Human Gene PUS3 (ENST00000227474.8_9) from GENCODE V47lift37

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Description: pseudouridine synthase 3, transcript variant 1 (from RefSeq NM_031307.4)
Gencode Transcript: ENST00000227474.8_9
Gencode Gene: ENSG00000110060.9_11
Transcript (Including UTRs)
Position: hg19 chr11:125,763,380-125,773,101 Size: 9,722 Total Exon Count: 4 Strand: -
Coding Region
Position: hg19 chr11:125,763,680-125,766,179 Size: 2,500 Coding Exon Count: 3

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr11:125,763,380-125,773,101)			mRNA (may differ from genome)		Protein (481 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: PUS3_HUMAN DESCRIPTION: RecName: Full=tRNA pseudouridine(38/39) synthase; EC=5.4.99.45; AltName: Full=tRNA pseudouridine synthase 3; AltName: Full=tRNA pseudouridylate synthase 3; AltName: Full=tRNA-uridine isomerase 3; FUNCTION: Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs (By similarity). CATALYTIC ACTIVITY: tRNA uridine(38/39) = tRNA pseudouridine(38/39). SUBCELLULAR LOCATION: Nucleus (Potential). SIMILARITY: Belongs to the tRNA pseudouridine synthase TruA family.

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: PUS3 Diseases sorted by gene-association score: mental retardation, autosomal recessive 55* (969) * = Manually curated disease association

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone C016403 2,4-dinitrotoluene D000082 Acetaminophen D001564 Benzo(a)pyrene D002794 Choline D002945 Cisplatin D019327 Copper Sulfate D003375 Coumestrol D003993 Dibutyl Phthalate D005492 Folic Acid more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 7.12 RPKM in Liver Total median expression: 183.42 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-22.60	83	-0.272	Picture	PostScript	Text
3' UTR	-59.60	300	-0.199	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR020103 - PsdUridine_synth_cat_dom
IPR001406 - PsdUridine_synth_TruA
IPR020097 - PsdUridine_synth_TruA_a/b_dom
IPR020095 - PsdUridine_synth_TruA_C
IPR020094 - PsdUridine_synth_TruA_N

Pfam Domains:
PF01416 - tRNA pseudouridine synthase

SCOP Domains:
55120 - Pseudouridine synthase

ModBase Predicted Comparative 3D Structure on Q9BZE2


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser	Genome Browser
Gene Details	Gene Details		Gene Details	Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase	SGD
				Protein Sequence	Protein Sequence
				Alignment	Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003723 RNA binding GO:0009982 pseudouridine synthase activity GO:0016853 isomerase activity Biological Process: GO:0001522 pseudouridine synthesis GO:0006400 tRNA modification GO:0008033 tRNA processing GO:0009451 RNA modification GO:0031119 tRNA pseudouridine synthesis GO:1990481 mRNA pseudouridine synthesis Cellular Component: GO:0005634 nucleus GO:0005737 cytoplasm GO:0005829 cytosol

Descriptions from all associated GenBank mRNAs


	BC013427 - Homo sapiens pseudouridylate synthase 3, mRNA (cDNA clone IMAGE:3896889), partial cds. BC004822 - Homo sapiens pseudouridylate synthase 3, mRNA (cDNA clone MGC:5252 IMAGE:3451112), complete cds. AK055702 - Homo sapiens cDNA FLJ31140 fis, clone IMR322001218, highly similar to Mus musculus pseudouridine synthase 3 (Pus3) mRNA. AF325689 - Homo sapiens FKSG32 (FKSG32) mRNA, complete cds. JD099826 - Sequence 80850 from Patent EP1572962. AK074218 - Homo sapiens cDNA FLJ23638 fis, clone CAS09913, highly similar to Pseudouridine synthase 3. AK314251 - Homo sapiens cDNA, FLJ94997. EU176455 - Synthetic construct Homo sapiens clone IMAGE:100006633; FLH264110.01X; RZPDo839E06257D pseudouridylate synthase 3 (PUS3) gene, encodes complete protein. DQ896653 - Synthetic construct Homo sapiens clone IMAGE:100011113; FLH263595.01L; RZPDo839B06155D pseudouridylate synthase 3 (PUS3) gene, encodes complete protein. DQ896654 - Synthetic construct Homo sapiens clone IMAGE:100011114; FLH196338.01L; RZPDo839B07155D pseudouridylate synthase 3 (PUS3) gene, encodes complete protein. EU176796 - Synthetic construct Homo sapiens clone IMAGE:100011573; FLH263596.01L; RZPDo839F05256D pseudouridylate synthase 3 (PUS3) gene, encodes complete protein.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q9BZE2 (Reactome details) participates in the following event(s): R-HSA-8870289 PUS3 transforms uridine-39 to pseudouridine-39 in tRNA R-HSA-6782315 tRNA modification in the nucleus and cytosol R-HSA-72306 tRNA processing R-HSA-8953854 Metabolism of RNA

Other Names for This Gene


	Alternate Gene Symbols: B2RAM0, ENST00000227474.1, ENST00000227474.2, ENST00000227474.3, ENST00000227474.4, ENST00000227474.5, ENST00000227474.6, ENST00000227474.7, FKSG32, NM_031307, PUS3_HUMAN, Q96D17, Q96J23, Q96NB4, Q9BZE2, uc317dms.1, uc317dms.2 UCSC ID: ENST00000227474.8_9 RefSeq Accession: NM_031307.4 Protein: Q9BZE2 (aka PUS3_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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