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Aliases for RPUSD3 Gene

Aliases for RPUSD3 Gene

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

External Ids for RPUSD3 Gene

Previous GeneCards Identifiers for RPUSD3 Gene

  • GC03M009855
  • GC03M009856
  • GC03M009817
  • GC03M009879

Summaries for RPUSD3 Gene

Entrez Gene Summary for RPUSD3 Gene

  • This gene encodes a protein that functions in the assembly of the mitochondrial ribosome by adding a pseudouridine group to 16S rRNA. Loss of this gene results in causes defects in mitochondrial protein production. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2017]

GeneCards Summary for RPUSD3 Gene

RPUSD3 (RNA Pseudouridylate Synthase Domain Containing 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include pseudouridine synthase activity. An important paralog of this gene is RPUSD4.

UniProtKB/Swiss-Prot for RPUSD3 Gene

  • Major enzyme responsible for the conversion of uridine to pseudouridine (PSI) at position 390 in mitochondrial COXI (MT-CO1) mRNA and at position 697-699 in mitochondrial COXIII (MT-CO3) mRNA, modulating the efficiency of mitochondrial protein synthesis without changes in transcript abundance or stability.

Additional gene information for RPUSD3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPUSD3 Gene

Genomics for RPUSD3 Gene

GeneHancer (GH) Regulatory Elements for RPUSD3 Gene

Promoters and enhancers for RPUSD3 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
GH03I009843 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 593.7 +0.7 736 1.7 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF213 RPUSD3 BRPF1 THUMPD3 GHRLOS FANCD2 TADA3 GC03M009840 PIR36573 TTLL3 GC03M009835
GH03I009394 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.8 +445.6 445611 9.8 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SETD5 THUMPD3-AS1 GC03P009403 BRPF1 RAD18 GHRLOS TTLL3 FANCD2 JAGN1 SEC13
GH03I009985 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 11.1 -142.5 -142530 2.5 HDGF PKNOX1 CLOCK MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B EMC3-AS1 EMC3 FANCD2 BRPF1 BRK1 GHRLOS RNU6-670P FANCD2OS PRRT3 SETD5
GH03I009648 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.8 +194.8 194812 2.2 HDGF PKNOX1 CLOCK FOXA2 MLX ARNT ARID4B SIN3A ZNF2 IRF4 MTMR14 BRPF1 SETD5 RAD18 JAGN1 THUMPD3 GHRLOS RPUSD3 FANCD2 SEC13
GH03I009896 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 11.3 -55.6 -55606 8.2 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A YBX1 DMAP1 YY1 IL17RE GC03P009923 GC03P009922 IL17RC JAGN1 FANCD2 CRELD1 PRRT3-AS1 RPUSD3 PRRT3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RPUSD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RPUSD3 gene promoter:

Genomic Locations for RPUSD3 Gene

Genomic Locations for RPUSD3 Gene
chr3:9,837,849-9,844,602
(GRCh38/hg38)
Size:
6,754 bases
Orientation:
Minus strand
chr3:9,879,533-9,886,286
(GRCh37/hg19)

Genomic View for RPUSD3 Gene

Genes around RPUSD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPUSD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPUSD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPUSD3 Gene

Proteins for RPUSD3 Gene

  • Protein details for RPUSD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6P087-RUSD3_HUMAN
    Recommended name:
    Mitochondrial mRNA pseudouridine synthase RPUSD3
    Protein Accession:
    Q6P087
    Secondary Accessions:
    • B4DS39
    • Q6P6A9
    • Q8N1B2
    • Q8NAV3

    Protein attributes for RPUSD3 Gene

    Size:
    351 amino acids
    Molecular mass:
    38461 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH62362.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH65741.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for RPUSD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RPUSD3 Gene

Post-translational modifications for RPUSD3 Gene

  • Ubiquitination at isoforms=2, 368

Antibody Products

  • Abcam antibodies for RPUSD3
  • Santa Cruz Biotechnology (SCBT) Antibodies for RPUSD3

No data available for DME Specific Peptides for RPUSD3 Gene

Domains & Families for RPUSD3 Gene

Gene Families for RPUSD3 Gene

Protein Domains for RPUSD3 Gene

Graphical View of Domain Structure for InterPro Entry

Q6P087

UniProtKB/Swiss-Prot:

RUSD3_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 RPUSD3: view

Function for RPUSD3 Gene

Molecular function for RPUSD3 Gene

UniProtKB/Swiss-Prot Function:
Major enzyme responsible for the conversion of uridine to pseudouridine (PSI) at position 390 in mitochondrial COXI (MT-CO1) mRNA and at position 697-699 in mitochondrial COXIII (MT-CO3) mRNA, modulating the efficiency of mitochondrial protein synthesis without changes in transcript abundance or stability.

Enzyme Numbers (IUBMB) for RPUSD3 Gene

Phenotypes From GWAS Catalog for RPUSD3 Gene

Gene Ontology (GO) - Molecular Function for RPUSD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA,IEA 22658674
GO:0005515 protein binding IPI 25416956
GO:0009982 pseudouridine synthase activity IEA,IBA --
GO:0016853 isomerase activity IEA --
GO:0019239 contributes_to deaminase activity IBA --
genes like me logo Genes that share ontologies with RPUSD3: view

Phenotypes for RPUSD3 Gene

genes like me logo Genes that share phenotypes with RPUSD3: view

miRNA for RPUSD3 Gene

miRTarBase miRNAs that target RPUSD3

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPUSD3 Gene

Localization for RPUSD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPUSD3 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 RPUSD3 gene
Compartment Confidence
mitochondrion 4
nucleus 3
cytosol 2
extracellular 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RPUSD3 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 RPUSD3: view

Pathways & Interactions for RPUSD3 Gene

SuperPathways for RPUSD3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RPUSD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:0009451 RNA modification IEA --
GO:0031119 tRNA pseudouridine synthesis IBA --
genes like me logo Genes that share ontologies with RPUSD3: view

No data available for Pathways by source and SIGNOR curated interactions for RPUSD3 Gene

Drugs & Compounds for RPUSD3 Gene

(1) Additional Compounds for RPUSD3 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 RPUSD3: view

Transcripts for RPUSD3 Gene

Unigene Clusters for RPUSD3 Gene

RNA pseudouridylate synthase domain containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RPUSD3 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11a ·
SP1: - - - - - - - - -
SP2: - - - - - - - - - -
SP3: - - - - - - - - - -
SP4: - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - - -
SP7: - - - - - - - -
SP8: - - - - - - - - - - - - - -
SP9: - - -
SP10: - - - - - - - - -
SP11: - -
SP12: - - -
SP13: - - -
SP14: -
SP15: - -
SP16: -

ExUns: 11b · 11c · 11d ^ 12a · 12b · 12c
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: - - -
SP9:
SP10:
SP11:
SP12: - - -
SP13:
SP14:
SP15:
SP16:

Relevant External Links for RPUSD3 Gene

GeneLoc Exon Structure for
RPUSD3
ECgene alternative splicing isoforms for
RPUSD3

Expression for RPUSD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RPUSD3 Gene

Protein differential expression in normal tissues from HIPED for RPUSD3 Gene

This gene is overexpressed in Lung (52.2) and Breast (14.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RPUSD3 Gene



Protein tissue co-expression partners for RPUSD3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RPUSD3 Gene:

RPUSD3

SOURCE GeneReport for Unigene cluster for RPUSD3 Gene:

Hs.33719

Evidence on tissue expression from TISSUES for RPUSD3 Gene

  • Nervous system(4.6)
  • Bone marrow(4.2)
  • Eye(4.1)
genes like me logo Genes that share expression patterns with RPUSD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPUSD3 Gene

Orthologs for RPUSD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RPUSD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RPUSD3 33 34
  • 92.77 (n)
dog
(Canis familiaris)
Mammalia RPUSD3 33 34
  • 85.75 (n)
cow
(Bos Taurus)
Mammalia RPUSD3 33 34
  • 84.06 (n)
mouse
(Mus musculus)
Mammalia Rpusd3 33 16 34
  • 78.04 (n)
rat
(Rattus norvegicus)
Mammalia Rpusd3 33
  • 77.32 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RPUSD3 34
  • 51 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RPUSD3 34
  • 48 (a)
OneToOne
chicken
(Gallus gallus)
Aves RPUSD3 33
  • 57.4 (n)
lizard
(Anolis carolinensis)
Reptilia RPUSD3 34
  • 46 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rpusd3 33
  • 53.26 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.3147 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3295 34
  • 17 (a)
OneToMany
Species where no ortholog for RPUSD3 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)
  • zebrafish (Danio rerio)

Evolution for RPUSD3 Gene

ENSEMBL:
Gene Tree for RPUSD3 (if available)
TreeFam:
Gene Tree for RPUSD3 (if available)

Paralogs for RPUSD3 Gene

Paralogs for RPUSD3 Gene

genes like me logo Genes that share paralogs with RPUSD3: view

Variants for RPUSD3 Gene

Sequence variations from dbSNP and Humsavar for RPUSD3 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs142932960 likely-pathogenic, Inborn genetic diseases 9,839,148(-) G/A coding_sequence_variant, intron_variant, missense_variant
rs767103943 likely-pathogenic, Inborn genetic diseases 9,840,238(-) G/A/T coding_sequence_variant, missense_variant
rs1000941594 -- 9,841,108(-) C/G intron_variant
rs1001033478 -- 9,839,984(-) G/A/T intron_variant
rs1001089270 -- 9,845,384(-) C/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RPUSD3 Gene

Variant ID Type Subtype PubMed ID
nsv1010768 CNV gain 25217958
nsv834615 CNV loss 17160897

Variation tolerance for RPUSD3 Gene

Residual Variation Intolerance Score: 92.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.40; 42.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPUSD3 Gene

Human Gene Mutation Database (HGMD)
RPUSD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPUSD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPUSD3 Gene

Disorders for RPUSD3 Gene

Additional Disease Information for RPUSD3

No disorders were found for RPUSD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RPUSD3 Gene

Publications for RPUSD3 Gene

  1. A pseudouridine synthase module is essential for mitochondrial protein synthesis and cell viability. (PMID: 27974379) Antonicka H … Shoubridge EA (EMBO reports 2017) 3 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules. (PMID: 28082677) Zaganelli S … Martinou JC (The Journal of biological chemistry 2017) 4 58

Products for RPUSD3 Gene

Sources for RPUSD3 Gene

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