UTP15

gene
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Also known as FLJ12787NET21FLJ23637

Summary

UTP15 (UTP15 small subunit processome component, HGNC:25758) is a protein-coding gene on chromosome 5q13.2, encoding U3 small nucleolar RNA-associated protein 15 homolog (Q8TED0). Ribosome biogenesis factor. It is a common-essential gene (DepMap: required in 99.9% of cancer cell lines).

Enables RNA binding activity. Involved in positive regulation of rRNA processing; positive regulation of transcription by RNA polymerase I; and ribosomal small subunit biogenesis. Located in endoplasmic reticulum and fibrillar center. Part of small-subunit processome.

Source: NCBI Gene 84135 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 63 total
  • Cancer dependency (DepMap): dependent in 99.9% of screened cell lines (common-essential)
  • MANE Select transcript: NM_032175

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25758
Approved symbolUTP15
NameUTP15 small subunit processome component
Location5q13.2
Locus typegene with protein product
StatusApproved
AliasesFLJ12787, NET21, FLJ23637
Ensembl geneENSG00000164338
Ensembl biotypeprotein_coding
OMIM616194
Entrez84135

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 retained_intron

ENST00000296792, ENST00000508491, ENST00000508686, ENST00000509005, ENST00000510478, ENST00000512550, ENST00000513824, ENST00000543251, ENST00000862251, ENST00000862252, ENST00000862253, ENST00000918458, ENST00000918459, ENST00000918460

RefSeq mRNA: 3 — MANE Select: NM_032175 NM_001284430, NM_001284431, NM_032175

CCDS: CCDS34186, CCDS68893, CCDS68894

Canonical transcript exons

ENST00000296792 — 13 exons

ExonStartEnd
ENSE000010836357356726273567434
ENSE000010836547357785673578005
ENSE000010836557357875173578852
ENSE000010836577357931773579375
ENSE000010836617357901773579150
ENSE000014035117357987773583380
ENSE000034756117356574373565912
ENSE000035010287356949773569675
ENSE000035263947357058673570711
ENSE000035295437357695273577036
ENSE000035469407356842073568604
ENSE000035834947356823573568327
ENSE000036701647357248973572624

Expression profiles

Bgee: expression breadth ubiquitous, 206 present calls, max score 91.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.0920 / max 169.1686, expressed in 1792 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
5704416.56131783
570452.86441281
570460.6663386

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370191.88gold quality
epithelial cell of pancreasCL:000008391.27gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.00gold quality
adrenal tissueUBERON:001830386.05gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.72gold quality
skin of abdomenUBERON:000141684.42gold quality
skin of legUBERON:000151183.84gold quality
islet of LangerhansUBERON:000000683.76gold quality
rectumUBERON:000105283.19gold quality
monocyteCL:000057682.81gold quality
leukocyteCL:000073882.53gold quality
zone of skinUBERON:000001482.25gold quality
smooth muscle tissueUBERON:000113582.11gold quality
vermiform appendixUBERON:000115481.86gold quality
tendonUBERON:000004381.54gold quality
bone marrow cellCL:000209281.05gold quality
muscle of legUBERON:000138380.18gold quality
gastrocnemiusUBERON:000138880.06gold quality
mucosa of stomachUBERON:000119979.95gold quality
body of stomachUBERON:000116179.77gold quality
pancreasUBERON:000126479.59gold quality
esophagus mucosaUBERON:000246979.38gold quality
stromal cell of endometriumCL:000225579.25gold quality
left adrenal glandUBERON:000123479.20gold quality
hindlimb stylopod muscleUBERON:000425279.03gold quality
left uterine tubeUBERON:000130379.01gold quality
left adrenal gland cortexUBERON:003582579.00gold quality
right adrenal gland cortexUBERON:003582778.98gold quality
lymph nodeUBERON:000002978.96gold quality
adrenal glandUBERON:000236978.83gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

94 targeting UTP15, 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-3613-3P100.0076.367965
HSA-MIR-340-5P100.0072.504437
HSA-MIR-432-3P100.0067.86705
HSA-MIR-3163100.0077.238605
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-477599.9875.006394
HSA-MIR-314899.9775.066478
HSA-MIR-50799.9770.111915
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-55799.9670.011640
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-450399.8571.451869
HSA-MIR-94499.8270.853042
HSA-MIR-4799-5P99.8270.602663
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-4802-3P99.7270.131273
HSA-MIR-494-3P99.7071.452795
HSA-MIR-5580-3P99.7069.412052
HSA-MIR-7154-5P99.6970.521900
HSA-MIR-580-3P99.6769.231841
HSA-MIR-182799.6368.573265
HSA-MIR-613499.6365.681537

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.9% of screened cell lines, common-essential.

