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Aliases for RPUSD4 Gene

Aliases for RPUSD4 Gene

  • RNA Pseudouridylate Synthase Domain Containing 4 2 3 5
  • RNA Pseudouridylate Synthase Domain-Containing Protein 4 4
  • EC 5.4.99.- 4

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. Gene Ontology (GO) annotations related to this gene include pseudouridine synthase activity. An important paralog of this gene is RPUSD3.

UniProtKB/Swiss-Prot for RPUSD4 Gene

  • Converts specific uridines to pseudouridine (PSI) in different mitochondrial RNA substrates. Acts on position 1397 in 16S mitochondrial ribosomal RNA (16S mt-rRNA). This modification is required for the assembly of 16S mt-rRNA into a functional mitochondrial ribosome (PubMed:27974379). Acts on position 39 in mitochondrial tRNA(Phe) (PubMed:28082677).

Additional gene information for RPUSD4 Gene

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

Genomics for RPUSD4 Gene

GeneHancer (GH) Regulatory Elements for RPUSD4 Gene

Promoters and enhancers for RPUSD4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I126210 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 -0.3 -336 3 CLOCK FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF143 FAM118B RPUSD4 FOXRED1 ENSG00000254694 STT3A SRPRA CDON RNU4-86P
GH11I126280 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 10.7 -70.8 -70755 4.2 HDGF ATF1 ARID4B SIN3A DMAP1 ZNF48 YY1 ZNF143 RXRA SP5 TIRAP FOXRED1 FAM118B ENSG00000254694 DCPS HP11014 RPUSD4 RNU4-86P ENSG00000254905
GH11I125901 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 10 +308.7 308695 2 PKNOX1 ATF1 ARID4B SIN3A DMAP1 YY1 ETS1 POLR2B ZNF766 ZNF207 DDX25 PUS3 ENSG00000254790 ENSG00000254694 FAM118B RPUSD4 PIR36090 ENSG00000255027
GH11I126188 Enhancer 1.1 ENCODE dbSUPER 16.1 +22.5 22469 2.1 PKNOX1 MLX ARID4B ZNF48 ATF7 RUNX3 SP5 NFYC JUNB PPARG FAM118B FOXRED1 RPUSD4 ENSG00000254833 ENSG00000254790 RNU4-86P DCPS ENSG00000254771 ENSG00000254694
GH11I125904 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 10 +307.3 307324 0.3 RING1 MXI1 USF1 MAX SIN3A USF2 POLR2A EZH2 DDX25 PUS3 ENSG00000254790 FAM118B RPUSD4 ENSG00000254694 GC11P125928 ENSG00000255027
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RPUSD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RPUSD4 gene promoter:

Genomic Locations for RPUSD4 Gene

Genomic Locations for RPUSD4 Gene
chr11:126,202,094-126,211,692
(GRCh38/hg38)
Size:
9,599 bases
Orientation:
Minus strand
chr11:126,071,989-126,081,587
(GRCh37/hg19)

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:
    Q96CM3-RUSD4_HUMAN
    Recommended name:
    Mitochondrial RNA pseudouridine synthase RPUSD4
    Protein Accession:
    Q96CM3
    Secondary Accessions:
    • E9PML2
    • Q96K56

    Protein attributes for RPUSD4 Gene

    Size:
    377 amino acids
    Molecular mass:
    42205 Da
    Quaternary structure:
    • Interacts with 16S mt-rRNA, mt-tRNA(Phe) and mt-tRNA(Met).
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for RPUSD4 Gene

Post-translational modifications for RPUSD4 Gene

No Post-translational modifications

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

Q96CM3

UniProtKB/Swiss-Prot:

RUSD4_HUMAN :
  • Belongs to the pseudouridine synthase RluA family.
Family:
  • Belongs to the pseudouridine synthase RluA family.
genes like me logo Genes that share domains with RPUSD4: view

Function for RPUSD4 Gene

Molecular function for RPUSD4 Gene

UniProtKB/Swiss-Prot Function:
Converts specific uridines to pseudouridine (PSI) in different mitochondrial RNA substrates. Acts on position 1397 in 16S mitochondrial ribosomal RNA (16S mt-rRNA). This modification is required for the assembly of 16S mt-rRNA into a functional mitochondrial ribosome (PubMed:27974379). Acts on position 39 in mitochondrial tRNA(Phe) (PubMed:28082677).

Enzyme Numbers (IUBMB) 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 HDA,IEA 22658674
GO:0005515 protein binding IPI 17577209
GO:0009982 pseudouridine synthase activity IBA,IEA --
GO:0016853 isomerase activity IEA --
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 Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPUSD4 Gene

Localization for RPUSD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPUSD4 Gene

Mitochondrion matrix. Note=Localizes to mitochondrial RNA granules, platforms for post-transcriptional RNA modification and ribosome assembly. {ECO:0000269 PubMed:27974379, ECO:0000269 PubMed:28082677}.

Subcellular locations from

COMPARTMENTS
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 --
GO:0005759 mitochondrial matrix IEA --
genes like me logo Genes that share ontologies with RPUSD4: view

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:0008033 tRNA processing IEA --
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
pseudouridine
  • 5-(b-D-Ribofuranosyl)uracil
  • 5-(b-delta-Ribofuranosyl)uracil
  • 5-b-D-Ribofuranosyl-Uracil
  • 5-beta-delta-Ribofuranosyl-Uracil
  • 5-Ribosyluracil
1445-07-4
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: -
SP5:
SP6: - - - - - -
SP7:
SP8: - - - - - - - - - -

Relevant External Links for RPUSD4 Gene

GeneLoc Exon Structure for
RPUSD4
ECgene alternative splicing isoforms for
RPUSD4

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:

RPUSD4

SOURCE GeneReport for Unigene cluster for RPUSD4 Gene:

Hs.150458

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
chimpanzee
(Pan troglodytes)
Mammalia RPUSD4 33 34
  • 99.47 (n)
dog
(Canis familiaris)
Mammalia RPUSD4 33 34
  • 85.23 (n)
cow
(Bos Taurus)
Mammalia RPUSD4 33 34
  • 84.75 (n)
mouse
(Mus musculus)
Mammalia Rpusd4 33 16 34
  • 82.32 (n)
rat
(Rattus norvegicus)
Mammalia Rpusd4 33
  • 81.87 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RPUSD4 34
  • 66 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RPUSD4 34
  • 62 (a)
OneToOne
chicken
(Gallus gallus)
Aves RPUSD4 33 34
  • 64.24 (n)
lizard
(Anolis carolinensis)
Reptilia RPUSD4 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC734064 33
  • 56 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.10103 33
zebrafish
(Danio rerio)
Actinopterygii rpusd4 33 34
  • 57.02 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3295 34
  • 25 (a)
OneToMany
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

ENSEMBL:
Gene Tree for RPUSD4 (if available)
TreeFam:
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 Variation AA Info Type
rs1000001988 -- 126,211,625(-) C/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1000215244 -- 126,202,829(-) T/C 3_prime_UTR_variant
rs1000218423 -- 126,205,964(-) A/G intron_variant
rs1000337269 -- 126,208,342(-) A/G intron_variant
rs1000959384 -- 126,210,017(-) A/G intron_variant

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

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

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)

Additional Variant Information for RPUSD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPUSD4

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

Disorders for RPUSD4 Gene

Additional Disease Information for RPUSD4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 4 58
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. A pseudouridine synthase module is essential for mitochondrial protein synthesis and cell viability. (PMID: 27974379) Antonicka H … Shoubridge EA (EMBO reports 2017) 4 58

Products for RPUSD4 Gene

Sources for RPUSD4 Gene

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