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Aliases for RPUSD4 Gene

Aliases for RPUSD4 Gene

  • RNA Pseudouridylate Synthase Domain Containing 4 2 3 5

External Ids for RPUSD4 Gene

Previous GeneCards Identifiers for RPUSD4 Gene

  • GC11M125578
  • GC11M126071
  • GC11M122013

Summaries for RPUSD4 Gene

GeneCards Summary for RPUSD4 Gene

RPUSD4 (RNA Pseudouridylate Synthase Domain Containing 4) is a Protein Coding gene. GO annotations related to this gene include poly(A) RNA binding and pseudouridine synthase activity. An important paralog of this gene is RPUSD3.

Additional gene information for RPUSD4 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPUSD4 Gene

Genomics for RPUSD4 Gene

Regulatory Elements for RPUSD4 Gene

Enhancers for RPUSD4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11H126188 1.2 ENCODE dbSUPER 16.1 +22.5 22470 2.1 PKNOX1 MLX ARID4B ATF7 RUNX3 SP5 NFYC JUNB PPARG KAT8 FAM118B FOXRED1 RPUSD4 ENSG00000254833 ENSG00000254790 RNU4-86P DCPS ENSG00000254771 ENSG00000254694
GH11H126418 1.8 FANTOM5 Ensembl ENCODE dbSUPER 9.6 -211.4 -211419 10.1 ATF1 ARNT SIN3A YY1 TCF12 ZNF766 GATA2 ELK1 ATF7 RUNX3 HP11014 ST3GAL4 DCPS ENSG00000254694 FAM118B RPUSD4 LOC105369558 FEZ1 ENSG00000278215 KIRREL3-AS1
GH11H126190 0.8 ENCODE dbSUPER 16.2 +20.7 20709 1.2 NFIC NFIB HNF4A ZNF548 KDM1A RAD21 FAM118B RPUSD4 RNU4-86P ENSG00000254790 DCPS ENSG00000254771 ENSG00000254694
GH11H126280 1 ENCODE 10.7 -70.8 -70755 4.2 HDGF ATF1 ARID4B SIN3A DMAP1 YY1 ELK1 ZNF143 SP5 REST FOXRED1 FAM118B ENSG00000254694 DCPS HP11014 RPUSD4 RNU4-86P TIRAP ENSG00000254905
GH11H125901 1 ENCODE 10 +308.7 308700 2 PKNOX1 ATF1 ARID4B SIN3A DMAP1 YY1 ETS1 ZNF766 ELK1 ZNF207 DDX25 ENSG00000254790 ENSG00000254694 FAM118B RPUSD4 PUS3 PIR36090
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RPUSD4 on UCSC Golden Path with GeneCards custom track

Promoters for RPUSD4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000046612 -8 1801 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF143 FOS SP3

Genomic Locations for RPUSD4 Gene

Genomic Locations for RPUSD4 Gene
9,599 bases
Minus strand

Genomic View for RPUSD4 Gene

Genes around RPUSD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPUSD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPUSD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPUSD4 Gene

Proteins for RPUSD4 Gene

  • Protein details for RPUSD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    RNA pseudouridylate synthase domain-containing protein 4
    Protein Accession:
    Secondary Accessions:
    • E9PML2
    • Q96K56

    Protein attributes for RPUSD4 Gene

    377 amino acids
    Molecular mass:
    42205 Da
    Quaternary structure:
    No Data Available
    • Sequence=AK308059; Type=Frameshift; Positions=101; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RPUSD4 Gene

    Alternative splice isoforms for RPUSD4 Gene


neXtProt entry for RPUSD4 Gene

Post-translational modifications for RPUSD4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RPUSD4 Gene

No data available for DME Specific Peptides for RPUSD4 Gene

Domains & Families for RPUSD4 Gene

Gene Families for RPUSD4 Gene

Suggested Antigen Peptide Sequences for RPUSD4 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the pseudouridine synthase RluA family.
  • Belongs to the pseudouridine synthase RluA family.
genes like me logo Genes that share domains with RPUSD4: view

Function for RPUSD4 Gene

Phenotypes From GWAS Catalog for RPUSD4 Gene

Gene Ontology (GO) - Molecular Function for RPUSD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,IDA 22658674
GO:0005515 protein binding IPI 17577209
GO:0009982 pseudouridine synthase activity IEA,IBA --
GO:0019239 contributes_to deaminase activity IBA --
genes like me logo Genes that share ontologies with RPUSD4: view

Phenotypes for RPUSD4 Gene

GenomeRNAi human phenotypes for RPUSD4:
genes like me logo Genes that share phenotypes with RPUSD4: view

miRNA for RPUSD4 Gene

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPUSD4 Gene

Localization for RPUSD4 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RPUSD4 gene
Compartment Confidence
mitochondrion 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RPUSD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IBA --
genes like me logo Genes that share ontologies with RPUSD4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for RPUSD4 Gene

