TRUB1

gene
On this page

Also known as PUS4

Summary

TRUB1 (TruB pseudouridine synthase family member 1, HGNC:16060) is a protein-coding gene on chromosome 10q25.3, encoding Pseudouridylate synthase TRUB1 (Q8WWH5). Pseudouridine synthase that catalyzes pseudouridylation of mRNAs and tRNAs.

Pseudouridine is an abundant component of rRNAs and tRNAs and is enzymatically generated by isomerization of uridine by pseudouridine synthase (Zucchini et al., 2003 [PubMed 12736709]).

Source: NCBI Gene 142940 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 34 total
  • MANE Select transcript: NM_139169

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16060
Approved symbolTRUB1
NameTruB pseudouridine synthase family member 1
Location10q25.3
Locus typegene with protein product
StatusApproved
AliasesPUS4
Ensembl geneENSG00000165832
Ensembl biotypeprotein_coding
OMIM610726
Entrez142940

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000298746, ENST00000485065, ENST00000900221, ENST00000900222, ENST00000900223, ENST00000922143, ENST00000948779

RefSeq mRNA: 1 — MANE Select: NM_139169 NM_139169

CCDS: CCDS7591

Canonical transcript exons

ENST00000298746 — 8 exons

ExonStartEnd
ENSE00001097026114959726114959807
ENSE00001097091114970368114970440
ENSE00001131261114974329114974385
ENSE00001131265114972135114972274
ENSE00001194052114975123114977676
ENSE00001194057114938195114938539
ENSE00003485263114942645114942743
ENSE00003679685114951094114951149

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 95.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.9191 / max 172.2434, expressed in 1792 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
10716916.91911792

Top tissues by expression

259 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
adrenal tissueUBERON:001830395.88gold quality
left ventricle myocardiumUBERON:000656695.80gold quality
cardiac muscle of right atriumUBERON:000337994.79silver quality
myocardiumUBERON:000234993.16gold quality
Brodmann (1909) area 46UBERON:000648390.32gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.72gold quality
kidney epitheliumUBERON:000481989.18silver quality
calcaneal tendonUBERON:000370189.07gold quality
right adrenal gland cortexUBERON:003582788.79gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.65gold quality
ileal mucosaUBERON:000033188.62gold quality
adrenal glandUBERON:000236988.59gold quality
heart right ventricleUBERON:000208088.50gold quality
islet of LangerhansUBERON:000000688.48gold quality
left adrenal glandUBERON:000123488.43gold quality
mucosa of sigmoid colonUBERON:000499388.22gold quality
superior frontal gyrusUBERON:000266188.00gold quality
adrenal cortexUBERON:000123587.96gold quality
right adrenal glandUBERON:000123387.88gold quality
left adrenal gland cortexUBERON:003582587.73gold quality
pigmented layer of retinaUBERON:000178287.66gold quality
retinaUBERON:000096687.64gold quality
postcentral gyrusUBERON:000258187.30gold quality
cauda epididymisUBERON:000436087.23gold quality
colonic mucosaUBERON:000031787.21gold quality
prefrontal cortexUBERON:000045186.99gold quality
Brodmann (1909) area 23UBERON:001355486.42gold quality
oocyteCL:000002386.41gold quality
entorhinal cortexUBERON:000272886.38gold quality
caput epididymisUBERON:000435886.33gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no3.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

166 targeting TRUB1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3646100.0073.565283
HSA-MIR-3163100.0077.238605
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-186-5P99.9970.833707
HSA-MIR-548AW99.9972.573559
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-366299.9973.825684
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-569699.9872.364487
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-477599.9875.006394
HSA-MIR-480399.9871.993117
HSA-MIR-548N99.9871.944170
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-495-3P99.9672.814197
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-568899.9673.234504
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-590-3P99.9674.346478

Literature-anchored findings (GeneRIF, showing 6)

  • TRUB1 gene encodes a 349-amino acid product, with a VFAVHKPKGPTSA box in positions 71-83 corresponding to motif I of the TruB family (PMID:12736709)
  • The tRNA pseudouridine synthase TruB1 regulates the maturation of let-7 miRNA. (PMID:32926445)
  • Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmic PUS10 produce conserved pseudouridine 55 in different sets of tRNA. (PMID:33023933)
  • Human TRUB1 is a highly conserved pseudouridine synthase responsible for the formation of Psi55 in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro. (PMID:36018806)
  • Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. (PMID:36302989)
  • Structural basis of pri-let-7 recognition by human pseudouridine synthase TruB1. (PMID:38776834)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotrub1ENSDARG00000053805
mus_musculusTrub1ENSMUSG00000025086
rattus_norvegicusTrub1ENSRNOG00000017321

Protein

Protein identifiers

Pseudouridylate synthase TRUB1Q8WWH5 (reviewed: Q8WWH5)

