U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 84881, updated on 11-Apr-2024

Summary

Go to the top of the page Help
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 mitochondrial tRNA pseudouridine synthesis and positive regulation of mitochondrial translation. Located in mitochondrion; nucleoplasm; and ribonucleoprotein granule. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 9.5), lymph node (RPKM 7.9) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
11q24.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (126202096..126211650, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (126231624..126241182, complement)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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 (32) 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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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 
Component Evidence Code Pubs
located_in mitochondrial matrix IEA
Inferred from Electronic Annotation
more info
  
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

Go to the top of the page Help
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)

Go to the top of the page Help

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.

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_2023_10

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous