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

    Gene ID: 1615, updated on 5-May-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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    See DARS1 in Genome Data Viewer
    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
    		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)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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