TARS3

gene
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Also known as FLJ25005ThrRS-L

Summary

TARS3 (threonyl-tRNA synthetase 3, HGNC:24728) is a protein-coding gene on chromosome 15q26.3, encoding Threonine–tRNA ligase 2, cytoplasmic (A2RTX5). Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr).

Predicted to enable threonine-tRNA ligase activity. Predicted to be involved in threonyl-tRNA aminoacylation. Predicted to be located in cytoplasm and nucleus. Predicted to be active in mitochondrion.

Source: NCBI Gene 123283 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 140 total
  • MANE Select transcript: NM_152334

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24728
Approved symbolTARS3
Namethreonyl-tRNA synthetase 3
Location15q26.3
Locus typegene with protein product
StatusApproved
AliasesFLJ25005, ThrRS-L
Ensembl geneENSG00000185418
Ensembl biotypeprotein_coding
Entrez123283

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 14 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000335968, ENST00000539112, ENST00000557811, ENST00000558533, ENST00000559492, ENST00000560150, ENST00000615656, ENST00000907978, ENST00000907979, ENST00000907980, ENST00000907981, ENST00000907982, ENST00000911609, ENST00000947768, ENST00000947769, ENST00000947770, ENST00000947771, ENST00000947772, ENST00000947773

RefSeq mRNA: 1 — MANE Select: NM_152334 NM_152334

CCDS: CCDS10394

Canonical transcript exons

ENST00000335968 — 19 exons

ExonStartEnd
ENSE00001295990101701086101701184
ENSE00001303704101714840101714963
ENSE00001303811101702239101702385
ENSE00001312103101657785101657857
ENSE00001324218101721126101721322
ENSE00001352874101703859101703937
ENSE00001352899101723093101723164
ENSE00001368541101705683101705747
ENSE00001373829101711880101712001
ENSE00001387081101708793101708910
ENSE00001876578101724091101724473
ENSE00001957517101653596101654730
ENSE00003482557101675600101675737
ENSE00003493619101685896101686062
ENSE00003512652101671671101671748
ENSE00003594310101661712101661816
ENSE00003626558101684075101684237
ENSE00003669552101671486101671586
ENSE00003686532101656922101657036

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 95.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.0943 / max 182.0954, expressed in 1789 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
15184517.95341789
1518440.140958

Top tissues by expression

255 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
corpus callosumUBERON:000233695.83gold quality
vastus lateralisUBERON:000137995.13gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450294.86gold quality
biceps brachiiUBERON:000150794.84gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451194.73gold quality
deltoidUBERON:000147694.72gold quality
quadriceps femorisUBERON:000137794.43gold quality
skeletal muscle tissueUBERON:000113494.26gold quality
left ventricle myocardiumUBERON:000656694.04gold quality
medial globus pallidusUBERON:000247793.15gold quality
sural nerveUBERON:001548893.11gold quality
gastrocnemiusUBERON:000138892.99gold quality
muscle of legUBERON:000138392.96gold quality
globus pallidusUBERON:000187592.90gold quality
hindlimb stylopod muscleUBERON:000425292.90gold quality
inferior vagus X ganglionUBERON:000536392.85gold quality
muscle tissueUBERON:000238592.50gold quality
C1 segment of cervical spinal cordUBERON:000646992.23gold quality
Brodmann (1909) area 46UBERON:000648392.05gold quality
calcaneal tendonUBERON:000370191.78gold quality
spinal cordUBERON:000224091.70gold quality
tibialis anteriorUBERON:000138591.12gold quality
nucleus accumbensUBERON:000188290.75gold quality
lateral globus pallidusUBERON:000247690.59gold quality
substantia nigraUBERON:000203890.52gold quality
subthalamic nucleusUBERON:000190690.50gold quality
putamenUBERON:000187490.45gold quality
caudate nucleusUBERON:000187390.44gold quality
myocardiumUBERON:000234990.23gold quality
cerebellar hemisphereUBERON:000224590.19gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.00
E-ENAD-20no57.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting TARS3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-428299.9975.366408
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-454-3P99.9174.011925
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-430299.8967.941187
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-MIR-1211999.8768.351653
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-7856-5P99.7569.992901
HSA-MIR-548O-3P99.7469.302228
HSA-MIR-494-3P99.7071.452795
HSA-MIR-3158-5P99.6567.511763
HSA-MIR-426199.5970.303415
HSA-MIR-467299.5071.582893
HSA-MIR-580-5P99.2870.941776
HSA-MIR-4667-3P99.2665.451608
HSA-MIR-569099.2567.581012
HSA-MIR-664A-3P99.2271.082696
HSA-MIR-125798.9768.021133

