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DARS1 aspartyl-tRNA synthetase 1 [ Homo sapiens (human) ]

Gene ID: 1615, updated on 7-Apr-2024

Summary

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Official Symbol
DARS1provided by HGNC
Official Full Name
aspartyl-tRNA synthetase 1provided by HGNC
Primary source
HGNC:HGNC:2678
See related
Ensembl:ENSG00000115866 MIM:603084; AllianceGenome:HGNC:2678
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
DARS; HBSL; aspRS
Summary
This gene encodes a member of a multienzyme complex that functions in mediating the attachment of amino acids to their cognate tRNAs. The encoded protein ligates L-aspartate to tRNA(Asp). Mutations in this gene have been found in patients showing hypomyelination with brainstem and spinal cord involvement and leg spasticity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
Expression
Ubiquitous expression in thyroid (RPKM 24.7), lymph node (RPKM 20.9) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
2q21.3
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (135905881..135985684, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (136350305..136430110, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (136663451..136743254, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:136633103-136633638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16579 Neighboring gene minichromosome maintenance complex component 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:136656467-136656966 Neighboring gene MANEAL pseudogene 1 Neighboring gene uncharacterized LOC124906078 Neighboring gene MPRA-validated peak3879 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr2:136718531-136719032 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16580 Neighboring gene DARS1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16583 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:136846458-136846659 Neighboring gene NANOG hESC enhancer GRCh37_chr2:136850708-136851567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16585 Neighboring gene C-X-C motif chemokine receptor 4 Neighboring gene heterogeneous nuclear ribonucleoprotein K pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Functional genomics screening identifies aspartyl-tRNA synthetase as a novel prognostic marker and a therapeutic target for gastric cancers. Liu B, et al. J Pathol, 2022 Oct. PMID 35696251
  2. Developmental delay and late onset HBSL pathology in hypomorphic Dars1(M256L) mice. Klugmann M, et al. Neurochem Res, 2022 Jul. PMID 35357600, Free PMC Article
  3. Association of DARS gene polymorphisms with the risk of isolated ventricular septal defects in the Chinese Han population. Feng Y, et al. Ital J Pediatr, 2016 Nov 21. PMID 27871331, Free PMC Article
  4. Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex. Kim KR, et al. Proteins, 2013 Oct. PMID 23609930, Free PMC Article
  5. Lysyl-tRNA synthetase interacts with EF1alpha, aspartyl-tRNA synthetase and p38 in vitro. Guzzo CM, et al. Biochem Biophys Res Commun, 2008 Jan 25. PMID 18029264

See all (161) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Functional genomics screening identifies aspartyl-tRNA synthetase as a novel prognostic marker and a therapeutic target for gastric cancers.
    Title: Functional genomics screening identifies aspartyl-tRNA synthetase as a novel prognostic marker and a therapeutic target for gastric cancers.
  2. Developmental delay and late onset HBSL pathology in hypomorphic Dars1(M256L) mice.
    Title: Developmental delay and late onset HBSL pathology in hypomorphic Dars1(M256L) mice.
  3. This study demonstrates that human mitochondrial AspRS, ArgRS, and LysRS, each have a specific sub-mitochondrial distribution, with ArgRS being exclusively localized in the membrane, LysRS exclusively in the soluble fraction, and AspRS being present in both.
    Title: Three human aminoacyl-tRNA synthetases have distinct sub-mitochondrial localizations that are unaffected by disease-associated mutations.
  4. Genetic variants of the DARS gene may influence individual susceptibility to isolated VSD in Chinese Han population. Risk of VSD was significantly associated with rs2164331 [G/A; odds ratio (OR) = 0.78, 95% confidence interval (CI) = 0.69-0.91; P = 3.17 x 10(-3)], rs6738266 [G/A; OR = 1.17, 95% CI = 1.05-1.29, P = 1.83 x 10(-3)], and rs309143 [G/A; OR = 1.09, 95% CI = 1.01-1.17; P = 3.12 x 10(-2)].
    Title: Association of DARS gene polymorphisms with the risk of isolated ventricular septal defects in the Chinese Han population.
  5. Report on the crystal structure of human cytosolic aspartyl-tRNA synthetase (DRS) at a resolution of 2.25 A.
    Title: Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex.
  6. Mutations in DARS cause hypomyelination with brain stem and spinal cord involvement and leg spasticity.
    Title: Mutations in DARS cause hypomyelination with brain stem and spinal cord involvement and leg spasticity.
  7. the N-terminus shows a less-ordered structure with flexible beta-turn, suggesting that when tRNA is stretched, the dissociation rate of Asp-tRNA from aspartyl-tRNA synthetase is reduced, giving time for elongation factor 1alpha to interact with Asp-tRNA.
    Title: Structure of the N-terminal extension of human aspartyl-tRNA synthetase: implications for its biological function.
Submit: New GeneRIF Correction

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
Hypomyelination with brain stem and spinal cord involvement and leg spasticity
MedGen: C4755254 OMIM: 615281 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify aspartyl-tRNA synthetase (DARS), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify aspartyl-tRNA synthetase (DARS), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify aspartyl-tRNA synthetase (DARS), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify aspartyl-tRNA synthetase (DARS), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
matrix gag HIV-1 MA is identified to have a physical interaction with aspartyl-tRNA synthetase (DARS) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC111579, DKFZp781B11202

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables aminoacylase activity TAS
Traceable Author Statement
more info
 PubMed 
enables aspartate-tRNA ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in aspartyl-tRNA aminoacylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein-containing complex assembly TAS
Traceable Author Statement
more info
 PubMed 
involved_in translation TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of aminoacyl-tRNA synthetase multienzyme complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of aminoacyl-tRNA synthetase multienzyme complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm TAS
Traceable Author Statement
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in membrane HDA PubMed 
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
aspartate--tRNA ligase, cytoplasmic
Names
aspartate tRNA ligase 1, cytoplasmic
aspartyl-tRNA synthetase, cytoplasmic
cell proliferation-inducing gene 40 protein
testicular tissue protein Li 192
NP_001280241.1
NP_001340.2

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

  1. NG_034149.1 RefSeqGene

    Range
    5059..84804
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001293312.1 → NP_001280241.1  aspartate--tRNA ligase, cytoplasmic isoform 2

    See identical proteins and their annotated locations for NP_001280241.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AC011999, BC000629, BU615302, BX101357, CR749809, DA597505
    Conserved Domains (3) summary
    cd00776
    Location:74 → 397
    AsxRS_core; Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as ...
    cd04320
    Location:1 → 58
    AspRS_cyto_N; AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. ...
    pfam00152
    Location:75 → 395
    tRNA-synt_2; tRNA synthetases class II (D, K and N)

  2. NM_001349.4 → NP_001340.2  aspartate--tRNA ligase, cytoplasmic isoform 1

    See identical proteins and their annotated locations for NP_001340.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC011999, BC000629, BU615302, BX101357, DA597505
    Consensus CDS
    CCDS2180.1
    UniProtKB/Swiss-Prot
    A8K3J2, D3DP77, P14868, Q2TNI3, Q32Q69, Q53HV4, Q53YC5, Q68CR9, Q9BW52
    UniProtKB/TrEMBL
    A0A140VJW5
    Related
    ENSP00000264161.4, ENST00000264161.9
    Conserved Domains (1) summary
    cl27743
    Location:3 → 501
    tRNA-synt_2; tRNA synthetases class II (D, K and N)

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

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    135905881..135985684 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    136350305..136430110 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P14868.2 GenPept UniProtKB/Swiss-Prot:P14868

Gene LinkOut

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