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NOL11

gene
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Also known as DKFZP586L0724

Summary

NOL11 (nucleolar protein 11, HGNC:24557) is a protein-coding gene on chromosome 17q24.2, encoding Nucleolar protein 11 (Q9H8H0). Ribosome biogenesis factor. It is a selective cancer dependency (DepMap: 50.4% of cell lines).

Enables RNA binding activity. Involved in maturation of SSU-rRNA and positive regulation of transcription of nucleolar large rRNA by RNA polymerase I. Located in nucleolus. Part of t-UTP complex.

Source: NCBI Gene 25926 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 113 total
  • Cancer dependency (DepMap): dependent in 50.4% of screened cell lines
  • MANE Select transcript: NM_015462

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24557
Approved symbolNOL11
Namenucleolar protein 11
Location17q24.2
Locus typegene with protein product
StatusApproved
AliasesDKFZP586L0724
Ensembl geneENSG00000130935
Ensembl biotypeprotein_coding
OMIM615366
Entrez25926

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 14 protein_coding, 5 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000253247, ENST00000577687, ENST00000580833, ENST00000580914, ENST00000581106, ENST00000581375, ENST00000581966, ENST00000583021, ENST00000583108, ENST00000584032, ENST00000584942, ENST00000898239, ENST00000898240, ENST00000898241, ENST00000898242, ENST00000918418, ENST00000918419, ENST00000918420, ENST00000918421, ENST00000918422, ENST00000955840

RefSeq mRNA: 2 — MANE Select: NM_015462 NM_001303272, NM_015462

CCDS: CCDS11671

Canonical transcript exons

ENST00000253247 — 18 exons

ExonStartEnd
ENSE000010146516772258067722637
ENSE000026937256774374367744531
ENSE000027250156771793667718088
ENSE000034604666773812267738355
ENSE000034621296771990667719962
ENSE000034765606773436367734439
ENSE000034766156773666667736754
ENSE000034838426772404967724193
ENSE000035031426773590067736023
ENSE000035663496772646067726648
ENSE000035931896771967467719787
ENSE000035980716773951667739608
ENSE000036139106774347967743586
ENSE000036235646772137867721526
ENSE000036418736773784767737972
ENSE000036421986773750867737692
ENSE000036478506773893267739010
ENSE000036804206773707167737145

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 95.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 36.9689 / max 689.6874, expressed in 1799 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
16234935.81881798
1623481.1501489

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305395.71gold quality
embryoUBERON:000092295.30gold quality
cortical plateUBERON:000534395.24gold quality
ganglionic eminenceUBERON:000402394.98gold quality
epithelium of nasopharynxUBERON:000195194.04gold quality
nasopharynxUBERON:000172894.03gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.99gold quality
calcaneal tendonUBERON:000370193.99gold quality
cartilage tissueUBERON:000241893.83gold quality
mucosa of transverse colonUBERON:000499193.55gold quality
tibiaUBERON:000097993.49gold quality
adrenal tissueUBERON:001830393.37gold quality
hair follicleUBERON:000207393.34gold quality
mucosa of sigmoid colonUBERON:000499393.12gold quality
parietal pleuraUBERON:000240092.96gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451192.92gold quality
oral cavityUBERON:000016792.85gold quality
choroid plexus epitheliumUBERON:000391192.69gold quality
esophagus squamous epitheliumUBERON:000692092.68gold quality
islet of LangerhansUBERON:000000692.66gold quality
pleuraUBERON:000097792.43gold quality
lymph nodeUBERON:000002992.25gold quality
germinal epithelium of ovaryUBERON:000130492.16gold quality
bone marrowUBERON:000237192.13gold quality
right lobe of liverUBERON:000111492.01gold quality
endometriumUBERON:000129591.97gold quality
colonic mucosaUBERON:000031791.94gold quality
colonic epitheliumUBERON:000039791.93gold quality
rectumUBERON:000105291.93gold quality
vastus lateralisUBERON:000137991.93gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.98
E-HCAD-29no92.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting NOL11, 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-3163100.0077.238605
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-477599.9875.006394
HSA-MIR-590-3P99.9674.346478
HSA-MIR-153-5P99.8973.866317
HSA-MIR-442899.7366.411733
HSA-MIR-471999.7372.103329
HSA-MIR-464399.4967.631791
HSA-MIR-127699.3668.181642
HSA-MIR-770299.0665.95698
HSA-MIR-480198.9669.422096
HSA-MIR-4711-5P98.8968.00965
HSA-MIR-316198.7167.14816
HSA-MIR-4731-3P98.5668.601860
HSA-MIR-397798.0068.171500
HSA-MIR-311697.0765.781324