Alternative names: TruB pseudouridine synthase homolog 1, tRNA pseudouridine 55 synthase TRUB1

All UniProt accessions (1): Q8WWH5

UniProt curated annotations — full annotation on UniProt →

Function. Pseudouridine synthase that catalyzes pseudouridylation of mRNAs and tRNAs. Mediates pseudouridylation of mRNAs with the consensus sequence 5’-GUUCNANNC-3’, harboring a stem-loop structure. Constitutes the major pseudouridine synthase acting on mRNAs. Also catalyzes pseudouridylation of some tRNAs, including synthesis of pseudouridine(55) from uracil-55, in the psi GC loop of a subset of tRNAs. Promotes the processing of pri-let-7 microRNAs (pri-miRNAs) independently of its RNA pseudouridylate synthase activity. Acts by binding to the stem-loop structure on pri-let-7, preventing LIN28-binding (LIN28A and/or LIN28B), thereby enhancing the interaction between pri-let-7 and the microprocessor DGCR8, which mediates miRNA maturation.

Subcellular location. Nucleus. Cytoplasm. Cytosol.

Tissue specificity. Highly expressed in heart, skeletal muscle and liver. Expressed at lower levels in lung, small intestine, kidney and spleen.

Similarity. Belongs to the pseudouridine synthase TruB family.

RefSeq proteins (1): NP_631908* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002501PsdUridine_synth_NDomain
IPR014780tRNA_psdUridine_synth_TruBFamily
IPR020103PsdUridine_synth_cat_dom_sfHomologous_superfamily

Pfam: PF01509

Catalyzed reactions (Rhea), 3 shown:

  • uridine(55) in tRNA = pseudouridine(55) in tRNA (RHEA:42532)
  • a uridine in tRNA = a pseudouridine in tRNA (RHEA:54572)
  • a uridine in mRNA = a pseudouridine in mRNA (RHEA:56644)

UniProt features (11 total): mutagenesis site 3, modified residue 2, sequence variant 2, initiator methionine 1, chain 1, sequence conflict 1, active site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
8JFXX-RAY DIFFRACTION2.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WWH5-F181.450.64

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 121 (nucleophile)

Post-translational modifications (2): 2, 11

Mutagenesis-validated functional residues (3):

PositionPhenotype
121abolished pseudouridine synthase activity without affecting ability to promote processing of let-7 mirnas; when associat
147abolished rna-binding and ability to promote processing of let-7 mirnas.
163abolished pseudouridine synthase activity without affecting ability to promote processing of let-7 mirnas; when associat

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 168 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_TRNA_METABOLIC_PROCESS, GGAMTNNNNNTCCY_UNKNOWN, GOBP_MRNA_MODIFICATION, GOBP_PSEUDOURIDINE_SYNTHESIS, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_RNA_MODIFICATION, DODD_NASOPHARYNGEAL_CARCINOMA_UP, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, SENESE_HDAC1_TARGETS_UP, GOBP_PRE_MIRNA_PROCESSING, GOBP_TRNA_PROCESSING, DURCHDEWALD_SKIN_CARCINOGENESIS_UP, GOBP_TRNA_MODIFICATION

GO Biological Process (9): mRNA processing (GO:0006397), tRNA modification (GO:0006400), tRNA pseudouridine synthesis (GO:0031119), mRNA pseudouridine synthesis (GO:1990481), positive regulation of pre-miRNA processing (GO:2000633), pseudouridine synthesis (GO:0001522), RNA processing (GO:0006396), tRNA processing (GO:0008033), RNA modification (GO:0009451)

GO Molecular Function (7): pseudouridine synthase activity (GO:0009982), pre-miRNA binding (GO:0070883), tRNA pseudouridine(55) synthase activity (GO:0160148), RNA binding (GO:0003723), protein binding (GO:0005515), isomerase activity (GO:0016853), tRNA pseudouridine synthase activity (GO:0106029)

GO Cellular Component (4): nucleus (GO:0005634), mitochondrion (GO:0005739), cytosol (GO:0005829), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
RNA modification2
pseudouridine synthesis2
intracellular membrane-bounded organelle2
cytoplasm2
cellular anatomical structure2
mRNA metabolic process1
tRNA processing1
tRNA modification1
mRNA modification1
pre-miRNA processing1
positive regulation of miRNA processing1
regulation of pre-miRNA processing1
gene expression1
RNA biosynthetic process1
primary metabolic process1
tRNA metabolic process1
RNA metabolic process1
macromolecule modification1
intramolecular transferase activity1
RNA binding1
tRNA pseudouridine synthase activity1
nucleic acid binding1
binding1
catalytic activity1
pseudouridine synthase activity1
catalytic activity, acting on a tRNA1
intracellular anatomical structure1

