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Aliases for PUS3 Gene

Aliases for PUS3 Gene

  • Pseudouridylate Synthase 3 2 3 5
  • TRNA Pseudouridylate Synthase 3 3 4
  • TRNA Pseudouridine Synthase 3 3 4
  • TRNA-Uridine Isomerase 3 3 4
  • TRNA Pseudouridine(38/39) Synthase 3
  • 2610020J05Rik 3
  • EC 4
  • FKSG32 3
  • MRT55 3

External Ids for PUS3 Gene

Previous GeneCards Identifiers for PUS3 Gene

  • GC11M125268
  • GC11M125763
  • GC11M121705

Summaries for PUS3 Gene

Entrez Gene Summary for PUS3 Gene

  • The protein encoded by this gene catalyzes the formation of tRNA pseudouridine from tRNA uridine at position 39 in the anticodon stem and loop of transfer RNAs. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

GeneCards Summary for PUS3 Gene

PUS3 (Pseudouridylate Synthase 3) is a Protein Coding gene. Diseases associated with PUS3 include Mental Retardation, Autosomal Recessive 55. Among its related pathways are Gene Expression and tRNA processing. Gene Ontology (GO) annotations related to this gene include RNA binding and pseudouridine synthase activity.

UniProtKB/Swiss-Prot for PUS3 Gene

  • Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs.

Additional gene information for PUS3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PUS3 Gene

Genomics for PUS3 Gene

GeneHancer (GH) Regulatory Elements for PUS3 Gene

Promoters and enhancers for PUS3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I125901 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 557.7 +0.4 372 2 PKNOX1 ATF1 ARID4B SIN3A DMAP1 YY1 ETS1 POLR2B ZNF766 ZNF207 DDX25 PUS3 ENSG00000254790 ENSG00000254694 FAM118B RPUSD4 PIR36090 ENSG00000255027
GH11I125904 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 550.8 -1.0 -999 0.3 RING1 MXI1 USF1 MAX SIN3A USF2 POLR2A EZH2 DDX25 PUS3 ENSG00000254790 FAM118B RPUSD4 ENSG00000254694 GC11P125928 ENSG00000255027
GH11I125493 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.2 +407.9 407941 2.9 ZSCAN4 INSM2 KLF17 ZNF76 SIN3A ZNF2 ZNF335 GLIS2 ZNF213 ZNF366 FEZ1 LOC403312 PUS3 DDX25 PKNOX2
GH11I125568 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 5.3 +333.3 333336 2.5 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF213 EI24 FEZ1 DDX25 PUS3 RNU6-1156P STT3A-AS1
GH11I125624 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 4.8 +277.3 277299 3.4 MLX ZFP64 DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF548 SP3 MEF2D CHEK1 HP11014 TMEM218 TIRAP MSANTD2 FEZ1 STT3A CCDC15 ACRV1 PUS3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PUS3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PUS3 gene promoter:

Genomic Locations for PUS3 Gene

Genomic Locations for PUS3 Gene
9,885 bases
Minus strand

Genomic View for PUS3 Gene

Genes around PUS3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PUS3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PUS3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PUS3 Gene

Proteins for PUS3 Gene

  • Protein details for PUS3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    tRNA pseudouridine(38/39) synthase
    Protein Accession:
    Secondary Accessions:
    • B2RAM0
    • Q96D17
    • Q96J23
    • Q96NB4

    Protein attributes for PUS3 Gene

    481 amino acids
    Molecular mass:
    55647 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PUS3 Gene

Post-translational modifications for PUS3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PUS3 Gene

Domains & Families for PUS3 Gene

Gene Families for PUS3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for PUS3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the tRNA pseudouridine synthase TruA family.
  • Belongs to the tRNA pseudouridine synthase TruA family.
genes like me logo Genes that share domains with PUS3: view

Function for PUS3 Gene

Molecular function for PUS3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
tRNA uridine(38/39) = tRNA pseudouridine(38/39).
UniProtKB/Swiss-Prot Function:
Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs.

Enzyme Numbers (IUBMB) for PUS3 Gene

Phenotypes From GWAS Catalog for PUS3 Gene

Gene Ontology (GO) - Molecular Function for PUS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0009982 pseudouridine synthase activity IEA,IMP 27055666
GO:0016853 isomerase activity IEA --
genes like me logo Genes that share ontologies with PUS3: view
genes like me logo Genes that share phenotypes with PUS3: view

Human Phenotype Ontology for PUS3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for PUS3

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PUS3 Gene

Localization for PUS3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PUS3 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 PUS3 gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PUS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with PUS3: view

