UTP11

Summary

UTP11 (UTP11 small subunit processome component, HGNC:24329) is a protein-coding gene on chromosome 1p34.3, encoding Probable U3 small nucleolar RNA-associated protein 11 (Q9Y3A2). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. It is a common-essential gene (DepMap: required in 93.5% of cancer cell lines).

Enables RNA binding activity. Involved in nervous system development; positive regulation of apoptotic process; and ribosomal small subunit biogenesis. Located in cytosol; extracellular space; and nuclear lumen. Part of small-subunit processome.

Source: NCBI Gene 51118 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 18 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 93.5% of screened cell lines (common-essential)
• MANE Select transcript: NM_016037

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24329
Approved symbol	UTP11
Name	UTP11 small subunit processome component
Location	1p34.3
Locus type	gene with protein product
Status	Approved
Aliases	CGI-94
Ensembl gene	ENSG00000183520
Ensembl biotype	protein_coding
OMIM	609440
Entrez	51118

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000373014, ENST00000483182, ENST00000486563, ENST00000488453, ENST00000890280, ENST00000920260, ENST00000920261

RefSeq mRNA: 1 — MANE Select: NM_016037 NM_016037

CCDS: CCDS429

Canonical transcript exons

ENST00000373014 — 8 exons

Exon	Start	End
ENSE00001459301	38023545	38024820
ENSE00001884229	38012734	38012865
ENSE00003503764	38019253	38019383
ENSE00003513811	38019059	38019152
ENSE00003540886	38018464	38018577
ENSE00003572268	38017668	38017770
ENSE00003600240	38016359	38016420
ENSE00003694084	38022699	38022809

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 98.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 64.6665 / max 1950.0620, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2239	55.0386	1819
2240	9.6279	1741

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
biceps brachii	UBERON:0001507	98.36	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	98.20	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	97.93	gold quality
gastrocnemius	UBERON:0001388	97.69	gold quality
triceps brachii	UBERON:0001509	97.64	gold quality
skeletal muscle tissue	UBERON:0001134	97.54	gold quality
muscle of leg	UBERON:0001383	97.52	gold quality
muscle organ	UBERON:0001630	97.52	gold quality
deltoid	UBERON:0001476	97.49	gold quality
vastus lateralis	UBERON:0001379	97.43	gold quality
quadriceps femoris	UBERON:0001377	97.40	gold quality
tibialis anterior	UBERON:0001385	97.33	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.99	gold quality
body of tongue	UBERON:0011876	95.78	gold quality
muscle tissue	UBERON:0002385	95.74	gold quality
diaphragm	UBERON:0001103	95.53	gold quality
gluteal muscle	UBERON:0002000	95.19	gold quality
heart right ventricle	UBERON:0002080	94.44	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	93.31	gold quality
tongue	UBERON:0001723	91.83	gold quality
ganglionic eminence	UBERON:0004023	91.75	gold quality
calcaneal tendon	UBERON:0003701	91.37	gold quality
islet of Langerhans	UBERON:0000006	90.98	gold quality
smooth muscle tissue	UBERON:0001135	90.34	gold quality
monocyte	CL:0000576	90.27	gold quality
mononuclear cell	CL:0000842	90.18	gold quality
cortical plate	UBERON:0005343	89.94	gold quality
left ventricle myocardium	UBERON:0006566	89.91	gold quality
leukocyte	CL:0000738	89.89	gold quality
cardiac ventricle	UBERON:0002082	89.89	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-106540	yes	332.42
E-ANND-3	yes	10.78
E-MTAB-7303	no	134.04
E-MTAB-7606	no	117.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting UTP11, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 93.5% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

• CGI-94 is down-regulated at the mRNA level in the hippocampus of early stage AD brain (PMID:11860508)
• UTP11 deficiency suppresses cancer development via nucleolar stress and ferroptosis. (PMID:37087976)
• UTP11 promotes the growth of hepatocellular carcinoma by enhancing the mRNA stability of Oct4. (PMID:38233795)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	utp11	ENSDARG00000039958
mus_musculus	Utp11	ENSMUSG00000028907
rattus_norvegicus	Utp11	ENSRNOG00000007174
drosophila_melanogaster	CG1789	FBGN0030063
caenorhabditis_elegans		WBGENE00007623