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 50.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • NOL11 is a novel protein required for the early stages of ribosome biogenesis in humans and is implicated in the pathogenesis of North American Indian childhood cirrhosis. (PMID:22916032)
  • Identification of a novel nucleolar protein complex required for mitotic chromosome segregation through centromeric accumulation of Aurora B. (PMID:32479628)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerionol11ENSDARG00000026767
mus_musculusNol11ENSMUSG00000018433
rattus_norvegicusNol11ENSRNOG00000052934
drosophila_melanogasterCG9300FBGN0036886

Protein

Protein identifiers

Nucleolar protein 11 — Q9H8H0 (reviewed: Q9H8H0)

All UniProt accessions (4): Q9H8H0, J3QKV1, J3QLQ6, J3QR28

UniProt curated annotations — full annotation on UniProt →

Function. Ribosome biogenesis factor. May be required for both optimal rDNA transcription and small subunit (SSU) pre-rRNA processing at sites A’, A0, 1 and 2b.

Subunit / interactions. Interacts with UTP4. Interacts with FBL/fibrillarin in a transcription-dependent manner. May associate with the proposed t-UTP subcomplex of the SSU processome containing at least UTP4, WDR43, HEATR1, UTP15, WDR75.

Subcellular location. Nucleus. Nucleolus.

Miscellaneous. Is the likely candidate for being the functional analog of yeast Utp8. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H8H0-11yes
Q9H8H0-22

RefSeq proteins (2): NP_001290201, NP_056277* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR012584NOL11_NDomain
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR042859NOL11Family
IPR048897Nol11_CDomain

Pfam: PF08168, PF20998

UniProt features (5 total): splice variant 2, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
7MQAELECTRON MICROSCOPY2.7
7MQ8ELECTRON MICROSCOPY3.6
7MQ9ELECTRON MICROSCOPY3.87

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H8H0-F178.910.38

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 (1): 346

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: 141 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, GOBP_RIBOSOME_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA, GOBP_RRNA_TRANSCRIPTION, WEI_MYCN_TARGETS_WITH_E_BOX, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GNF2_FBL, GARY_CD5_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, REACTOME_METABOLISM_OF_RNA, GOCC_PRERIBOSOME, GOCC_SMALL_SUBUNIT_PROCESSOME

GO Biological Process (4): maturation of SSU-rRNA (GO:0030490), positive regulation of transcription of nucleolar large rRNA by RNA polymerase I (GO:1901838), rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254)

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

GO Cellular Component (4): nucleoplasm (GO:0005654), nucleolus (GO:0005730), t-UTP complex (GO:0034455), 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
nuclear lumen2
rRNA processing1
ribosomal small subunit biogenesis1
nucleolar large rRNA transcription by RNA polymerase I1
positive regulation of transcription by RNA polymerase I1
regulation of transcription of nucleolar large rRNA by RNA polymerase I1
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
ribonucleoprotein complex biogenesis1
nucleic acid binding1
binding1
cellular anatomical structure1
intracellular membraneless organelle1
nucleolus1
nuclear protein-containing complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

