UTP25

gene
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Also known as MGC29875DEF

Summary

UTP25 (UTP25 small subunit processome component, HGNC:28440) is a protein-coding gene on chromosome 1q32.2, encoding U3 small nucleolar RNA-associated protein 25 homolog (Q68CQ4). Component of the ribosomal small subunit processome for the biogenesis of ribosomes, functions in pre-ribosomal RNA (pre-rRNA) processing. It is a selective cancer dependency (DepMap: 87.5% of cell lines).

Enables RNA binding activity. Involved in several processes, including protein catabolic process; protein destabilization; and protein localization to nucleolus. Located in nucleolus.

Source: NCBI Gene 27042 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 126 total
  • Cancer dependency (DepMap): dependent in 87.5% of screened cell lines
  • MANE Select transcript: NM_014388

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28440
Approved symbolUTP25
NameUTP25 small subunit processome component
Location1q32.2
Locus typegene with protein product
StatusApproved
AliasesMGC29875, DEF
Ensembl geneENSG00000117597
Ensembl biotypeprotein_coding
OMIM619663
Entrez27042

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000457820, ENST00000491415, ENST00000852869, ENST00000852870, ENST00000915424

RefSeq mRNA: 1 — MANE Select: NM_014388 NM_014388

CCDS: CCDS1493

Canonical transcript exons

ENST00000491415 — 12 exons

ExonStartEnd
ENSE00000792137209830108209830147
ENSE00000792138209830803209831043
ENSE00000792139209833185209833358
ENSE00000792140209835075209835163
ENSE00000792141209836801209837211
ENSE00000792142209838909209839128
ENSE00000792143209840853209841055
ENSE00000792144209842265209842447
ENSE00000792145209842583209842695
ENSE00000792146209843451209843696
ENSE00001443261209827972209828170
ENSE00001933838209851204209857565

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 90.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.0498 / max 642.6341, expressed in 1785 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
837020.04981785

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011590.02gold quality
germinal epithelium of ovaryUBERON:000130482.97gold quality
epithelium of nasopharynxUBERON:000195182.85gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.68gold quality
cartilage tissueUBERON:000241881.79gold quality
cervix squamous epitheliumUBERON:000692281.45gold quality
epithelial cell of pancreasCL:000008380.76gold quality
hair follicleUBERON:000207380.49gold quality
amniotic fluidUBERON:000017379.44gold quality
squamous epitheliumUBERON:000691478.50gold quality
stromal cell of endometriumCL:000225578.49gold quality
cortical plateUBERON:000534378.29gold quality
tibiaUBERON:000097978.10gold quality
esophagus squamous epitheliumUBERON:000692078.01gold quality
cauda epididymisUBERON:000436077.86gold quality
pancreatic ductal cellCL:000207977.85silver quality
caput epididymisUBERON:000435877.36gold quality
oviduct epitheliumUBERON:000480477.02gold quality
islet of LangerhansUBERON:000000676.80gold quality
epithelium of esophagusUBERON:000197676.72gold quality
gingival epitheliumUBERON:000194976.48gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047376.34gold quality
pericardiumUBERON:000240776.25gold quality
ventricular zoneUBERON:000305376.04gold quality
adrenal tissueUBERON:001830375.56gold quality
bronchial epithelial cellCL:000232875.52gold quality
tibialis anteriorUBERON:000138575.31gold quality
cranial nerve IIUBERON:000094175.29gold quality
mucosa of paranasal sinusUBERON:000503075.10gold quality
calcaneal tendonUBERON:000370174.99gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no5.29

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): BRD1

miRNA regulators (miRDB)

205 targeting UTP25, 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-3134100.0066.43777
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-8485100.0077.574731
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-186-5P99.9970.833707
HSA-MIR-366299.9973.825684
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-1213699.9872.815713
HSA-MIR-616-5P99.9875.584775
HSA-MIR-373-5P99.9875.364753
HSA-MIR-548N99.9871.944170
HSA-MIR-314899.9775.066478
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-211099.9666.681930
HSA-MIR-426799.9666.532368
HSA-MIR-3682-5P99.9367.971163

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 87.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

