit 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_Ia_edit UniProtKB/TrEMBL
KEGG Report rno:363172 UniProtKB/TrEMBL
NCBI Gene 363172 ENTREZGENE
PANTHER LEUCINE--TRNA LIGASE, MITOCHONDRIAL UniProtKB/TrEMBL
  PTHR43740 UniProtKB/TrEMBL
Pfam Anticodon_1 UniProtKB/TrEMBL
  tRNA-synt_1 UniProtKB/TrEMBL
  tRNA-synt_1_2 UniProtKB/TrEMBL
PhenoGen Lars2 PhenoGen
PRINTS TRNASYNTHLEU UniProtKB/TrEMBL
PROSITE AA_TRNA_LIGASE_I UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004760 RatGTEx
Superfamily-SCOP Nucleotidylyl transferase UniProtKB/TrEMBL
  tRNAsyn_1a_bind UniProtKB/TrEMBL
  ValRS_IleRS_edit UniProtKB/TrEMBL
UniProt A0A0G2K9E5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZU78 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6G2M3 ENTREZGENE, UniProtKB/TrEMBL
  D3Z9N3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-27 Lars2  leucyl-tRNA synthetase 2, mitochondrial  Lars2  leucyl-tRNA synthetase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-12-23 Lars2  leucyl-tRNA synthetase 2  Lars2  leucyl-tRNA synthetase 2, mitochondrial  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-17 Lars2  leucyl-tRNA synthetase 2, mitochondrial  Lars2  leucyl-tRNA synthetase, mitochondrial   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Lars2  leucyl-tRNA synthetase, mitochondrial   Lars2_predicted  leucyl-tRNA synthetase, mitochondrial (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lars2_predicted  leucyl-tRNA synthetase, mitochondrial (predicted)      Symbol and Name status set to approved 70820 APPROVED