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    PUS1 pseudouridine synthase 1 [ Homo sapiens (human) ]

    Gene ID: 80324, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PUS1provided by HGNC
    Official Full Name
    pseudouridine synthase 1provided by HGNC
    Primary source
    HGNC:HGNC:15508
    See related
    Ensembl:ENSG00000177192 MIM:608109; AllianceGenome:HGNC:15508
    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
    MLASA1
    Summary
    This gene encodes a pseudouridine synthase that converts uridine to pseudouridine once it has been incorporated into an RNA molecule. The encoded enzyme may play an essential role in tRNA function and in stabilizing the secondary and tertiary structure of many RNAs. A mutation in this gene has been linked to mitochondrial myopathy and sideroblastic anemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Sep 2009]
    Expression
    Ubiquitous expression in appendix (RPKM 5.5), lymph node (RPKM 5.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PUS1 in Genome Data Viewer
    Location:
    12q24.33
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (131929276..131945896)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (131977320..131993946)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (132413821..132430441)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5102 Neighboring gene Sharpr-MPRA regulatory region 8404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132381351-132382148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132384711-132385228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132385229-132385746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132385901-132386674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132386675-132387447 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25936 Neighboring gene unc-51 like autophagy activating kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7373 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:132409300-132410176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5107 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25941 Neighboring gene PUS1 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 9670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5109 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132434951-132435658 Neighboring gene Sharpr-MPRA regulatory region 13568 Neighboring gene E1A binding protein p400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132470576-132471195 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132471868-132472518 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132473169-132473818 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:132490339-132491538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132498351-132499144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132499145-132499938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132499948-132500448 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:132508440-132509639 Neighboring gene Sharpr-MPRA regulatory region 9648 Neighboring gene small nucleolar RNA, H/ACA box 49 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132534021-132534992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132567429-132567930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5111 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132569347-132570207 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:132570983-132571159 Neighboring gene EP400 pseudogene 1 Neighboring gene uncharacterized LOC107987169

    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. Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1. Sibert BS, et al. RNA, 2008 Sep. PMID 18648068, Free PMC Article
    2. Nonsense mutation in pseudouridylate synthase 1 (PUS1) in two brothers affected by myopathy, lactic acidosis and sideroblastic anaemia (MLASA). Fernandez-Vizarra E, et al. J Med Genet, 2007 Mar. PMID 17056637, Free PMC Article
    3. Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA). Bykhovskaya Y, et al. Am J Hum Genet, 2004 Jun. PMID 15108122, Free PMC Article
    4. Steroid receptor RNA activator (SRA) modification by the human pseudouridine synthase 1 (hPus1p): RNA binding, activity, and atomic model. Huet T, et al. PLoS One, 2014. PMID 24722331, Free PMC Article
    5. In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities. Czudnochowski N, et al. J Mol Biol, 2013 Oct 23. PMID 23707380, Free PMC Article

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
      Title: Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
    2. These results demonstrate a structure-dependent mode of mRNA target recognition by a conserved pseudouridine synthase and implicate modulation of RNA structure as the probable mechanism to regulate mRNA pseudouridylation.
      Title: mRNA structure determines modification by pseudouridine synthase 1.
    3. results show that the NTD of ERalpha and AR contains a novel RBM that directly binds SRA, and that STR5 can serve as a novel class of RNA inhibitor of ERalpha and AR signaling by interfering with Pus1p-mediated SRA pseudouridylation
      Title: A small RNA derived from RNA coactivator SRA blocks steroid receptor signaling via inhibition of Pus1p-mediated pseudouridylation of SRA: evidence of a novel RNA binding domain in the N-terminus of steroid receptors.
    4. Investigation of the sequence and structural requirements for hPus1p activity on human tRNASer.
      Title: Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements.
    5. We identified one novel homozygous null mutation in a familial case. It predicts a nonsense mutation at glutamine 154 (Q154X) that would lead to a protein lacking the 266 C-terminal amino acids
      Title: Systematic molecular genetic analysis of congenital sideroblastic anemia: evidence for genetic heterogeneity and identification of novel mutations.
    6. Three residues (R116, Y173, R267) that correspond to amino acids known to compose the active site of TruA, a bacterial Psi synthase that is homologous to Pus1p, were mutated in human Pus1p.
      Title: Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1.
    7. Missense mutation in pseudouridine synthase 1 causes mitochondrial myopathy and sideroblastic anemia
      Title: Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA).
    8. MLASA is associated with absent or greatly reduced tRNA pseudouridylation at specific sites, implicating this pathway in its molecular pathogenesis.
      Title: Mitochondrial myopathy and sideroblastic anemia (MLASA): missense mutation in the pseudouridine synthase 1 (PUS1) gene is associated with the loss of tRNA pseudouridylation.
    9. A new homozygous stop mutation (E220X)predicts a protein missing 208/427 amino acid residues on the C terminus. The nuclear isoform has an N-terminal extension absent in the mature mitochondrial isoform.
      Title: Nonsense mutation in pseudouridylate synthase 1 (PUS1) in two brothers affected by myopathy, lactic acidosis and sideroblastic anaemia (MLASA).
    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
    Myopathy, lactic acidosis, and sideroblastic anemia 1
    MedGen: C4551958 OMIM: 600462 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

