U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    KARS1 lysyl-tRNA synthetase 1 [ Homo sapiens (human) ]

    Gene ID: 3735, updated on 27-Nov-2024

    Summary

    Official Symbol
    KARS1provided by HGNC
    Official Full Name
    lysyl-tRNA synthetase 1provided by HGNC
    Primary source
    HGNC:HGNC:6215
    See related
    Ensembl:ENSG00000065427 MIM:601421; AllianceGenome:HGNC:6215
    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
    KRS; KARS; KARS2; LEPID; CMTRIB; DEAPLE; DFNB89
    Summary
    Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. Lysyl-tRNA synthetase is a homodimer localized to the cytoplasm which belongs to the class II family of tRNA synthetases. It has been shown to be a target of autoantibodies in the human autoimmune diseases, polymyositis or dermatomyositis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 57.5), lymph node (RPKM 40.9) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See KARS1 in Genome Data Viewer
    Location:
    16q23.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (75627724..75647665, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (81676020..81695962, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (75661622..75681563, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75600739-75601492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11139 Neighboring gene GABA type A receptor associated protein like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11142 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75626991-75627988 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75627989-75628985 Neighboring gene adenosine deaminase tRNA specific 1 Neighboring gene Sharpr-MPRA regulatory region 14871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75655412-75655932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75655933-75656452 Neighboring gene H3K27ac hESC enhancers GRCh37_chr16:75656453-75656972 and GRCh37_chr16:75656973-75657492 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:75663368-75664567 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11144 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:75681635-75682592 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:75682593-75683548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11146 Neighboring gene TERF2 interacting protein Neighboring gene cytoplasmic polyadenylated homeobox like 2

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Autosomal recessive nonsyndromic hearing loss 89
    MedGen: C3151351 OMIM: 613916 GeneReviews: Not available
    not available
    Charcot-Marie-Tooth disease recessive intermediate B
    MedGen: C3150897 OMIM: 613641 GeneReviews: Not available
    not available
    Deafness, congenital, and adult-onset progressive leukoencephalopathy
    MedGen: C5543087 OMIM: 619196 GeneReviews: Not available
    not available
    Leukoencephalopathy, progressive, infantile-onset, with or without deafness
    MedGen: C5542996 OMIM: 619147 GeneReviews: Not available
    not available

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of lysyl-tRNA synthetase (KARS) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Gag-Pol gag-pol The Pol domain of HIV-1 Gag-Pol associates specifically with Lysyl-tRNA synthetase PubMed
    Pol gag-pol HIV-1 Pol interacts with lysyl-tRNA synthetase (LysRS). Sequences in Pol binding to LysRS are found within connection domain/RNaseH domain of RT PubMed
    gag-pol The p6 and Integrase (IN) domains of HIV-1 Pol act synergistically to build a strong and stable anchoring platform for its binding to LysRS. The catalytic domain (amino acids 237-597) of LysRS is involved in its interaction with Pol PubMed
    Pr55(Gag) gag Homodimeric lysyl-tRNA synthetase dissociates into a monomer that bridges between HIV-1 Gag and tRNA(Lys3) PubMed
    gag LysRS double mutants at positions I246D/R247A, I250D/I251D, and I254D/R255A in the helix 7 dimerization domain reduce its binding to HIV-1 Gag/delta p6 and CA-CTD PubMed
    gag A peptide containing 10 amino acid residues from helix4 of C-terminal domain of HIV-1 CA (CA-CTD) can form a helical structure upon binding to LysRS through strong hydrogen bond interactions between R247-Q219 and R241-E212 PubMed
    gag The interaction of Lysyl-tRNA synthetase with HIV-1 Gag is dependent upon Gag amino acids 310-363 (last 54 amino acids of the capsid domain) and amino acids 208-259 of Lysyl-tRNA synthetase PubMed
    gag Lysyl-tRNA synthetase is incorporated into HIV-1 virions through an interaction with HIV-1 Gag PubMed
    Vpr vpr Mitochondrial localization of lysyl-tRNA synthetase (LysRS) is altered in the presence of HIV-1 Vpr in HeLa cells PubMed
    vpr HIV-1 Vpr binds to Lysyl-tRNA synthetase (LysRS) and inhibits LysRS-mediated aminoacylation of tRNA-Lys, an effect that may influence the initiation of HIV-1 reverse transcription PubMed
    capsid gag LysRS double mutants at positions I246D/R247A, I250D/I251D, and I254D/R255A in the helix 7 dimerization domain reduce its binding to HIV-1 Gag/delta p6 and CA-CTD PubMed
    gag The Capsid domain of HIV-1 Gag is sufficient for the interaction of Gag with lysyl-tRNA synthetase in an in vitro pull-down assay PubMed
    gag Cyclic peptides inhibit the interaction of HIV-1 CA with lysyl-tRNA synthetase by binding to the helix 4 motif of the C-terminal domain of CA PubMed
    gag Peptides derived from the helix-4 of HIV-1 capsid C-terminal domain significantly bind to LysRS PubMed
    matrix gag HIV-1 MA is identified to have a physical interaction with lysyl-tRNA synthetase (KARS) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    retropepsin gag-pol Using a bioluminescence resonance energy transfer assay to directly measure HIV-1 protease activity in vivo indicates that the overexpression of lysyl tRNA synthetase (LysRS) in the cell reduces viral protease activity PubMed
    reverse transcriptase gag-pol HIV-1 Pol interacts with lysyl-tRNA synthetase (LysRS). Sequences in Pol binding to LysRS are found within connection domain/RNaseH domain of RT PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0070