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioutp15ENSDARG00000002720
mus_musculusUtp15ENSMUSG00000041747
rattus_norvegicusUtp15ENSRNOG00000016591
drosophila_melanogasterCG3071FBGN0023527
caenorhabditis_elegansY23H5B.5WBGENE00021276

Protein

Protein identifiers

U3 small nucleolar RNA-associated protein 15 homologQ8TED0 (reviewed: Q8TED0)

All UniProt accessions (4): A0A1Y8EI88, D6RF65, H0Y8P4, Q8TED0

UniProt curated annotations — full annotation on UniProt →

Function. Ribosome biogenesis factor. Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre-ribosomal RNA transcription by RNA polymerase I. Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome.

Subunit / interactions. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3. May be a component of the proposed t-UTP subcomplex of the ribosomal small subunit (SSU) processome containing at least UTP4, WDR43, HEATR1, UTP15, WDR75. Interacts directly with UTP4 and WDR43.

Subcellular location. Nucleus. Nucleolus.

Isoforms (3)

UniProt IDNamesCanonical?
Q8TED0-11yes
Q8TED0-22
Q8TED0-33

RefSeq proteins (3): NP_001271359, NP_001271360, NP_115551* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR018983U3_snoRNA-assocProt_15_CDomain
IPR019775WD40_repeat_CSConserved_site
IPR036322WD40_repeat_dom_sfHomologous_superfamily

Pfam: PF00400, PF09384

UniProt features (55 total): strand 30, repeat 7, sequence conflict 4, sequence variant 3, turn 3, splice variant 2, helix 2, initiator methionine 1, chain 1, cross-link 1, modified residue 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
7RUOX-RAY DIFFRACTION1.8
7MQAELECTRON MICROSCOPY2.7
7MQ8ELECTRON MICROSCOPY3.6
7MQ9ELECTRON MICROSCOPY3.87

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8TED0-F182.240.34

Functional residue map

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

Post-translational modifications (2): 249, 2

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-6790901rRNA modification in the nucleus and cytosol
R-HSA-6791226Major pathway of rRNA processing in the nucleolus and cytosol

MSigDB gene sets: 126 (showing top): GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_MATURATION_OF_SSU_RRNA, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GARY_CD5_TARGETS_DN, FISCHER_DREAM_TARGETS, ZHANG_BREAST_CANCER_PROGENITORS_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, CUI_TCF21_TARGETS_2_UP, REACTOME_METABOLISM_OF_RNA, GOCC_PRERIBOSOME, GOCC_SMALL_SUBUNIT_PROCESSOME, GOCC_NUCLEOLUS, GOCC_RIBONUCLEOPROTEIN_COMPLEX

GO Biological Process (5): rRNA processing (GO:0006364), ribosomal small subunit biogenesis (GO:0042274), positive regulation of transcription by RNA polymerase I (GO:0045943), positive regulation of rRNA processing (GO:2000234), ribosome biogenesis (GO:0042254)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (7): fibrillar center (GO:0001650), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), small-subunit processome (GO:0032040), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
rRNA processing in the nucleus and cytosol2

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
ribosome biogenesis2
ribonucleoprotein complex biogenesis2
nucleolus2
nuclear lumen2
intracellular membrane-bounded organelle2
RNA processing1
rRNA metabolic process1
regulation of transcription by RNA polymerase I1
transcription by RNA polymerase I1
positive regulation of DNA-templated transcription1
rRNA processing1
positive regulation of RNA metabolic process1
regulation of rRNA processing1
nucleic acid binding1
binding1
intracellular membraneless organelle1
intracellular anatomical structure1
cytoplasm1
endomembrane system1
preribosome1
t-UTP complex1
nuclear protein-containing complex1

Protein interactions and networks

STRING

2645 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
UTP15WDR43Q15061982
UTP15UTP4Q969X6981
UTP15HEATR1Q9H583972
UTP15WDR75Q8IWA0941
UTP15BMS1Q14692778
UTP15NOP58Q9Y2X3753
UTP15UTP6Q9NYH9744
UTP15UTP18Q9Y5J1728
UTP15NOP56O00567710
UTP15WDR36Q8NI36710
UTP15UTP14AQ9BVJ6704
UTP15NOL10Q9BSC4699
UTP15NOP14P78316645
UTP15MPHOSPH10O00566629
UTP15BYSLQ13895627

IntAct

91 interactions, top by confidence:

ABTypeScore
UTP4UTP15psi-mi:“MI:0407”(direct interaction)0.810
C1DZFC3H1psi-mi:“MI:0914”(association)0.640
EXOSC5ZFC3H1psi-mi:“MI:0914”(association)0.640
NOL7WDR43psi-mi:“MI:0914”(association)0.640
NOP53RRP8psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
WDR43UTP15psi-mi:“MI:0407”(direct interaction)0.590
ZNF324BZNF316psi-mi:“MI:0914”(association)0.530
LAMP3METTL15psi-mi:“MI:0914”(association)0.530
NOL11WDR43psi-mi:“MI:0914”(association)0.530
WDR75WDR43psi-mi:“MI:0914”(association)0.530
FBLZNF316psi-mi:“MI:0914”(association)0.530
TBC1D15MYO9Apsi-mi:“MI:0914”(association)0.530
CSGALNACT2GOLIM4psi-mi:“MI:0914”(association)0.530
UTP4ANKRD28psi-mi:“MI:0914”(association)0.530
RBM4NVLpsi-mi:“MI:0914”(association)0.530
WDR43WDR75psi-mi:“MI:0914”(association)0.530
TBC1D15UBXN8psi-mi:“MI:0914”(association)0.530
NOL7IPO5psi-mi:“MI:0914”(association)0.530
CSGALNACT2TPST1psi-mi:“MI:0914”(association)0.530
PARP2UTP15psi-mi:“MI:0557”(adp ribosylation reaction)0.440
UTP15H4C16psi-mi:“MI:0915”(physical association)0.400
UTP15PGK2psi-mi:“MI:0915”(physical association)0.400
ATMRBM47psi-mi:“MI:0914”(association)0.350
NcaphATP5MF-PTCD1psi-mi:“MI:0914”(association)0.350
HDAC6GLOD5psi-mi:“MI:0914”(association)0.350
SORT1SH3PXD2Bpsi-mi:“MI:0914”(association)0.350

BioGRID (159): UTP15 (Affinity Capture-MS), UTP15 (Affinity Capture-MS), UTP15 (Affinity Capture-MS), UTP15 (Affinity Capture-MS), UTP15 (Affinity Capture-MS), NPM1 (Co-fractionation), TBL3 (Co-fractionation), UTP15 (Co-fractionation), UTP15 (Co-fractionation), UTP15 (Co-fractionation), UTP15 (Co-fractionation), UTP15 (Co-fractionation), UTP15 (Co-fractionation), UTP15 (Co-fractionation), UTP15 (Co-fractionation)

ESM2 similar proteins: A2RRU3, A7MB12, A8XSW2, A8XYW9, G5ECZ4, G5EFW7, O13282, O14053, O43071, O75529, O94365, P25635, P38328, P40968, P42000, P49846, P87177, P91341, Q04199, Q04305, Q05946, Q05BV3, Q12220, Q15269, Q20059, Q3MKM6, Q5F3D7, Q5REE0, Q5RFQ3, Q5XGE2, Q6ED65, Q7ZW33, Q7ZXZ2, Q8BHB4, Q8BQM8, Q8BU03, Q8C7V3, Q8SQS4, Q8TED0, Q8VYZ5

Diamond homologs: A2RRU3, A7MB12, O02482, O82266, O94365, Q10282, Q5F3D7, Q5REE0, Q5XGE2, Q7ZW33, Q7ZXZ2, Q8C7V3, Q8TED0, B6QC56, B8AP31, C0NRC6, C6HTE8, O35828, P49177, Q40687, Q5RBW3, A0A1W2PR48, O13166, O13168, O14435, O42469, O42470, O42478, P16371, P16520, P40066, P63002, P63003, P79083, Q04724, Q04725, Q04726, Q04727, Q07141, Q08117

SIGNOR signaling

1 interactions.

AEffectBMechanism
UTP15“form complex”“UTP-A complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 116 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
rRNA modification in the nucleus and cytosol923.4×3e-08
Nuclear RNA decay521.4×5e-04
Major pathway of rRNA processing in the nucleolus and cytosol1311.2×3e-08

GO biological processes:

GO termPartnersFoldFDR
ribosomal small subunit biogenesis1023.0×1e-08
ribosomal large subunit biogenesis522.4×7e-04
rRNA processing1115.7×4e-08
RNA processing511.1×9e-03
RNA splicing87.1×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance58
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1838 predictions. Top by Δscore:

VariantEffectΔscore
5:73568232:A:AGacceptor_gain1.0000
5:73568233:A:Gacceptor_gain1.0000
5:73568326:GA:Gdonor_gain1.0000
5:73568328:G:GGdonor_gain1.0000
5:73568418:A:AGacceptor_gain1.0000
5:73568419:G:GGacceptor_gain1.0000
5:73568605:G:GGdonor_gain1.0000
5:73572620:GA:Gdonor_gain1.0000
5:73576948:TTAGG:Tacceptor_loss1.0000
5:73576949:TAGG:Tacceptor_loss1.0000
5:73576951:G:GTacceptor_loss1.0000
5:73577034:GCA:Gdonor_gain1.0000
5:73577035:CA:Cdonor_gain1.0000
5:73577037:G:GGdonor_gain1.0000
5:73577852:TTAGC:Tacceptor_loss1.0000
5:73577854:A:AGacceptor_gain1.0000
5:73577855:G:GTacceptor_gain1.0000
5:73577855:GC:Gacceptor_gain1.0000
5:73577983:G:GTdonor_gain1.0000
5:73577984:A:Tdonor_gain1.0000
5:73577996:G:GTdonor_gain1.0000
5:73578003:CGGGT:Cdonor_loss1.0000
5:73578006:G:Adonor_loss1.0000
5:73578007:T:Adonor_loss1.0000
5:73578744:A:AGacceptor_gain1.0000
5:73578746:TGCA:Tacceptor_loss1.0000
5:73578747:GCA:Gacceptor_loss1.0000
5:73578748:CAGGA:Cacceptor_loss1.0000
5:73578749:A:AGacceptor_gain1.0000
5:73578749:A:ATacceptor_loss1.0000

AlphaMissense

3387 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:73568311:T:AV56D0.999
5:73572561:A:TK249I0.999
5:73567420:T:AW26R0.998
5:73567420:T:CW26R0.998
5:73568266:T:AV41D0.998
5:73568308:C:AA55D0.998
5:73568429:T:GY65D0.998
5:73568502:G:CR89P0.998
5:73568520:T:CL95P0.998
5:73569573:T:AW149R0.998
5:73569573:T:CW149R0.998
5:73570586:G:AG183E0.998
5:73572614:T:CS267P0.998
5:73578809:T:CL368P0.998
5:73579108:G:CR413P0.998
5:73569543:T:CS139P0.997
5:73572509:T:AW232R0.997
5:73572509:T:CW232R0.997
5:73572562:A:CK249N0.997
5:73572562:A:TK249N0.997
5:73572612:G:AG266D0.997
5:73577881:G:AG307E0.997
5:73578836:T:CL377P0.997
5:73579099:T:CL410P0.997
5:73568507:G:CD91H0.996
5:73568508:A:TD91V0.996
5:73568526:C:AA97D0.996
5:73568529:G:AG98D0.996
5:73568553:T:CL106P0.996
5:73569516:T:CF130L0.996

dbSNP variants (sampled 300 via entrez): RS1000107909 (5:73580753 A>G), RS1000120750 (5:73564025 T>G), RS1000218021 (5:73573409 G>A), RS1000316267 (5:73565931 C>G,T), RS1000327010 (5:73573654 G>A), RS1000329196 (5:73566316 C>T), RS1000462808 (5:73571927 G>A), RS1000657839 (5:73564881 G>A,T), RS1000721020 (5:73565395 G>A), RS1000808385 (5:73569292 T>C), RS1001072354 (5:73577836 A>C), RS1001392620 (5:73575512 A>C), RS1001413388 (5:73565696 C>G), RS1001466679 (5:73565798 T>C,G), RS1001522088 (5:73578055 A>G)

Disease associations

OMIM: gene MIM:616194 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cadmium Chloridedecreases expression, increases abundance, increases expression3
bisphenol Adecreases expression, affects cotreatment, increases expression2
sodium arseniteincreases abundance, increases expression, decreases expression, affects cotreatment2
Formaldehydedecreases expression2
Tetrachlorodibenzodioxindecreases expression2
Valproic Acidaffects expression, decreases expression2
Cyclosporineincreases expression2
aristolochic acid Idecreases expression1
bisphenol Faffects cotreatment, increases expression1
TAK-243decreases sumoylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
sodium arsenatedecreases expression1
arseniteaffects binding, increases reaction1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
nivalenolincreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
jinfukangdecreases expression1
LDN 193189affects cotreatment, decreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Leflunomideincreases expression1
Arsenicincreases abundance, increases expression, affects cotreatment1
Cadmiumincreases abundance, increases expression1
Dexamethasoneaffects cotreatment, increases expression1
Diethylstilbestrolincreases expression1

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.