Pathways & Interactions for PUS3 Gene

genes like me logo Genes that share pathways with PUS3: view

Pathways by source for PUS3 Gene

Gene Ontology (GO) - Biological Process for PUS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006400 tRNA modification TAS --
GO:0008033 tRNA processing IEA --
GO:0009451 RNA modification IEA --
GO:0031119 tRNA pseudouridine synthesis IMP,IEA 27055666
GO:1990481 mRNA pseudouridine synthesis IBA --
genes like me logo Genes that share ontologies with PUS3: view

No data available for SIGNOR curated interactions for PUS3 Gene

Drugs & Compounds for PUS3 Gene

(1) Drugs for PUS3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Uridine Experimental, Investigational Pharma 0

(1) Additional Compounds for PUS3 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 PUS3: view

Transcripts for PUS3 Gene

Unigene Clusters for PUS3 Gene

Pseudouridylate synthase 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PUS3 Gene

No ASD Table

Relevant External Links for PUS3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PUS3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PUS3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PUS3 Gene

This gene is overexpressed in Heart (51.8) and Adipocyte (12.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PUS3 Gene

Protein tissue co-expression partners for PUS3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PUS3 Gene:


SOURCE GeneReport for Unigene cluster for PUS3 Gene:


Evidence on tissue expression from TISSUES for PUS3 Gene

  • Lung(4.2)
  • Pancreas(4.1)
genes like me logo Genes that share expression patterns with PUS3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PUS3 Gene

Orthologs for PUS3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PUS3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PUS3 33 34
  • 99.58 (n)
(Bos Taurus)
Mammalia PUS3 33 34
  • 89.86 (n)
(Canis familiaris)
Mammalia PUS3 33 34
  • 89.07 (n)
(Mus musculus)
Mammalia Pus3 33 16 34
  • 86.93 (n)
(Rattus norvegicus)
Mammalia Pus3 33
  • 85.51 (n)
(Monodelphis domestica)
Mammalia PUS3 34
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia PUS3 34
  • 64 (a)
(Gallus gallus)
Aves PUS3 33 34
  • 68.13 (n)
(Anolis carolinensis)
Reptilia PUS3 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pus3 33
  • 60.84 (n)
(Danio rerio)
Actinopterygii pus3 33 34
  • 59.03 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010807 33
  • 52.36 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3045 33 34
  • 49.96 (n)
(Caenorhabditis elegans)
Secernentea tag-124 33 34
  • 50.4 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E14345g 33
  • 53.73 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DEG1 33 34 36
  • 53.14 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGL003W 33
  • 51.54 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC25B8.05 33
  • 52.33 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 32 (a)
Species where no ortholog for PUS3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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)

Evolution for PUS3 Gene

Gene Tree for PUS3 (if available)
Gene Tree for PUS3 (if available)

Paralogs for PUS3 Gene

No data available for Paralogs for PUS3 Gene

Variants for PUS3 Gene

Sequence variations from dbSNP and Humsavar for PUS3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs104894232 pathogenic, Hydrolethalus syndrome, Hydrolethalus syndrome 1 125,900,000(-) A/G intron_variant
rs117414825 uncertain-significance, Hydrolethalus syndrome 125,900,597(-) T/G intron_variant
rs138284572 uncertain-significance, Hydrolethalus syndrome 125,899,836(-) A/G intron_variant
rs145788945 uncertain-significance, Hydrolethalus syndrome 125,900,344(-) C/T intron_variant
rs200146258 uncertain-significance, Hydrolethalus syndrome 125,899,454(-) A/C/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PUS3 Gene

Variant ID Type Subtype PubMed ID
dgv248n67 CNV gain 20364138
esv32964 CNV gain+loss 17666407
nsv468888 CNV loss 19166990
nsv556525 CNV gain 21841781
nsv556526 CNV loss 21841781

Variation tolerance for PUS3 Gene

Residual Variation Intolerance Score: 75.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.36; 85.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PUS3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PUS3 Gene

Disorders for PUS3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PUS3 Gene - From: HGMD, OMIM, ClinVar, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, autosomal recessive 55
  • mrt55
- elite association - COSMIC cancer census association via MalaCards
Search PUS3 in MalaCards View complete list of genes associated with diseases


  • Mental retardation, autosomal recessive 55 (MRT55) [MIM:617051]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269 PubMed:27055666}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PUS3

genes like me logo Genes that share disorders with PUS3: view

No data available for Genatlas for PUS3 Gene

Publications for PUS3 Gene

  1. A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition. (PMID: 27055666) Shaheen R … Alkuraya FS (Human genetics 2016) 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. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. 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
  5. Pseudouridine synthase 3 from mouse modifies the anticodon loop of tRNA. (PMID: 11027153) Chen J … Patton JR (Biochemistry 2000) 3 22 58

Products for PUS3 Gene

Sources for PUS3 Gene

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