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP:ADP adenylyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ATP:ADP adenylyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables amino acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables lysine-tRNA ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables lysine-tRNA ligase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables tRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables tRNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in ERK1 and ERK2 cascade IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in basophil activation involved in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in basophil activation involved in immune response IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in diadenosine tetraphosphate biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in diadenosine tetraphosphate biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in diadenosine tetraphosphate biosynthetic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in lysyl-tRNA aminoacylation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in lysyl-tRNA aminoacylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of inflammatory response to antigenic stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of macrophage activation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of macrophage activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to X-ray IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in tRNA processing NAS
    Non-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 
    is_active_in cytoplasm 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 space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
     
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    lysine--tRNA ligase
    Names
    lysRS
    lysine tRNA ligase
    NP_001123561.1
    NP_001365077.1
    NP_005539.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_028025.1 RefSeqGene

      Range
      5001..24964
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_366

    mRNA and Protein(s)

    1. NM_001130089.2NP_001123561.1  lysine--tRNA ligase isoform 1

      See identical proteins and their annotated locations for NP_001123561.1

      Status: REVIEWED

      Source sequence(s)
      AC025287
      Consensus CDS
      CCDS45532.1
      UniProtKB/Swiss-Prot
      Q15046
      Related
      ENSP00000325448.5, ENST00000319410.9
      Conserved Domains (3) summary
      PLN02502
      Location:48605
      PLN02502; lysyl-tRNA synthetase
      cd00775
      Location:265603
      LysRS_core; Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three ...
      cd04322
      Location:153262
      LysRS_N; LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. ...
    2. NM_001378148.1NP_001365077.1  lysine--tRNA ligase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC025287
      Conserved Domains (1) summary
      PLN02502
      Location:1421
      PLN02502; lysyl-tRNA synthetase
    3. NM_005548.3NP_005539.1  lysine--tRNA ligase isoform 2

      See identical proteins and their annotated locations for NP_005539.1

      Status: REVIEWED

      Source sequence(s)
      AA503390, AF285758, AK315687
      Consensus CDS
      CCDS10923.1
      UniProtKB/Swiss-Prot
      A8MSK1, D3DUK4, O14946, Q15046, Q96J25, Q9HB23
      Related
      ENSP00000303043.3, ENST00000302445.8
      Conserved Domains (1) summary
      PLN02502
      Location:12577
      PLN02502; lysyl-tRNA synthetase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      75627724..75647665 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      81676020..81695962 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)