Protein

Protein identifiers

Probable U3 small nucleolar RNA-associated protein 11 — Q9Y3A2 (reviewed: Q9Y3A2)

Alternative names: UTP11-like protein

All UniProt accessions (1): Q9Y3A2

UniProt curated annotations — full annotation on UniProt →

Function. 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. Involved in nucleolar processing of pre-18S ribosomal RNA.

Subunit / interactions. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the UTP11 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y3A2-1	1	yes
Q9Y3A2-2	2

RefSeq proteins (1): NP_057121* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007144	SSU_processome_Utp11	Family

Pfam: PF03998

UniProt features (20 total): cross-link 13, sequence conflict 2, modified residue 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
7MQA	ELECTRON MICROSCOPY	2.7
7MQ8	ELECTRON MICROSCOPY	3.6
7MQ9	ELECTRON MICROSCOPY	3.87

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y3A2-F1	91.31	0.71

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 (15): 144, 180, 211, 218, 235, 236, 246, 90, 241, 74, 83, 86, 103, 120, 143

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

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

MSigDB gene sets: 177 (showing top): GOBP_RIBOSOME_BIOGENESIS, TGCGCANK_UNKNOWN, MODULE_255, GOBP_MATURATION_OF_SSU_RRNA, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, MODULE_317, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, chr1p34, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, MULLIGHAN_NPM1_SIGNATURE_3_DN, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3, GRADE_COLON_AND_RECTAL_CANCER_UP, REACTOME_METABOLISM_OF_RNA, GOCC_PRERIBOSOME

GO Biological Process (4): rRNA processing (GO:0006364), nervous system development (GO:0007399), ribosomal small subunit biogenesis (GO:0042274), positive regulation of apoptotic process (GO:0043065)

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

GO Cellular Component (7): obsolete extracellular space (GO:0005615), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), small-subunit processome (GO:0032040), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	2

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
ribosome biogenesis	2
nuclear lumen	2
RNA processing	1
rRNA metabolic process	1
system development	1
ribonucleoprotein complex biogenesis	1
apoptotic process	1
regulation of apoptotic process	1
positive regulation of programmed cell death	1
nucleic acid binding	1
binding	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
cytoplasm	1
nucleolus	1
preribosome	1
t-UTP complex	1
nuclear protein-containing complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2103 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UTP11	UTP3	Q9NQZ2	833
UTP11	WDR46	O15213	785
UTP11	UTP18	Q9Y5J1	742
UTP11	UTP20	O75691	723
UTP11	DNTTIP2	Q5QJE6	692
UTP11	NOP14	P78316	672
UTP11	FCF1	Q9Y324	628
UTP11	HEATR1	Q9H583	625
UTP11	UTP6	Q9NYH9	624
UTP11	UTP15	Q8TED0	590
UTP11	EBNA1BP2	Q99848	577
UTP11	BYSL	Q13895	573
UTP11	UTP14A	Q9BVJ6	560
UTP11	KRR1	Q13601	559
UTP11	ISY1	Q9ULR0	538

IntAct

98 interactions, top by confidence:

A	B	Type	Score
PIK3CA	PIK3R2	psi-mi:“MI:0914”(association)	0.900
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
RPS14	CCZ1B	psi-mi:“MI:0914”(association)	0.640
SUMO1	CBX4	psi-mi:“MI:0914”(association)	0.600
CEP70	UTP11	psi-mi:“MI:0915”(physical association)	0.560
UTP11	CEP70	psi-mi:“MI:0915”(physical association)	0.560
N	RBM47	psi-mi:“MI:0914”(association)	0.530
KIF2C	KIF2A	psi-mi:“MI:0914”(association)	0.530
PDGFRL	ANKRD28	psi-mi:“MI:0914”(association)	0.530
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
UTP11	RSL1D1	psi-mi:“MI:0915”(physical association)	0.400
UTP11	PLEC	psi-mi:“MI:0915”(physical association)	0.400
UTP11	MTUS2	psi-mi:“MI:0915”(physical association)	0.370
UTP11	CCNDBP1	psi-mi:“MI:0915”(physical association)	0.370
Cul1	GPS1	psi-mi:“MI:0914”(association)	0.350
RRP1B	ZNF785	psi-mi:“MI:0914”(association)	0.350
APBB1	SSPOP	psi-mi:“MI:0914”(association)	0.350
Mecom	ESYT2	psi-mi:“MI:0914”(association)	0.350
APP	ZNF724	psi-mi:“MI:0914”(association)	0.350
MRPL34	IPO5	psi-mi:“MI:0914”(association)	0.350
UTP11	KLHL41	psi-mi:“MI:0914”(association)	0.350
IKZF5	PEX14	psi-mi:“MI:0914”(association)	0.350
RASGRF2	SNRPA	psi-mi:“MI:0914”(association)	0.350
ORF4a	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350

BioGRID (112): CEP70 (Two-hybrid), THNSL1 (Affinity Capture-MS), KLHL41 (Affinity Capture-MS), SPRR3 (Affinity Capture-MS), CRNN (Affinity Capture-MS), RRP15 (Co-fractionation), UTP11L (Affinity Capture-MS), UTP11L (Affinity Capture-MS), UTP11L (Affinity Capture-MS), UTP11L (Affinity Capture-MS), UTP11L (Affinity Capture-MS), KLHL41 (Affinity Capture-MS), THNSL1 (Affinity Capture-MS), CRNN (Affinity Capture-MS), UTP11L (Affinity Capture-MS)

ESM2 similar proteins: A1C8E1, A3LU29, B0JZ89, B2W2Y7, O43082, O45766, O94389, O95926, P0CM66, P0CM67, P53188, Q0C7E6, Q0UVD1, Q0V389, Q1E554, Q28HN4, Q28IN9, Q28XK6, Q2HDR6, Q2TVY9, Q3B748, Q4I5Z5, Q568A0, Q59WI7, Q5B020, Q68EY7, Q6BIC4, Q6BWR0, Q6C1V5, Q6CNQ3, Q6DD17, Q6DGP2, Q6DKE6, Q6FVC7, Q6NVR5, Q6PHE8, Q752U2, Q7SDA6, Q7ZY35, Q8AVQ6

Diamond homologs: A6ZZL7, B5VM59, G0SF32, P34247, Q09462, Q10106, Q55C50, Q8R5K5, Q8S1Z1, Q9CZJ1, Q9M223, Q9U178, Q9W3C0, Q9Y3A2, Q8I4V5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1266 predictions. Top by Δscore:

Variant	Effect	Δscore
1:38012824:GCGGC:G	donor_gain	1.0000
1:38012861:GCCAG:G	donor_gain	1.0000
1:38012863:CAGG:C	donor_loss	1.0000
1:38012865:GGTA:G	donor_loss	1.0000
1:38012866:GTA:G	donor_loss	1.0000
1:38016357:A:AG	acceptor_gain	1.0000
1:38016358:G:GG	acceptor_gain	1.0000
1:38016358:GC:G	acceptor_gain	1.0000
1:38016416:GCAGA:G	donor_gain	1.0000
1:38016419:GA:G	donor_gain	1.0000
1:38016419:GAGT:G	donor_loss	1.0000
1:38016421:G:GG	donor_gain	1.0000
1:38016421:GT:G	donor_loss	1.0000
1:38016426:T:G	donor_gain	1.0000
1:38016483:C:G	donor_gain	1.0000
1:38016490:GCC:G	donor_gain	1.0000
1:38016492:C:CG	donor_gain	1.0000
1:38016492:C:G	donor_gain	1.0000
1:38016507:GGGA:G	donor_gain	1.0000
1:38017641:AT:A	acceptor_gain	1.0000
1:38017642:T:G	acceptor_gain	1.0000
1:38017642:T:TA	acceptor_gain	1.0000
1:38017654:A:AG	acceptor_gain	1.0000
1:38017654:AACCT:A	acceptor_gain	1.0000
1:38017658:T:A	acceptor_gain	1.0000
1:38017663:TTTAG:T	acceptor_loss	1.0000
1:38017664:TTAGT:T	acceptor_loss	1.0000
1:38017665:TAG:T	acceptor_loss	1.0000
1:38017666:A:AG	acceptor_gain	1.0000
1:38017666:A:T	acceptor_loss	1.0000

AlphaMissense

1668 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:38017738:T:C	F66L	0.998
1:38017740:C:A	F66L	0.998
1:38017740:C:G	F66L	0.998
1:38016416:G:C	A41P	0.994
1:38017752:G:A	M70I	0.994
1:38017752:G:C	M70I	0.994
1:38017752:G:T	M70I	0.994
1:38022745:G:C	R205P	0.994
1:38023605:T:C	F247L	0.994
1:38023607:T:A	F247L	0.994
1:38023607:T:G	F247L	0.994
1:38016413:C:A	R40S	0.993
1:38022754:G:C	R208P	0.993
1:38017751:T:C	M70T	0.992
1:38016391:G:C	E32D	0.990
1:38016391:G:T	E32D	0.990
1:38022736:T:C	L202P	0.990
1:38012856:G:C	E18D	0.987
1:38012856:G:T	E18D	0.987
1:38016403:T:A	D36E	0.987
1:38016403:T:G	D36E	0.987
1:38016393:A:T	K33I	0.986
1:38016401:G:C	D36H	0.986
1:38019320:G:C	R168S	0.986
1:38019320:G:T	R168S	0.986
1:38016394:A:C	K33N	0.985
1:38016394:A:T	K33N	0.985
1:38017703:T:C	L54P	0.985
1:38017739:T:C	F66S	0.985
1:38019084:T:C	L123P	0.985

dbSNP variants (sampled 300 via entrez): RS1000068982 (1:38013233 G>C), RS1000085597 (1:38019681 G>A), RS1001312702 (1:38024418 C>A,T), RS1001364393 (1:38018857 T>C), RS1001589185 (1:38012701 C>A,G,T), RS1002425655 (1:38012174 A>G), RS1002481689 (1:38018314 G>A), RS1002647726 (1:38024938 A>G), RS1003218904 (1:38023654 C>G), RS1003225041 (1:38017116 C>G), RS1003291815 (1:38022163 A>G), RS1003313298 (1:38021504 G>A), RS1003647202 (1:38011767 G>A), RS1003708157 (1:38017508 A>G), RS1003981599 (1:38012049 T>A,C,G)

Disease associations

OMIM: gene MIM:609440 | 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: yes

ChEMBL targets (1): CHEMBL6066350 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
Tobacco Smoke Pollution	increases expression	2
Cyclosporine	increases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
kojic acid	increases expression	1
beta-lapachone	increases expression	1
arsenite	increases reaction, affects binding	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
cupric chloride	increases expression	1
cupric oxide	increases expression	1
di-n-butylphosphoric acid	affects expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
bisphenol S	increases expression, affects cotreatment	1
7-(benzylamino)-1,3,4,8-tetrahydropyrrolo(4,3,2-de)quinolin-8(1H)-one	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Arbutin	increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Copper	affects binding, decreases expression	1
Dexamethasone	increases expression, affects cotreatment	1
Disulfiram	affects binding, decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Ozone	affects expression, increases abundance	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5549110	Binding	Induction of UTP11 degradation in human H1975-TM cells at 50 nM incubated for 24 hrs	Design, Synthesis, and Biological Evaluation of Novel EGFR PROTACs Targeting C797S Mutation. — J Med Chem

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3L3	Abcam HEK293T UTP11 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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