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

Gene ID: 84881, updated on 5-Aug-2022

Summary

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
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Genomic context

See RPUSD4 in Genome Data Viewer
Location:
11q24.2
Exon count:
7
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (126202096..126211650, complement)
110 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 LOC105369591 Neighboring gene uncharacterized LOC124902783 Neighboring gene HNF4 motif-containing MPRA enhancer 115 Neighboring gene family with sequence similarity 118 member B Neighboring gene RNA, U4 small nuclear 86, pseudogene Neighboring gene SRP receptor subunit alpha Neighboring gene RNA, 7SL, cytoplasmic 351, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 IBA
Inferred from Biological aspect of Ancestor
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 
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
 
involved_in enzyme-directed rRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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

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

NCBI Reference Sequences (RefSeq)

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_001144827.2NP_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
    UniProtKB/Swiss-Prot
    Q96CM3
    Related
    ENSP00000433065.1, ENST00000533628.5
    Conserved Domains (2) summary
    cd02869
    Location:106298
    PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family
    COG0564
    Location:73315
    RluA; Pseudouridylate synthase, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]
  2. NM_001363516.2NP_001350445.1  pseudouridylate synthase RPUSD4, mitochondrial isoform c

    Status: VALIDATED

    Source sequence(s)
    AP001893
    Conserved Domains (1) summary
    cd02869
    Location:106328
    PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family
  3. NM_032795.3NP_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
    Q96CM3, Q96K56
    Related
    ENSP00000298317.4, ENST00000298317.9
    Conserved Domains (1) summary
    cd02869
    Location:106329
    PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_011543039.3XP_011541341.1  mitochondrial RNA pseudouridine synthase RPUSD4 isoform X1

    See identical proteins and their annotated locations for XP_011541341.1

    UniProtKB/TrEMBL
    B4DUN4
    Conserved Domains (1) summary
    cd02869
    Location:28136
    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)