  • characterization of the related zebrafish protein (PMID:16322560)
  • Colonic tissue from patients with Hirschsprung’s disease showed lower expression levels of digestive-organ expansion factor (DIEXF). (PMID:25007945)
  • DEF is highly expressed in human neuroblastoma, and its depletion in human neuroblastoma cell lines induces apoptosis. (PMID:28263972)
  • Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. (PMID:32041475)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioutp25ENSDARG00000017696
mus_musculusUtp25ENSMUSG00000016181
rattus_norvegicusUtp25ENSRNOG00000004789
drosophila_melanogasterCG3735FBGN0034933
caenorhabditis_elegansWBGENE00012756

Protein

Protein identifiers

U3 small nucleolar RNA-associated protein 25 homologQ68CQ4 (reviewed: Q68CQ4)

Alternative names: Digestive organ expansion factor homolog, UTP25 small subunit processor component

All UniProt accessions (2): H7C2R4, Q68CQ4

UniProt curated annotations — full annotation on UniProt →

Function. Component of the ribosomal small subunit processome for the biogenesis of ribosomes, functions in pre-ribosomal RNA (pre-rRNA) processing. Essential for embryonic development in part through the regulation of p53 pathway. Controls the expansion growth of digestive organs and liver. Also involved in the sympathetic neuronal development. Mediates, with CAPN3, the proteasome-independent degradation of p53/TP53.

Subunit / interactions. Interacts with CAPN3; the interaction is required for CAPN3 translocation to the nucleolus.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Expressed in colon.

Post-translational modifications. Phosphorylated. Phosphorylation is required to promote p53/TP53 degradation in the nucleolus which promotes cell cycle progression and liver development.

Induction. Down-regulated by the miRNA MIR195.

Similarity. Belongs to the UTP25 family.

RefSeq proteins (1): NP_055203* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR010678UTP25Family
IPR027417P-loop_NTPaseHomologous_superfamily
IPR053939UTP25_CDomain
IPR053940UTP25_NTPase-likeDomain

Pfam: PF06862, PF22916

UniProt features (18 total): modified residue 7, region of interest 4, compositionally biased region 3, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q68CQ4-F178.780.54

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 (7): 52, 58, 60, 62, 64, 10, 50

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: 227 (showing top): GOBP_RIBOSOME_BIOGENESIS, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_MATURATION_OF_SSU_RRNA, CHUANG_OXIDATIVE_STRESS_RESPONSE_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_PROTEIN_DESTABILIZATION, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, GOBP_REGULATION_OF_PROTEIN_STABILITY, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FREAC4_01, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE

GO Biological Process (7): maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462), protein catabolic process (GO:0030163), protein destabilization (GO:0031648), positive regulation of embryonic development (GO:0040019), embryonic organ development (GO:0048568), protein localization to nucleolus (GO:1902570), rRNA processing (GO:0006364)

GO Molecular Function (4): RNA binding (GO:0003723), rRNA binding (GO:0019843), U3 snoRNA binding (GO:0034511), protein binding (GO:0005515)

GO Cellular Component (4): nucleoplasm (GO:0005654), nucleolus (GO:0005730), 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
embryo development2
nuclear lumen2
maturation of SSU-rRNA1
macromolecule catabolic process1
protein metabolic process1
regulation of protein stability1
regulation of embryonic development1
positive regulation of developmental process1
positive regulation of multicellular organismal process1
animal organ development1
protein localization to nucleus1
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
nucleic acid binding1
RNA binding1
snoRNA binding1
binding1
cellular anatomical structure1
intracellular membraneless organelle1
nucleolus1
preribosome1
t-UTP complex1
nuclear protein-containing complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1546 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
UTP25UTP3Q9NQZ2744
UTP25MPHOSPH10O00566729
UTP25IRF6O14896717
UTP25DDX49Q9Y6V7714
UTP25PDCD11Q14690680
UTP25BYSLQ13895667
UTP25ABT1Q9ULW3663
UTP25ESF1Q9H501639
UTP25WDR36Q8NI36622
UTP25RCL1Q9Y2P8606
UTP25UTP18Q9Y5J1605
UTP25DHX8Q14562597
UTP25NOP14P78316579
UTP25NOM1Q5C9Z4563
UTP25PWP2Q15269545

IntAct

102 interactions, top by confidence:

ABTypeScore
MAPKAPK3MAPK11psi-mi:“MI:0914”(association)0.870
MED17MED19psi-mi:“MI:0914”(association)0.840
CEP70UTP25psi-mi:“MI:0915”(physical association)0.830
UTP25CEP70psi-mi:“MI:0915”(physical association)0.830
UTP25RUFY1psi-mi:“MI:0915”(physical association)0.740
RUFY1UTP25psi-mi:“MI:0915”(physical association)0.740
UTP25MIPOL1psi-mi:“MI:0915”(physical association)0.670
MIPOL1UTP25psi-mi:“MI:0915”(physical association)0.670
UTP25RUFY1psi-mi:“MI:0915”(physical association)0.670
UTP25AP2M1psi-mi:“MI:0915”(physical association)0.670
IMP3MPHOSPH10psi-mi:“MI:0914”(association)0.670
FGL1LCMT2psi-mi:“MI:0914”(association)0.640
MAGEA11UTP25psi-mi:“MI:0915”(physical association)0.560
UTP25MID2psi-mi:“MI:0915”(physical association)0.560
UTP25MAGEA11psi-mi:“MI:0915”(physical association)0.560
MID2UTP25psi-mi:“MI:0915”(physical association)0.560
UTP25MEOX2psi-mi:“MI:0915”(physical association)0.560

BioGRID (130): DIEXF (Two-hybrid), DIEXF (Two-hybrid), RUFY1 (Two-hybrid), CEP70 (Two-hybrid), MIPOL1 (Two-hybrid), DIEXF (Affinity Capture-MS), DIEXF (Affinity Capture-MS), DIEXF (Affinity Capture-MS), DIEXF (Two-hybrid), DIEXF (Co-fractionation), DIEXF (Co-fractionation), MYO18A (Co-fractionation), DIEXF (Affinity Capture-MS), DIEXF (Affinity Capture-MS), DIEXF (Affinity Capture-MS)

ESM2 similar proteins: A0AVT1, A4QN59, A6H630, A6QXC6, A7SBF0, A7SKJ3, F4JZC2, O01757, O70467, P49958, P87115, Q09454, Q0J7N5, Q10206, Q17QF2, Q4KLT3, Q58EM4, Q5AWA2, Q5M9G7, Q5TYS0, Q5XI55, Q5ZIE6, Q5ZJM3, Q5ZKI2, Q5ZLG3, Q642T7, Q655R6, Q68CQ4, Q6DE00, Q6DJA3, Q6NTR1, Q6NUA1, Q6PEH4, Q7SXP2, Q8C7R4, Q8GWT4, Q8GXR5, Q8JFW4, Q8K224, Q922H1

Diamond homologs: A1CQH8, A1D3E2, A2QQ09, A3LXV1, A4R0E6, A5DFC2, A5E1F6, A6RT94, A6ZVI6, A7EZP8, A7THH1, B0XQ54, B2B4I8, B2W0B1, B3LTT8, B6H768, B6JX19, B6Q702, B8LVD6, B9WM88, C0NQU6, C0SG20, C1G2D1, C1GPD0, C4JTH6, C4R2K0, C4XWY8, C4YMA4, C5DMP2, C5DPB7, C5G0N1, C5GAH0, C5JMX0, C5M3P0, C5P5Z4, C6HQ17, C7GKL8, C7YRJ1, C8ZAF8, D1Z6B1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 94 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
Signaling by NTRK1 (TRKA)516.7×3e-03
rRNA modification in the nucleus and cytosol515.9×3e-03
Signaling by NTRKs515.4×3e-03
Diseases of signal transduction by growth factor receptors and second messengers76.7×6e-03

GO biological processes:

GO termPartnersFoldFDR
ribosomal small subunit biogenesis615.5×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance108
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2194 predictions. Top by Δscore:

VariantEffectΔscore
1:209828180:G:Tdonor_gain1.0000
1:209830797:TTTTA:Tacceptor_loss1.0000
1:209830799:TTA:Tacceptor_loss1.0000
1:209830800:TA:Tacceptor_loss1.0000
1:209830801:A:AGacceptor_gain1.0000
1:209830801:A:ATacceptor_loss1.0000
1:209830802:G:GGacceptor_gain1.0000
1:209830802:GT:Gacceptor_gain1.0000
1:209830802:GTC:Gacceptor_gain1.0000
1:209830802:GTCA:Gacceptor_gain1.0000
1:209831039:AGAGA:Adonor_gain1.0000
1:209831040:GAGA:Gdonor_gain1.0000
1:209831040:GAGAG:Gdonor_gain1.0000
1:209831041:AGA:Adonor_gain1.0000
1:209831042:GA:Gdonor_gain1.0000
1:209831042:GAG:Gdonor_gain1.0000
1:209831044:G:Cdonor_loss1.0000
1:209831044:G:GGdonor_gain1.0000
1:209831045:T:Gdonor_loss1.0000
1:209833316:G:GTdonor_gain1.0000
1:209833370:GT:Gdonor_gain1.0000
1:209835164:G:GGdonor_gain1.0000
1:209836799:A:AGacceptor_gain1.0000
1:209836799:AGT:Aacceptor_gain1.0000
1:209836800:G:GAacceptor_gain1.0000
1:209836800:GT:Gacceptor_gain1.0000
1:209836800:GTG:Gacceptor_gain1.0000
1:209837208:CAAGG:Cdonor_loss1.0000
1:209837210:AGGTG:Adonor_loss1.0000
1:209837213:T:Adonor_loss1.0000

AlphaMissense

5042 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:209838931:G:CR362P0.998
1:209839119:T:CF425L0.998
1:209839121:C:AF425L0.998
1:209839121:C:GF425L0.998
1:209840904:C:GS445W0.998
1:209840931:G:AG454D0.998
1:209842323:G:CR515P0.998
1:209843552:G:CR628P0.998
1:209839021:T:CF392S0.997
1:209840853:G:AG428E0.997
1:209841037:G:CQ489H0.997
1:209841037:G:TQ489H0.997
1:209838913:T:CL356P0.996
1:209839113:G:CD423H0.996
1:209840907:A:TD446V0.996
1:209840922:C:TS451F0.996
1:209841040:C:AN490K0.996
1:209841040:C:GN490K0.996
1:209841041:T:AW491R0.996
1:209841041:T:CW491R0.996
1:209842365:G:CR529P0.996
1:209843672:C:TT668I0.996
1:209837204:G:CR352T0.995
1:209837204:G:TR352M0.995
1:209839120:T:CF425S0.995
1:209840922:C:AS451Y0.995
1:209843546:G:CR626P0.995
1:209839114:A:TD423V0.994
1:209839128:G:AG428R0.994
1:209839128:G:CG428R0.994

dbSNP variants (sampled 300 via entrez): RS1000127283 (1:209845973 C>T), RS1000296113 (1:209835473 A>G), RS1000331843 (1:209855322 G>A), RS1000517735 (1:209842293 C>G), RS1000564380 (1:209844036 GT>G), RS1000745860 (1:209854949 ATCTTCATTACCAAATTTCTACTCCACACT>A), RS1000790681 (1:209848887 T>C), RS1001018397 (1:209844346 T>C), RS1001333845 (1:209855308 T>G), RS1001394189 (1:209855885 G>A), RS1001503288 (1:209849505 G>A,T), RS1001672786 (1:209843089 A>G), RS1001869963 (1:209828969 T>G), RS1001885024 (1:209832325 T>A), RS1001885872 (1:209857686 G>A,C)

Disease associations

OMIM: gene MIM:619663 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST003996_12Monobrow2.000000e-11
GCST004131_1Inflammatory bowel disease1.000000e-08
GCST004132_85Crohn’s disease7.000000e-07
GCST004166_10Nonsyndromic cleft lip with cleft palate9.000000e-19
GCST004866_6Alopecia areata2.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007906synophrys measurement
EFO:0003959cleft lip

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, decreases methylation4
Arsenicincreases expression, increases methylation, affects cotreatment, increases abundance2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Cyclosporineincreases expression2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases expression1
arseniteincreases methylation1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
zinc chromateincreases abundance, increases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
potassium chromate(VI)decreases expression1
chromium hexavalent ionincreases abundance, increases expression1
perfluoro-n-nonanoic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Sunitinibincreases expression1
Leflunomideincreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Cisplatindecreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Doxorubicindecreases expression1
Estradiolincreases expression1
Ethyl Methanesulfonatedecreases expression1
Hydrogen Peroxideaffects expression1
Leaddecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): alopecia areata