Literature-anchored findings (GeneRIF, showing 3)

  • TARSL2 is potentially a new component of aminoacyl-tRNA synthetase core-complex (PMID:24312579)
  • Newly acquired N-terminal extension targets threonyl-tRNA synthetase-like protein into the multiple tRNA synthetase complex. (PMID:31287872)
  • miR-720 is a key regulator of glioma migration and invasion by controlling TARSL2 expression. (PMID:34024034)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioENSDARG00000075385
mus_musculusTars3ENSMUSG00000030515
rattus_norvegicusTars3ENSRNOG00000024460
drosophila_melanogasterThrRSFBGN0027081
caenorhabditis_elegansWBGENE00006617

Paralogs (4): TARS1 (ENSG00000113407), TARS2 (ENSG00000143374), MRPL39 (ENSG00000154719), PARS2 (ENSG00000162396)

Protein

Protein identifiers

Threonine–tRNA ligase 2, cytoplasmicA2RTX5 (reviewed: A2RTX5)

Alternative names: Threonyl-tRNA synthetase, Threonyl-tRNA synthetase protein 3

All UniProt accessions (3): A2RTX5, B7ZLP8, H0YKB9

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged tRNA(Thr) via its editing domain, at the post-transfer stage.

Subunit / interactions. May be a component of the multisynthetase complex (MSC), a large multi-subunit complex which contains at least eight different aminoacyl-tRNA synthetases plus three auxillary subunits AIMP1, AIMP2 and EEF1E1. Interacts with the MSC components EPRS1, AIMP1, AIMP2 and KARS1.

Subcellular location. Cytoplasm. Nucleus.

Similarity. Belongs to the class-II aminoacyl-tRNA synthetase family.

Isoforms (2)

UniProt IDNamesCanonical?
A2RTX5-11yes
A2RTX5-22

RefSeq proteins (1): NP_689547* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002314aa-tRNA-synt_IIbDomain
IPR002320Thr-tRNA-ligase_IIaFamily
IPR004095TGSDomain
IPR004154Anticodon-bdDomain
IPR006195aa-tRNA-synth_IIDomain
IPR012675Beta-grasp_dom_sfHomologous_superfamily
IPR012676TGS-likeHomologous_superfamily
IPR012947tRNA_SADDomain
IPR018163Thr/Ala-tRNA-synth_IIc_editHomologous_superfamily
IPR033728ThrRS_coreDomain
IPR036621Anticodon-bd_dom_sfHomologous_superfamily
IPR045864aa-tRNA-synth_II/BPL/LPLHomologous_superfamily
IPR047246ThrRS_anticodonDomain

Pfam: PF00587, PF02824, PF03129, PF07973

Catalyzed reactions (Rhea), 1 shown:

  • tRNA(Thr) + L-threonine + ATP = L-threonyl-tRNA(Thr) + AMP + diphosphate + H(+) (RHEA:24624)

UniProt features (18 total): sequence conflict 6, modified residue 2, coiled-coil region 2, compositionally biased region 2, initiator methionine 1, chain 1, splice variant 1, domain 1, region of interest 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A2RTX5-F187.910.72

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 453, 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_AMINO_ACID_ACTIVATION, GOBP_TRNA_METABOLIC_PROCESS, GOBP_TRANSLATION, NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON, KEGG_AMINOACYL_TRNA_BIOSYNTHESIS, BASAKI_YBX1_TARGETS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, HNF4ALPHA_Q6, chr15q26, GOMF_LIGASE_ACTIVITY_FORMING_CARBON_OXYGEN_BONDS, GOMF_ADENYL_NUCLEOTIDE_BINDING, CHYLA_CBFA2T3_TARGETS_DN, GOMF_CATALYTIC_ACTIVITY_ACTING_ON_RNA

GO Biological Process (4): threonyl-tRNA aminoacylation (GO:0006435), translation (GO:0006412), tRNA aminoacylation for protein translation (GO:0006418), tRNA aminoacylation (GO:0043039)

GO Molecular Function (6): threonine-tRNA ligase activity (GO:0004829), ATP binding (GO:0005524), nucleotide binding (GO:0000166), aminoacyl-tRNA ligase activity (GO:0004812), protein binding (GO:0005515), ligase activity (GO:0016874)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
tRNA aminoacylation for protein translation1
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
translation1
tRNA aminoacylation1
tRNA metabolic process1
amino acid activation1
aminoacyl-tRNA ligase activity1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
ligase activity, forming carbon-oxygen bonds1
catalytic activity, acting on a tRNA1
binding1
catalytic activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

