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    FARSB phenylalanyl-tRNA synthetase subunit beta [ Homo sapiens (human) ]

    Gene ID: 10056, updated on 28-Oct-2024

    Summary

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    Official Symbol
    FARSBprovided by HGNC
    Official Full Name
    phenylalanyl-tRNA synthetase subunit betaprovided by HGNC
    Primary source
    HGNC:HGNC:17800
    See related
    Ensembl:ENSG00000116120 MIM:609690; AllianceGenome:HGNC:17800
    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
    FRSB; RJBS; PheHB; PheRS; FARSLB; RILDBC; HSPC173; NEDBLLA; RILDBC1
    Summary
    This gene encodes a highly conserved enzyme that belongs to the aminoacyl-tRNA synthetase class IIc subfamily. This enzyme comprises the regulatory beta subunits that form a tetramer with two catalytic alpha subunits. In the presence of ATP, this tetramer is responsible for attaching L-phenylalanine to the terminal adenosine of the appropriate tRNA. A pseudogene located on chromosome 10 has been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
    Expression
    Ubiquitous expression in brain (RPKM 8.3), testis (RPKM 8.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FARSB in Genome Data Viewer
    Location:
    2q36.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (222566899..222656092, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (223052236..223141156, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223431618..223520811, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene sphingosine-1-phosphate phosphatase 2 Neighboring gene RNA, U6 small nuclear 619, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223383170-223383762 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 49 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:223400343-223400843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12372 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:223502966-223503113 Neighboring gene uncharacterized LOC105373902 Neighboring gene tripartite motif containing 60 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17167 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:223521038-223521234 Neighboring gene uncharacterized LOC124907985 Neighboring gene monoacylglycerol O-acyltransferase 1 Neighboring gene RRAS2 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 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. Phenylalanyl-tRNA synthetase of the human placenta. Evidence for different enzymatic forms in equilibrium. Archambault de Vencay J, et al. FEBS Lett, 1978 May 1. PMID 658405
    2. FARSB Facilitates Hepatocellular Carcinoma Progression by Activating the mTORC1 Signaling Pathway. Wang Y, et al. Int J Mol Sci, 2023 Nov 24. PMID 38069034, Free PMC Article
    3. Recognition nucleotides for human phenylalanyl-tRNA synthetase. Nazarenko IA, et al. Nucleic Acids Res, 1992 Feb 11. PMID 1741281, Free PMC Article
    4. Use of germline polymorphisms in predicting concurrent chemoradiotherapy response in esophageal cancer. Chen PC, et al. Int J Radiat Oncol Biol Phys, 2012 Apr 1. PMID 21596488
    5. Role of low-molecular-weight substrates in functional binding of the tRNAPhe acceptor end by phenylalanyl-tRNA synthetase. Vasil'eva IA, et al. Biochemistry (Mosc), 2004 Feb. PMID 15000680