    Clone Names

    • MGC11268

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables pseudouridine synthase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables pseudouridine synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables pseudouridine synthase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables pseudouridine synthase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables steroid receptor RNA activator RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA pseudouridine synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA pseudouridine synthesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrial tRNA pseudouridine synthesis TAS
    Traceable Author Statement
    more info
    		  
    involved_in tRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA pseudouridine synthesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pseudouridylate synthase 1 homolog
    Names
    mitochondrial tRNA pseudouridine synthase A
    pseudouridylate synthase 1
    tRNA pseudouridine synthase 1
    tRNA pseudouridine synthase A, mitochondrial
    tRNA pseudouridine(38-40) synthase
    tRNA pseudouridylate synthase I
    tRNA uridine isomerase I
    NP_001002019.1
    NP_001002020.1
    NP_079491.2

    NCBI Reference Sequences (RefSeq)

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    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_013039.2 RefSeqGene

      Range
      5002..21622
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001002019.3 → NP_001002019.1  pseudouridylate synthase 1 homolog isoform 2

      See identical proteins and their annotated locations for NP_001002019.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AC131009, AF116238, AI566545, BM923133, BX340929
      Consensus CDS
      CCDS31928.1
      UniProtKB/TrEMBL
      E5KMT6, G8JLB3
      Conserved Domains (2) summary
      cd02568
      Location:60 → 312
      PseudoU_synth_PUS1_PUS2; Pseudouridine synthase, PUS1/ PUS2 like
      COG0101
      Location:56 → 335
      TruA; tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]

    2. NM_001002020.3 → NP_001002020.1  pseudouridylate synthase 1 homolog isoform 2

      See identical proteins and their annotated locations for NP_001002020.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AC131009, AI566545, BC002901, CB118952
      Consensus CDS
      CCDS31928.1
      UniProtKB/TrEMBL
      E5KMT6, G8JLB3
      Related
      ENSP00000392451.2, ENST00000443358.6
      Conserved Domains (2) summary
      cd02568
      Location:60 → 312
      PseudoU_synth_PUS1_PUS2; Pseudouridine synthase, PUS1/ PUS2 like
      COG0101
      Location:56 → 335
      TruA; tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]

    3. NM_025215.6 → NP_079491.2  pseudouridylate synthase 1 homolog isoform 1

      See identical proteins and their annotated locations for NP_079491.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC131009, AI566545, AK074659
      Consensus CDS
      CCDS9275.2
      UniProtKB/Swiss-Prot
      A8K877, B3KQC1, Q8WYT2, Q9BU44, Q9Y606
      UniProtKB/TrEMBL
      E5KMT5, G8JLB3
      Related
      ENSP00000365837.3, ENST00000376649.8
      Conserved Domains (2) summary
      cd02568
      Location:88 → 340
      PseudoU_synth_PUS1_PUS2; Pseudouridine synthase, PUS1/ PUS2 like
      COG0101
      Location:84 → 363
      TruA; tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      131929276..131945896
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      131977320..131993946
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y606.3 GenPept UniProtKB/Swiss-Prot:Q9Y606

    Gene LinkOut

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

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