1730 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TARS3LARS2Q15031978
TARS3LARS1Q9P2J5972
TARS3AARS1P49588895
TARS3IARS2Q9NSE4880
TARS3NARS1O43776873
TARS3NARS2Q96I59873
TARS3EPRS1P07814862
TARS3IARS1P41252856
TARS3VARS1P26640845
TARS3HARS1P12081828
TARS3PARS2Q7L3T8827
TARS3GARS1P41250826
TARS3AARS2Q5JTZ9821
TARS3HARS2P49590820
TARS3SARS1P49591820

IntAct

80 interactions, top by confidence:

ABTypeScore
TARS1TARS3psi-mi:“MI:0915”(physical association)0.720
TARS3TARS1psi-mi:“MI:0915”(physical association)0.720
TARS3psi-mi:“MI:0915”(physical association)0.560
TARS3psi-mi:“MI:0915”(physical association)0.560
TARS3TP53BP2psi-mi:“MI:0915”(physical association)0.560
TARS3ATF4psi-mi:“MI:0915”(physical association)0.560
TARS3ECSITpsi-mi:“MI:0915”(physical association)0.560
TARS3ARPC3psi-mi:“MI:0915”(physical association)0.560
TARS3LGALS14psi-mi:“MI:0915”(physical association)0.560
TARS3TARS2psi-mi:“MI:0915”(physical association)0.560
ALDH3B1UBA6psi-mi:“MI:0914”(association)0.530
SDCBPTARS3psi-mi:“MI:0914”(association)0.530
Spred2TARS3psi-mi:“MI:0914”(association)0.350
Sart3TARS3psi-mi:“MI:0914”(association)0.350
THOC1TARS3psi-mi:“MI:0914”(association)0.350
MYH7TARS3psi-mi:“MI:0914”(association)0.350
SLAIN2TARS3psi-mi:“MI:0914”(association)0.350
CCNB1TARS3psi-mi:“MI:0914”(association)0.350
MYCTARS3psi-mi:“MI:0914”(association)0.350
Tmed10TARS3psi-mi:“MI:0914”(association)0.350
ETAA1TARS3psi-mi:“MI:0914”(association)0.350
NCBP2TARS3psi-mi:“MI:0914”(association)0.350
JUNTPM3psi-mi:“MI:0914”(association)0.350

BioGRID (84): TARSL2 (Two-hybrid), TARSL2 (Affinity Capture-MS), TARSL2 (Affinity Capture-MS), TARSL2 (Affinity Capture-MS), TARSL2 (Affinity Capture-MS), TARSL2 (Affinity Capture-MS), AARS (Co-fractionation), FARSB (Co-fractionation), GARS (Co-fractionation), TARSL2 (Co-fractionation), TARSL2 (Co-fractionation), TARSL2 (Affinity Capture-MS), TARSL2 (Affinity Capture-MS), TARSL2 (Affinity Capture-MS), TARSL2 (Affinity Capture-MS)

ESM2 similar proteins: A0AVT1, A1L1C5, A1L259, A2RTX5, A3KMX8, A5PJD0, A6H630, A6NGE7, B8ZXI1, O60678, O70467, O75879, P32455, P32456, Q0V9S0, Q0ZDF7, Q22017, Q283N4, Q2KHV5, Q4R526, Q4R646, Q58EM4, Q5D1D6, Q5R998, Q5RBE1, Q5ZIE6, Q61107, Q68EH8, Q6AXB1, Q6AYT5, Q6DJ95, Q6DJA3, Q6ING7, Q6NTW6, Q6PA41, Q6ZN66, Q7SXP2, Q7T010, Q8BIJ6, Q8BLY2

Diamond homologs: A0PZN1, A1ARE5, A1U2C3, A1V3R3, A1WU53, A2BQ78, A2C155, A2RTX5, A2S2N6, A3DET1, A3MJT8, A3N8T1, A3NUI4, A3PBX1, A4G619, A4J4Y7, A5EVK6, A5I6L8, A5IJ45, A5N258, A6QNM8, A7FY87, A7GI05, A8F8Q8, A8G3W3, A9A078, A9ABF9, A9BHF0, B0B8F5, B0BA34, B0S169, B1IMV3, B1L0T7, B1L7W6, B2A5P2, B4UAM8, B7XIA1, B8FN26, B8J4E4, B8J823

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 59 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Cytosolic tRNA aminoacylation776.9×4e-10
tRNA Aminoacylation857.1×3e-10
Selenoamino acid metabolism629.5×4e-06
Transcriptional and post-translational regulation of MITF-M expression and activity626.8×6e-06
MITF-M-regulated melanocyte development720.0×4e-06
Translation812.4×1e-05
Metabolism of amino acids and derivatives711.8×9e-05
Transcriptional Regulation by TP5369.3×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

