Free for academic non-profit institutions. Other users need a Commercial license

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. 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

Regulatory Elements for PUS3 Gene

Enhancers for PUS3 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
GH11H125901 1 ENCODE 7.7 +0.4 377 2 PKNOX1 ATF1 ARID4B SIN3A DMAP1 YY1 ETS1 ZNF766 ELK1 ZNF207 DDX25 ENSG00000254790 RPUSD4 FAM118B ENSG00000254694 PUS3 PIR36090
GH11H125874 0.7 ENCODE 10.5 +28.7 28669 0.2 CTCF ZNF654 ATF1 SAP130 TRIM22 MAX MNT REST RAD21 TEAD3 DDX25 PUS3 PATE4 CHEK1 ENSG00000260209 HYLS1
GH11H125493 1.4 FANTOM5 ENCODE dbSUPER 5.2 +407.9 407942 2.9 ZSCAN4 INSM2 SIN3A ZNF76 KLF17 ZNF2 GLIS2 ZNF366 REST ZEB2 FEZ1 PUS3 DDX25 PKNOX2 LOC403312
GH11H126196 0.7 ENCODE dbSUPER 10.2 -294.1 -294123 2.6 MAFK RELA FOXRED1 FAM118B ENSG00000254790 SRPRA DDX25 PUS3 DCPS ENSG00000254694 ENSG00000254771
GH11H125568 1.1 ENCODE 5.3 +333.3 333334 2.5 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143 FEZ1 TIRAP HP11014 STT3A MSANTD2 TMEM218 DDX25 PUS3 RNU6-1156P EI24
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PUS3 on UCSC Golden Path with GeneCards custom track

Promoters for PUS3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000046540 269 1800 PKNOX1 ATF1 ARID4B SIN3A YY1 ETS1 ZNF766 ELK1 ZNF207 ZNF143
ENSR00000046541 -931 201 RING1 MXI1 POLR2A USF2 EZH2

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):
  • Enzymes
  • 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 IMP,IEA 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

Clone Products

No data available for Human Phenotype Ontology , 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 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 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 34 36 33
  • 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 Sequence Context AA Info Type
rs104894232 Pathogenic 125,900,000(+) GACAG(A/G)CCGGG intron-variant, reference, missense
rs774005569 Pathogenic 125,893,928(+) AATTC(A/G)TCCCC intron-variant, reference, utr-variant-3-prime, stop-gained
rs79600654 Likely benign 125,900,375(+) TTTAT(A/G)GTAAG intron-variant, utr-variant-3-prime
rs117414825 Uncertain significance 125,900,597(+) TGTTT(G/T)TTAAG intron-variant, utr-variant-3-prime
rs138284572 Uncertain significance 125,899,836(+) AACCT(A/G)CCACA intron-variant, reference, synonymous-codon

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

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

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)

Relevant External Links for PUS3 Gene

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

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, 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.

Relevant External Links for PUS3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 60
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  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 60
  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 60
  5. Pseudouridine synthase 3 from mouse modifies the anticodon loop of tRNA. (PMID: 11027153) Chen J … Patton JR (Biochemistry 2000) 3 22 60

Products for PUS3 Gene

Sources for PUS3 Gene

Loading form....