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    RPUSD3 RNA pseudouridine synthase D3 [ Homo sapiens (human) ]

    Gene ID: 285367, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RPUSD3provided by HGNC
    Official Full Name
    RNA pseudouridine synthase D3provided by HGNC
    Primary source
    HGNC:HGNC:28437
    See related
    Ensembl:ENSG00000156990 MIM:617759; AllianceGenome:HGNC:28437
    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
    Summary
    This gene encodes a protein that functions in the assembly of the mitochondrial ribosome by adding a pseudouridine group to 16S rRNA. Loss of this gene results in causes defects in mitochondrial protein production. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2017]
    Expression
    Ubiquitous expression in testis (RPKM 19.6), placenta (RPKM 7.8) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See RPUSD3 in Genome Data Viewer
    Location:
    3p25.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9837849..9844008, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9829856..9836015, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9879533..9885692, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene transcriptional adaptor 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9834089-9834615 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9834616-9835142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19409 Neighboring gene ARPC4-TTLL3 readthrough Neighboring gene actin related protein 2/3 complex subunit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14044 Neighboring gene tubulin tyrosine ligase like 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:9866222-9866442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9867034-9867534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9867535-9868035 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9868869-9869369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9876763-9877262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19411 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:9890179-9891039 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9895593-9896262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9901011-9901551 Neighboring gene MARK2 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 13942 Neighboring gene Sharpr-MPRA regulatory region 9891 Neighboring gene cell death inducing DFFA like effector c

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules. Zaganelli S, et al. J Biol Chem, 2017 Mar 17. PMID 28082677, Free PMC Article
    2. A pseudouridine synthase module is essential for mitochondrial protein synthesis and cell viability. Antonicka H, et al. EMBO Rep, 2017 Jan. PMID 27974379, Free PMC Article
    3. A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation. Arroyo JD, et al. Cell Metab, 2016 Dec 13. PMID 27667664, Free PMC Article
    4. The SARS-CoV-2 RNA interactome. Lee S, et al. Mol Cell, 2021 Jul 1. PMID 33989516, Free PMC Article
    5. A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome. Richter R, et al. EMBO J, 2010 Mar 17. PMID 20186120, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34707, FLJ37268, MGC29784

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables pseudouridine synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA pseudouridine synthesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of mitochondrial translation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    mitochondrial mRNA pseudouridine synthase RPUSD3
    Names
    RNA pseudouridylate synthase domain containing 3
    RNA pseudouridylate synthase domain-containing protein 3

    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_054931.1 RefSeqGene

      Range
      5011..11170
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001142547.3 → NP_001136019.2  mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC018809
      Consensus CDS
      CCDS46744.2
      UniProtKB/Swiss-Prot
      B4DS39, Q6P087, Q6P6A9, Q8N1B2, Q8NAV3
      Related
      ENSP00000398921.3, ENST00000433535.7
      Conserved Domains (1) summary
      cd02869
      Location:80 → 252
      PseudoU_synth_RluA_like; Pseudouridine synthase, RluA family

    2. NM_001351736.3 → NP_001338665.1  mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC018809, BC065741, BU197244, HY235216
      Consensus CDS
      CCDS87038.1
      UniProtKB/TrEMBL
      C9JM75, H7C454
      Related
      ENSP00000408693.1, ENST00000424438.5
      Conserved Domains (1) summary
      cd02869
      Location:58 → 210
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    3. NM_001351737.2 → NP_001338666.2  mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC018809
      UniProtKB/TrEMBL
      H7C454
      Related
      ENSP00000415616.2, ENST00000418713.6
      Conserved Domains (1) summary
      cd02869
      Location:82 → 234
      PseudoU_synth_RluA_like; Pseudouridine synthase, RluA family

    4. NM_001351738.2 → NP_001338667.2  mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC018809
      UniProtKB/TrEMBL
      H7C1H7
      Related
      ENSP00000400397.1, ENST00000427174.5
      Conserved Domains (1) summary
      cl00130
      Location:82 → 190
      PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

    5. NM_173659.5 → NP_775930.3  mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC018809
      Consensus CDS
      CCDS2586.3
      UniProtKB/Swiss-Prot
      B4DS39, Q6P087, Q6P6A9, Q8N1B2, Q8NAV3
      Related
      ENSP00000373331.6, ENST00000383820.10
      Conserved Domains (1) summary
      cd02869
      Location:82 → 267
      PseudoU_synth_RluA_like; Pseudouridine synthase, RluA family

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      9837849..9844008 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      9829856..9836015 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P087.3 GenPept UniProtKB/Swiss-Prot:Q6P087

    Gene LinkOut

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

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