140 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance112
Likely benign5
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3231 predictions. Top by Δscore:

VariantEffectΔscore
15:101654726:AACCA:Aacceptor_gain1.0000
15:101654727:ACCA:Aacceptor_gain1.0000
15:101654728:CCA:Cacceptor_gain1.0000
15:101654728:CCAC:Cacceptor_gain1.0000
15:101654729:CA:Cacceptor_gain1.0000
15:101654729:CAC:Cacceptor_gain1.0000
15:101654730:ACT:Aacceptor_loss1.0000
15:101654731:C:CCacceptor_gain1.0000
15:101654731:CT:Cacceptor_loss1.0000
15:101656937:A:ACdonor_gain1.0000
15:101656938:C:CCdonor_gain1.0000
15:101656941:AG:Adonor_gain1.0000
15:101656942:G:Cdonor_gain1.0000
15:101657035:ACCTA:Aacceptor_loss1.0000
15:101657036:CCTAG:Cacceptor_loss1.0000
15:101657038:T:Aacceptor_loss1.0000
15:101661706:ACTT:Adonor_loss1.0000
15:101661707:CTTA:Cdonor_loss1.0000
15:101661708:TTA:Tdonor_loss1.0000
15:101661709:T:TGdonor_loss1.0000
15:101661710:A:ACdonor_gain1.0000
15:101661710:A:Cdonor_loss1.0000
15:101661711:C:CCdonor_gain1.0000
15:101661813:CTTA:Cacceptor_gain1.0000
15:101661817:C:CCacceptor_gain1.0000
15:101671669:A:ACdonor_gain1.0000
15:101671670:C:CCdonor_gain1.0000
15:101671749:C:CCacceptor_gain1.0000
15:101671750:T:Cacceptor_gain1.0000
15:101671751:T:Cacceptor_gain1.0000

AlphaMissense

5357 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:101661713:A:GW691R0.998
15:101661713:A:TW691R0.998
15:101661742:G:TA681D0.998
15:101661779:G:CH669D0.998
15:101671678:C:TG620D0.998
15:101675617:A:GW591R0.998
15:101675617:A:TW591R0.998
15:101684107:C:GD540H0.998
15:101684163:C:GR521T0.998
15:101685919:T:AK488N0.998
15:101685919:T:GK488N0.998
15:101685999:A:GW462R0.998
15:101685999:A:TW462R0.998
15:101701152:A:CS418R0.998
15:101701152:A:TS418R0.998
15:101701154:T:GS418R0.998
15:101702327:C:TG378E0.998
15:101711984:A:CS236R0.998
15:101711984:A:TS236R0.998
15:101711986:T:GS236R0.998
15:101661763:C:TG674E0.997
15:101661775:C:GR670P0.997
15:101671683:A:CF618L0.997
15:101671683:A:TF618L0.997
15:101671685:A:GF618L0.997
15:101671744:A:GL598P0.997
15:101675615:C:AW591C0.997
15:101675615:C:GW591C0.997
15:101684101:C:GA542P0.997
15:101684114:G:CF537L0.997

dbSNP variants (sampled 300 via entrez): RS1000009398 (15:101726213 A>C), RS1000023609 (15:101716015 T>C), RS1000034446 (15:101716104 C>T), RS1000072527 (15:101715787 C>A,T), RS1000122567 (15:101715051 T>TG), RS1000152346 (15:101672996 GAGGACACAGGAC>G), RS1000163603 (15:101693751 C>T), RS1000218990 (15:101720947 C>T), RS1000243241 (15:101675804 T>C), RS1000318406 (15:101699267 C>T), RS1000351929 (15:101669843 T>C), RS1000367903 (15:101710388 G>A), RS1000474860 (15:101704841 C>G), RS1000529999 (15:101673990 C>T), RS1000532754 (15:101678978 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases methylation, decreases expression2
trichostatin Aaffects cotreatment, decreases expression2
(+)-JQ1 compoundincreases expression2
Cadmium Chlorideincreases abundance, increases expression, decreases expression2
dicrotophosdecreases expression1
sodium arseniteincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangaffects cotreatment, decreases expression1
Acetaminophenincreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Cadmiumincreases abundance, increases expression1
Cisplatinaffects cotreatment, decreases expression1
Estradiolaffects cotreatment, increases expression1
Formaldehydeincreases expression1
Methyl Methanesulfonateincreases expression1
Tretinoindecreases expression1
Okadaic Acidincreases expression1
Copper Sulfatedecreases expression1
Particulate Matterincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.