YARS1 tyrosyl-tRNA synthetase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: YARS1provided by HGNC
Official Full Name: tyrosyl-tRNA synthetase 1provided by HGNC
Primary source: HGNC:HGNC:12840
See related: Ensembl:ENSG00000134684 MIM:603623; AllianceGenome:HGNC:12840
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: YRS; YTS; YARS; TYRRS; CMTDIC; IMNEPD2
Summary: Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. Tyrosyl-tRNA synthetase belongs to the class I tRNA synthetase family. Cytokine activities have also been observed for the human tyrosyl-tRNA synthetase, after it is split into two parts, an N-terminal fragment that harbors the catalytic site and a C-terminal fragment found only in the mammalian enzyme. The N-terminal fragment is an interleukin-8-like cytokine, whereas the released C-terminal fragment is an EMAP II-like cytokine. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 25.7), brain (RPKM 24.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p35.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (32775239..32817358, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (32635023..32677140, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (33240840..33282959, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Tyrosyl-tRNA synthetase has a noncanonical function in actin bundling.
Title: Tyrosyl-tRNA synthetase has a noncanonical function in actin bundling.
The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype.
Title: The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype.
Novel partial loss-of-function variants in the tyrosyl-tRNA synthetase 1 (YARS1) gene involved in multisystem disease.
Title: Novel partial loss-of-function variants in the tyrosyl-tRNA synthetase 1 (YARS1) gene involved in multisystem disease.
Moonlighting matrix metalloproteinase substrates: Enhancement of proinflammatory functions of extracellular tyrosyl-tRNA synthetase upon cleavage.
Title: Moonlighting matrix metalloproteinase substrates: Enhancement of proinflammatory functions of extracellular tyrosyl-tRNA synthetase upon cleavage.
study revealed a new radiation protection mechanism for RSV, in which the acetylation of TyrRS and its translocation into the nucleus is promoted, and this mechanism may also represent a novel protective target against irradiation.
Title: Resveratrol targets TyrRS acetylation to protect against radiation-induced damage.
By revealing the existence of a YARS-PI3K-Akt signaling axis in gastric cancer, we discovered that tRNA synthetase YARS is a novel tumorigenic factor, characterized by its upregulation in tumor-derived specimens, as well as its functions in promoting gastric cancer progression.
Title: YARS as an oncogenic protein that promotes gastric cancer progression through activating PI3K-Akt signaling.
Analysis of YARS p.Pro167Thr in yeast complementation assays revealed a loss-of-function, hypomorphic allele that significantly impaired growth. Recombinant YARS p.Pro167Thr demonstrated normal subcellular localization, but greatly diminished ability to homodimerize in human embryonic kidney cells.
Title: Homozygosity for a mutation affecting the catalytic domain of tyrosyl-tRNA synthetase (YARS) causes multisystem disease.
conclusion is further supported by a positive correlation across brain regions between TyrRS expression and arginine-accelerated KTP production.
Title: Tyrosyl-tRNA synthetase: A potential kyotorphin synthetase in mammals.
Platelet replenishment by YRS(ACT) is independent of thrombopoietin (TPO), as evidenced by expansion of the megakaryocytes from induced pluripotent stem cell-derived hematopoietic stem cells from a patient deficient in TPO signaling.
Title: Tyrosyl-tRNA synthetase stimulates thrombopoietin-independent hematopoiesis accelerating recovery from thrombocytopenia.
These YARS variants occur in the catalytic domain and the C-terminal domain, respectively. Mutations in YARS have been previously associated with an autosomal dominant form of Charcot-Marie-Tooth (CMT); our findings suggest the disease spectrum associated with YARS dysregulation is broader than peripheral neuropathy.
Title: A novel multisystem disease associated with recessive mutations in the tyrosyl-tRNA synthetase (YARS) gene.

Submit: New GeneRIF Correction See all GeneRIFs (33)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Charcot-Marie-Tooth disease dominant intermediate C MedGen: C1842237 OMIM: 608323 GeneReviews: Not available	Compare labs
Neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset 2 MedGen: C5543623 OMIM: 619418 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of tyrosyl-tRNA synthetase (YARS) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 upregulates the expression of tyrosyl-tRNA synthetase in T-cell lines	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

SHGC-74484 (e-PCR)
- UniSTS:73497

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

D10S16 (e-PCR)
- UniSTS:155756

D15S1477 (e-PCR)
- UniSTS:474482

D1S1423 (e-PCR)
- UniSTS:149619

RH64745 (e-PCR)
- UniSTS:77942

D13S1552 (e-PCR)
- UniSTS:473481

SHGC-74549 (e-PCR)
- UniSTS:71311

D11S3114 (e-PCR)
- UniSTS:152207

D16S325 (e-PCR)
- UniSTS:147089

AL009604 (e-PCR)
- UniSTS:37019

SHGC-74542 (e-PCR)
- UniSTS:69830

STS-R16166 (e-PCR)
- UniSTS:200

SHGC-74550 (e-PCR)
- UniSTS:20947

stdJ1070N10T7 (e-PCR)
- UniSTS:181727

D1S233 (e-PCR), detects polymorphism
- UniSTS:49127

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables interleukin-8 receptor binding	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small molecule binding	IDA Inferred from Direct Assay more info	PubMed
enables tRNA binding	IEA Inferred from Electronic Annotation more info
enables tyrosine-tRNA ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables tyrosine-tRNA ligase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in apoptotic process	TAS Traceable Author Statement more info	PubMed
involved_in response to starvation	IDA Inferred from Direct Assay more info	PubMed
involved_in tyrosyl-tRNA aminoacylation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular space	TAS Traceable Author Statement more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: tyrosine--tRNA ligase, cytoplasmic

Names: tyrosine tRNA ligase 1, cytoplasmic; tyrosyl--tRNA ligase; tyrosyl-tRNA synthetase, cytoplasmic

NP_003671.1

EC 6.1.1.1

XP_011540649.1

EC 6.1.1.1

XP_054195307.1

EC 6.1.1.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008408.1 RefSeqGene

Range

5001..47794

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_273

mRNA and Protein(s)

NM_003680.4 → NP_003671.1 tyrosine--tRNA ligase, cytoplasmic

See identical proteins and their annotated locations for NP_003671.1

Status: REVIEWED

Source sequence(s)

AC114489, AC114493

Consensus CDS

CCDS368.1

UniProtKB/Swiss-Prot

B3KWK4, D3DPQ4, O43276, P54577, Q53EN1

UniProtKB/TrEMBL

A0A0S2Z4R1, A0A6Q8PFX2

Related

ENSP00000362576.4, ENST00000373477.9

Conserved Domains (2) summary

cl00015
Location:8 → 328

nt_trans; nucleotidyl transferase superfamily

cl26127
Location:327 → 528

PRK12267; methionyl-tRNA synthetase; Reviewed

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

32775239..32817358 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011542347.3 → XP_011540649.1 tyrosine--tRNA ligase, cytoplasmic isoform X1

See identical proteins and their annotated locations for XP_011540649.1

Conserved Domains (2) summary

cd02799
Location:153 → 258

tRNA_bind_EMAP-II_like; tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae ...

cl00015
Location:4 → 128

nt_trans; nucleotidyl transferase superfamily