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

Gene ID: 285367, updated on 2-Nov-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: 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. 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
  2. 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
  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)

Genotypes

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 positive regulation of mitochondrial translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in pseudouridine synthesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in mitochondrial matrix IEA
Inferred from Electronic Annotation
more info
  
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

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