Pathways & Interactions for RPUSD4 Gene

SuperPathways for RPUSD4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RPUSD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009451 RNA modification IEA --
GO:0031119 tRNA pseudouridine synthesis IBA --
genes like me logo Genes that share ontologies with RPUSD4: view

No data available for Pathways by source and SIGNOR curated interactions for RPUSD4 Gene

Drugs & Compounds for RPUSD4 Gene

(1) Additional Compounds for RPUSD4 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 5-(b-D-Ribofuranosyl)uracil
  • 5-(b-delta-Ribofuranosyl)uracil
  • 5-b-D-Ribofuranosyl-Uracil
  • 5-beta-delta-Ribofuranosyl-Uracil
  • 5-Ribosyluracil
genes like me logo Genes that share compounds with RPUSD4: view

Transcripts for RPUSD4 Gene

Unigene Clusters for RPUSD4 Gene

RNA pseudouridylate synthase domain containing 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RPUSD4 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b · 5c · 5d ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b
SP1: - - -
SP2: - - - - -
SP3: - - - - - - - - -
SP4: -
SP6: - - - - - -
SP8: - - - - - - - - - -

Relevant External Links for RPUSD4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RPUSD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RPUSD4 Gene

mRNA differential expression in normal tissues according to GTEx for RPUSD4 Gene

This gene is overexpressed in Muscle - Skeletal (x7.2).

Protein differential expression in normal tissues from HIPED for RPUSD4 Gene

This gene is overexpressed in Pancreas (34.8), Lung (24.6), and Adrenal (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RPUSD4 Gene

Protein tissue co-expression partners for RPUSD4 Gene

NURSA nuclear receptor signaling pathways regulating expression of RPUSD4 Gene:


SOURCE GeneReport for Unigene cluster for RPUSD4 Gene:


Evidence on tissue expression from TISSUES for RPUSD4 Gene

  • Lung(4.2)
  • Nervous system(3.9)
genes like me logo Genes that share expression patterns with RPUSD4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPUSD4 Gene

Orthologs for RPUSD4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RPUSD4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RPUSD4 33 34
  • 99.47 (n)
(Canis familiaris)
Mammalia RPUSD4 33 34
  • 85.23 (n)
(Bos Taurus)
Mammalia RPUSD4 33 34
  • 84.75 (n)
(Mus musculus)
Mammalia Rpusd4 33 16 34
  • 82.32 (n)
(Rattus norvegicus)
Mammalia Rpusd4 33
  • 81.87 (n)
(Ornithorhynchus anatinus)
Mammalia RPUSD4 34
  • 66 (a)
(Monodelphis domestica)
Mammalia RPUSD4 34
  • 62 (a)
(Gallus gallus)
Aves RPUSD4 33 34
  • 64.24 (n)
(Anolis carolinensis)
Reptilia RPUSD4 34
  • 59 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC734064 33
  • 56 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.10103 33
(Danio rerio)
Actinopterygii rpusd4 33 34
  • 57.02 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3295 34
  • 25 (a)
Species where no ortholog for RPUSD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RPUSD4 Gene

Gene Tree for RPUSD4 (if available)
Gene Tree for RPUSD4 (if available)

Paralogs for RPUSD4 Gene

Paralogs for RPUSD4 Gene

genes like me logo Genes that share paralogs with RPUSD4: view

Variants for RPUSD4 Gene

Sequence variations from dbSNP and Humsavar for RPUSD4 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000001988 -- 126,211,625(+) TCCAC(C/T)TGGGC upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs1000215244 -- 126,202,829(+) CTTCA(C/T)GTGTG utr-variant-3-prime
rs1000218423 -- 126,205,964(+) AGCTT(A/G)TCTTT intron-variant
rs1000337269 -- 126,208,342(+) CACAA(A/G)ATGCT intron-variant
rs1000959384 -- 126,210,017(+) CTCAG(A/G)CATAC intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for RPUSD4 Gene

Variant ID Type Subtype PubMed ID
nsv556529 CNV loss 21841781
nsv556528 CNV loss 21841781
nsv556527 CNV loss 21841781
nsv536 CNV deletion 18451855

Variation tolerance for RPUSD4 Gene

Residual Variation Intolerance Score: 58% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.11; 90.25% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RPUSD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPUSD4 Gene

Disorders for RPUSD4 Gene

Relevant External Links for RPUSD4

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for RPUSD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RPUSD4 Gene

Publications for RPUSD4 Gene

  1. The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules. (PMID: 28082677) Zaganelli S … Martinou JC (The Journal of biological chemistry 2017) 2 3 60
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  5. A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation. (PMID: 27667664) Arroyo JD … Mootha VK (Cell metabolism 2016) 3 60

Products for RPUSD4 Gene

Sources for RPUSD4 Gene

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