Protein interactions and networks

STRING

2624 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TRUB1PUS1Q9Y606876
TRUB1PUS7Q96PZ0873
TRUB1PUS3Q9BZE2838
TRUB1PUS10Q3MIT2833
TRUB1RPUSD2Q8IZ73811
TRUB1PUS7LQ9H0K6781
TRUB1TRMT1Q9NXH9766
TRUB1RPUSD3Q6P087724
TRUB1RPUSD4Q96CM3716
TRUB1TARBP1Q13395689
TRUB1TRMT6Q9UJA5676
TRUB1METTL1Q9UBP6665
TRUB1RPUSD1Q9UJJ7654
TRUB1PUSL1Q8N0Z8648
TRUB1WDR4P57081645
TRUB1NOP10Q9NPE3645

IntAct

33 interactions, top by confidence:

ABTypeScore
TRAF2HTRA2psi-mi:“MI:0914”(association)0.750
SETMARHSPA8psi-mi:“MI:0914”(association)0.530
TRUB1CAPGpsi-mi:“MI:0914”(association)0.500
TRUB1CAPGpsi-mi:“MI:0915”(physical association)0.500
TRUB1psi-mi:“MI:0407”(direct interaction)0.440
TRUB1SRPK2psi-mi:“MI:0217”(phosphorylation reaction)0.440
CD72TRUB1psi-mi:“MI:0915”(physical association)0.400
TRUB1E2psi-mi:“MI:0915”(physical association)0.370
TRUB1E7psi-mi:“MI:0915”(physical association)0.370
S100A9TRUB1psi-mi:“MI:0915”(physical association)0.370
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
CAND1GTPBP10psi-mi:“MI:0914”(association)0.350
SLC2A2APOBpsi-mi:“MI:0914”(association)0.350
TRUB1USP11psi-mi:“MI:0914”(association)0.350
PKMPAWRpsi-mi:“MI:0914”(association)0.350
SSBRPS3Apsi-mi:“MI:0914”(association)0.350
PRPS2SMCHD1psi-mi:“MI:0914”(association)0.350
SLC2A2CAPGpsi-mi:“MI:0914”(association)0.350
NUDT9WDR5Bpsi-mi:“MI:0914”(association)0.350
FECHGTPBP10psi-mi:“MI:0914”(association)0.350
SNW1psi-mi:“MI:0914”(association)0.350
CDC5Lpsi-mi:“MI:0914”(association)0.350
TRUB1E2psi-mi:“MI:0915”(physical association)0.000

BioGRID (47): TRUB1 (Co-fractionation), TRUB1 (Affinity Capture-MS), TRUB1 (Affinity Capture-MS), TRUB1 (Affinity Capture-MS), TRUB1 (Affinity Capture-MS), MTFMT (Affinity Capture-MS), USP11 (Affinity Capture-MS), TCEAL1 (Affinity Capture-MS), TRUB1 (Affinity Capture-MS), TRUB1 (Affinity Capture-MS), TRUB1 (Affinity Capture-MS), TRUB1 (Affinity Capture-MS), TRUB1 (Affinity Capture-MS), TRUB1 (Affinity Capture-MS), MTFMT (Affinity Capture-MS)

ESM2 similar proteins: A2ADA5, A4PCD4, A6H611, D3ZDM7, F6PHZ6, O75344, P04053, P09838, P17256, P36195, P47823, P55345, Q01992, Q03426, Q08602, Q0V8R7, Q13144, Q1L8I0, Q3MIT2, Q4KM92, Q4QQT0, Q5CZL1, Q5E9Z1, Q5I0L3, Q5M7T9, Q5M934, Q5RFE6, Q5XGM5, Q64350, Q6GQ53, Q7L3T8, Q80W22, Q86YJ6, Q8BYL4, Q8C0D0, Q8CHW4, Q8N0Z8, Q8WWH5, Q91XW8, Q92089

Diamond homologs: A6LLV6, O59721, O95900, Q5M934, Q5XFW2, Q5XGG2, Q8C0D0, Q8WWH5, Q91WG3, A0AIC9, A0JUU8, A0Q0Q4, A0Q7W5, A1R520, A1S464, A1ST47, A1U5Z8, A3MJW6, A3N007, A3NUL2, A4IWL0, A4QEY6, A4VPN8, A4XYD8, A5FQR4, A5IIS7, A5N845, A5UBU2, A5UF28, A5W985, A6LEL7, A6VCJ9, A6VNE2, A7GG03, A7GRE0, A7NAR1, A8FDD4, B0JJJ5, B0KHX6, B0TXH9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

34 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance22
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1052 predictions. Top by Δscore:

VariantEffectΔscore
10:114938518:TTG:Tdonor_gain1.0000
10:114938537:C:Tdonor_gain1.0000
10:114938537:CAGG:Cdonor_loss1.0000
10:114938539:GG:Gdonor_loss1.0000
10:114938540:G:Cdonor_loss1.0000
10:114938541:T:Gdonor_loss1.0000
10:114951088:TTGTA:Tacceptor_loss1.0000
10:114951089:TGTA:Tacceptor_loss1.0000
10:114951090:GTAGT:Gacceptor_loss1.0000
10:114951091:TA:Tacceptor_loss1.0000
10:114951092:A:AGacceptor_gain1.0000
10:114951092:A:Gacceptor_loss1.0000
10:114951092:AGTT:Aacceptor_gain1.0000
10:114951093:G:GGacceptor_gain1.0000
10:114951093:GT:Gacceptor_gain1.0000
10:114951093:GTT:Gacceptor_gain1.0000
10:114951093:GTTG:Gacceptor_gain1.0000
10:114970441:G:GGdonor_gain1.0000
10:114972111:T:Gacceptor_gain1.0000
10:114972125:A:AGacceptor_gain1.0000
10:114972126:T:Gacceptor_gain1.0000
10:114972130:A:AGacceptor_gain1.0000
10:114972131:C:Gacceptor_gain1.0000
10:114972132:A:AGacceptor_gain1.0000
10:114972133:A:Gacceptor_gain1.0000
10:114972272:TAGGT:Tdonor_loss1.0000
10:114972273:AGG:Adonor_loss1.0000
10:114972274:GGTAA:Gdonor_loss1.0000
10:114972275:G:GCdonor_loss1.0000
10:114972276:T:Adonor_loss1.0000

AlphaMissense

2228 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:114942702:G:AG115E0.997
10:114942734:G:AG126R0.996
10:114942734:G:CG126R0.996
10:114951100:G:AG131E0.996
10:114951149:G:CK147N0.996
10:114951149:G:TK147N0.996
10:114974339:T:GC249W0.996
10:114974368:T:AV259D0.996
10:114938481:G:CK76N0.995
10:114938481:G:TK76N0.995
10:114942704:C:GH116D0.995
10:114942708:G:AG117E0.995
10:114942735:G:AG126E0.995
10:114959742:G:AG153E0.995
10:114975153:T:CL275P0.995
10:114975212:T:AW295R0.995
10:114975212:T:CW295R0.995
10:114942741:T:CL128P0.994
10:114975138:C:AA270D0.994
10:114959729:T:CY149H0.993
10:114974359:G:CR256T0.993
10:114974380:G:AG263E0.993
10:114938479:A:GK76E0.992
10:114942721:C:AD121E0.992
10:114942721:C:GD121E0.992
10:114942738:T:AV127D0.992
10:114951097:T:AV130D0.992
10:114974337:T:CC249R0.992
10:114974359:G:TR256I0.992
10:114938519:T:CL89S0.991

dbSNP variants (sampled 300 via entrez): RS1000069781 (10:114943894 T>C), RS1000188759 (10:114961102 T>A,C), RS1000491323 (10:114967699 T>C), RS1000696970 (10:114961081 G>A), RS1000702805 (10:114954076 T>A,C), RS1000752470 (10:114953785 T>A,C,G), RS1000826824 (10:114972666 G>T), RS1000900460 (10:114973049 A>C), RS1000961749 (10:114948541 G>A,T), RS1001051388 (10:114960701 A>C), RS1001069800 (10:114942286 A>G), RS1001103945 (10:114942614 T>A,C), RS1001249814 (10:114955375 A>G), RS1001285459 (10:114950626 T>C), RS1001295534 (10:114950936 A>G)

Disease associations

OMIM: gene MIM:610726 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST010002_226Refractive error2.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

35 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression2
Acetaminophendecreases expression2
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
trichostatin Adecreases expression1
arseniteaffects binding, decreases reaction1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
coumarinincreases phosphorylation1
4-aminophenylarsenoxideaffects binding, decreases reaction1
1-nitropyreneincreases expression1
perfluorooctane sulfonic aciddecreases expression1
corosolic acidincreases expression1
jinfukangdecreases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-olincreases expression1
Arsenic Trioxideaffects binding, decreases reaction1
Vorinostatincreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneaffects methylation1
Caffeinedecreases phosphorylation1
Formaldehydeincreases expression1
Golddecreases expression1
Hydrogen Peroxideaffects expression1
Ivermectindecreases expression1
Manganeseincreases abundance, increases expression, affects cotreatment1
Methyl Methanesulfonateincreases expression1
Ribonucleotidesaffects binding1
Rotenonedecreases expression1
Testosteronedecreases expression1
Tretinoindecreases expression1
Tunicamycindecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E0SCUbigene HeLa TRUB1 KOCancer cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.