    See all (129) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FARSB Facilitates Hepatocellular Carcinoma Progression by Activating the mTORC1 Signaling Pathway.
      Title: FARSB Facilitates Hepatocellular Carcinoma Progression by Activating the mTORC1 Signaling Pathway.
    2. Contribution of upregulated aminoacyl-tRNA biosynthesis to metabolic dysregulation in gastric cancer.
      Title: Contribution of upregulated aminoacyl-tRNA biosynthesis to metabolic dysregulation in gastric cancer.
    3. FARSA mutations mimic phenylalanyl-tRNA synthetase deficiency caused by FARSB defects.
      Title: FARSA mutations mimic phenylalanyl-tRNA synthetase deficiency caused by FARSB defects.
    4. This study further implicates FARSB mutations in a multisystem, recessive, neurodevelopmental phenotype that share clinical features with the previously known aminoacyl-tRNA synthetase-related diseases.
      Title: Homozygosity for FARSB mutation leads to Phe-tRNA synthetase-related disease of growth restriction, brain calcification, and interstitial lung disease.
    5. Expression studies using fibroblasts isolated from the proband revealed a severe depletion of both FARSB and FARSA protein levels. These data indicate that the FARSB variants destabilize total phenylalanyl-tRNA synthetase levels, thus causing a loss-of-function effect.
      Title: Compound heterozygosity for loss-of-function FARSB variants in a patient with classic features of recessive aminoacyl-tRNA synthetase-related disease.
    6. Human PheRS recognizes C74, the G1-C72 base pair, and the "discriminator" base A73, proposed to contribute to tRNA(Phe) identity in the yeast mitochondrial enzyme.
      Title: Crystal structure of human mitochondrial PheRS complexed with tRNA(Phe) in the active "open" state.
    7. Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns
      Title: Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns.
    8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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
    Rajab interstitial lung disease with brain calcifications 1
    MedGen: C5436276 OMIM: 613658 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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables phenylalanine-tRNA ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in phenylalanyl-tRNA aminoacylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phenylalanyl-tRNA aminoacylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein heterotetramerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in translation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 
    part_of phenylalanine-tRNA ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of phenylalanine-tRNA ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of phenylalanine-tRNA ligase complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    phenylalanine--tRNA ligase beta subunit
    Names
    phenylalanine tRNA ligase 1, beta, cytoplasmic
    phenylalanine-tRNA ligase beta chain
    phenylalanine-tRNA synthetase-like, beta subunit
    phenylalanyl-tRNA synthetase beta chain
    phenylalanyl-tRNA synthetase beta subunit
    phenylalanyl-tRNA synthetase-like, beta subunit
    NP_005678.3
    XP_006712232.1
    XP_011508768.1
    XP_054196057.1
    XP_054196058.1

    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.

    mRNA and Protein(s)

    1. NM_005687.5 → NP_005678.3  phenylalanine--tRNA ligase beta subunit

      See identical proteins and their annotated locations for NP_005678.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
      Source sequence(s)
      AC097461, AF042346, BG721840
      Consensus CDS
      CCDS2454.1
      UniProtKB/Swiss-Prot
      B4DFM0, O95708, Q4ZFX1, Q57ZJ5, Q9NSD9, Q9NZZ6
      UniProtKB/TrEMBL
      A8K666
      Related
      ENSP00000281828.6, ENST00000281828.8
      Conserved Domains (4) summary
      smart00873
      Location:118 → 279
      B3_4; B3/4 domain
      PLN02265
      Location:1 → 589
      PLN02265; probable phenylalanyl-tRNA synthetase beta chain
      cd00769
      Location:392 → 588
      PheRS_beta_core; Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an ...
      pfam03484
      Location:310 → 374
      B5; tRNA synthetase B5 domain

    RNA

    1. NR_130154.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC097461, BC022273

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      222566899..222656092 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510466.3 → XP_011508768.1  phenylalanine--tRNA ligase beta subunit isoform X1

      See identical proteins and their annotated locations for XP_011508768.1

      UniProtKB/TrEMBL
      B7ZB32
      Conserved Domains (1) summary
      cl27259
      Location:1 → 490
      B5; tRNA synthetase B5 domain

    2. XM_006712169.3 → XP_006712232.1  phenylalanine--tRNA ligase beta subunit isoform X1

      See identical proteins and their annotated locations for XP_006712232.1

      UniProtKB/TrEMBL
      B7ZB32
      Conserved Domains (1) summary
      cl27259
      Location:1 → 490
      B5; tRNA synthetase B5 domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      223052236..223141156 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340083.1 → XP_054196058.1  phenylalanine--tRNA ligase beta subunit isoform X1

    2. XM_054340082.1 → XP_054196057.1  phenylalanine--tRNA ligase beta subunit isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NSD9.3 GenPept UniProtKB/Swiss-Prot:Q9NSD9

    Gene LinkOut

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