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    RPUSD4 RNA pseudouridine synthase D4 [ Homo sapiens (human) ]

    Gene ID: 84881, updated on 2-Nov-2024

    Summary

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    Official Symbol
    RPUSD4provided by HGNC
    Official Full Name
    RNA pseudouridine synthase D4provided by HGNC
    Primary source
    HGNC:HGNC:25898
    See related
    Ensembl:ENSG00000165526 MIM:617488; AllianceGenome:HGNC:25898
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables mitochondrial ribosomal large subunit rRNA binding activity; pseudouridine synthase activity; and tRNA binding activity. Involved in mRNA pseudouridine synthesis; mitochondrial tRNA pseudouridine synthesis; and positive regulation of mitochondrial translation. Located in mitochondrion; nucleoplasm; and ribonucleoprotein granule. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 9.5), lymph node (RPKM 7.9) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See RPUSD4 in Genome Data Viewer
    Location:
    11q24.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (126202096..126211650, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (126231624..126241182, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (126071991..126081545, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902784 Neighboring gene uncharacterized LOC105369591 Neighboring gene uncharacterized LOC124902783 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126016810-126017457 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126017458-126018104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:126029789-126030433 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126030434-126031078 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:126052865-126053364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:126055613-126056538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5703 Neighboring gene family with sequence similarity 118 member B Neighboring gene RNA, U4 small nuclear 86, pseudogene Neighboring gene MPRA-validated peak1502 silencer Neighboring gene MPRA-validated peak1503 silencer Neighboring gene SRP receptor subunit alpha Neighboring gene RNA, 7SL, cytoplasmic 351, pseudogene

    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. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. Martinez NM, et al. Mol Cell, 2022 Feb 3. PMID 35051350, 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. Association of genome-wide variation with the risk of incident heart failure in adults of European and African ancestry: a prospective meta-analysis from the cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium. Smith NL, et al. Circ Cardiovasc Genet, 2010 Jun. PMID 20445134, Free PMC Article
    4. 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
    5. The interactome of the histone gene regulatory factor HiNF-P suggests novel cell cycle related roles in transcriptional control and RNA processing. Miele A, et al. J Cell Biochem, 2007 Sep 1. PMID 17577209

    See all (33) 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. RPUSD4 binds 16S mt-rRNA, mt-tRNA(Met), and mt-tRNA(Phe), and is responsible for pseudouridylation of the latter.
      Title: The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    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

    EBI GWAS Catalog

    Description
    Association of genome-wide variation with the risk of incident heart failure in adults of European and African ancestry: a prospective meta-analysis from the cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium.
    EBI GWAS Catalog

    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

    • FLJ14494

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mitochondrial ribosomal large subunit rRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrial tRNA 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 
    involved_in rRNA processing 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 nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pseudouridylate synthase RPUSD4, mitochondrial
    Names
    RNA pseudouridylate synthase domain containing 4
    RNA pseudouridylate synthase domain-containing protein 4
    mitochondrial RNA pseudouridine synthase RPUSD4
    NP_001138299.1
    NP_001350445.1
    NP_116184.2
    XP_011541341.1
    XP_054226218.1

    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_001144827.2 → NP_001138299.1  pseudouridylate synthase RPUSD4, mitochondrial isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses two alternate in-frame splice sites in the coding region, compared to variant 1. This results in a shorter protein (isoform b) compared to isoform a.
      Source sequence(s)
      AK308059, BE260782, BU679173, DB051034
      Consensus CDS
      CCDS53721.1
      Related
      ENSP00000433065.1, ENST00000533628.5
      Conserved Domains (2) summary
      cd02869
      Location:106 → 298
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family
      COG0564
      Location:73 → 315
      RluA; Pseudouridylate synthase, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]

    2. NM_001363516.2 → NP_001350445.1  pseudouridylate synthase RPUSD4, mitochondrial isoform c

      Status: VALIDATED

      Source sequence(s)
      AP001893
      Conserved Domains (1) summary
      cd02869
      Location:106 → 328
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    3. NM_032795.3 → NP_116184.2  pseudouridylate synthase RPUSD4, mitochondrial isoform a

      See identical proteins and their annotated locations for NP_116184.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      BC014131, BU679173, DB542764
      Consensus CDS
      CCDS8469.1
      UniProtKB/Swiss-Prot
      E9PML2, Q96CM3, Q96K56
      Related
      ENSP00000298317.4, ENST00000298317.9
      Conserved Domains (1) summary
      cd02869
      Location:106 → 329
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD 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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      126202096..126211650 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543039.3 → XP_011541341.1  pseudouridylate synthase RPUSD4, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_011541341.1

      UniProtKB/TrEMBL
      B4DUN4
      Conserved Domains (1) summary
      cd02869
      Location:28 → 136
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      126231624..126241182 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370243.1 → XP_054226218.1  pseudouridylate synthase RPUSD4, mitochondrial isoform X1

      UniProtKB/TrEMBL
      B4DUN4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96CM3.1 GenPept UniProtKB/Swiss-Prot:Q96CM3

    Gene LinkOut

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

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