2032 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NOL11UTP4Q969X6889
NOL11WDR43Q15061760
NOL11UTP15Q8TED0548
NOL11HEATR1Q9H583545
NOL11WDR75Q8IWA0541
NOL11UTP6Q9NYH9490
NOL11UTP20O75691447
NOL11RRN3Q9NYV6413
NOL11TFAP2BQ92481400
NOL11POLIQ9UNA4387
NOL11NUTM2FA1L443385
NOL11MDN1Q9NU22378
NOL11TCOF1Q13428375
NOL11ENOPH1Q9UHY7370
NOL11PRRX2Q99811369

IntAct

96 interactions, top by confidence:

ABTypeScore
UTP4WDR43psi-mi:“MI:0914”(association)0.860
PIK3CBPIK3R1psi-mi:“MI:0914”(association)0.840
UTP4NOL11psi-mi:“MI:0915”(physical association)0.820
VAPBFAM83Gpsi-mi:“MI:0914”(association)0.730
MAD2L1INSRpsi-mi:“MI:0914”(association)0.700
MPHOSPH6MTREXpsi-mi:“MI:0914”(association)0.690
C1DZFC3H1psi-mi:“MI:0914”(association)0.640
VAPAFAM83Gpsi-mi:“MI:0914”(association)0.640
EXOSC5ZFC3H1psi-mi:“MI:0914”(association)0.640
NOL7WDR43psi-mi:“MI:0914”(association)0.640
FBLNOL11psi-mi:“MI:0915”(physical association)0.560
ARSIHSPA5psi-mi:“MI:0914”(association)0.530
NOL11WDR43psi-mi:“MI:0914”(association)0.530
FBLZNF316psi-mi:“MI:0914”(association)0.530
CD70METTL15psi-mi:“MI:0914”(association)0.530
UTP4ANKRD28psi-mi:“MI:0914”(association)0.530
WDR43WDR75psi-mi:“MI:0914”(association)0.530
FBXL19MED19psi-mi:“MI:0914”(association)0.530
NOL7IPO5psi-mi:“MI:0914”(association)0.530
MPHOSPH6ZFC3H1psi-mi:“MI:0914”(association)0.530
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
MAD2L1PPIP5K2psi-mi:“MI:0914”(association)0.530
ACSBG1NOL11psi-mi:“MI:0915”(physical association)0.400
GNB1NOL11psi-mi:“MI:0915”(physical association)0.370
JUNpsi-mi:“MI:0914”(association)0.350

BioGRID (153): NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), NOL11 (Affinity Capture-MS), UTP15 (Co-fractionation), NOL11 (Affinity Capture-MS), NOL11 (Proximity Label-MS), NOL11 (Proximity Label-MS)

ESM2 similar proteins: A0A1L8GXY4, A4D1P6, A8XSV3, B0JZ65, B0R160, B0WYR6, E9Q7R9, F1REV3, F6S215, O00443, O65418, P50748, Q09178, Q12769, Q17I16, Q19317, Q2TAW0, Q3MHH2, Q402B2, Q4V9P9, Q5R6T6, Q5RAY1, Q5RB52, Q5RE88, Q5ZJY3, Q5ZL79, Q5ZLL7, Q6DTM3, Q6GM71, Q6INI5, Q6P996, Q6X9E4, Q6ZQQ6, Q7TMQ7, Q86XI2, Q8BJW5, Q8BMQ2, Q8C3Y4, Q8K3E5, Q8N157

Diamond homologs: Q3MHH2, Q4V9P9, Q5RB52, Q5ZL79, Q6INI5, Q8BJW5, Q9H8H0

SIGNOR signaling

1 interactions.

AEffectBMechanism
NOL11“form complex”“UTP-A complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 127 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
Nuclear RNA decay517.9×2e-03
Major pathway of rRNA processing in the nucleolus and cytosol117.9×7e-05

GO biological processes:

GO termPartnersFoldFDR
ribosomal large subunit biogenesis519.1×1e-03
ribosomal small subunit biogenesis713.7×7e-04
positive regulation of fibroblast proliferation512.7×6e-03
rRNA processing89.8×7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance86
Likely benign7
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2434 predictions. Top by Δscore:

VariantEffectΔscore
17:67718379:C:Gdonor_gain1.0000
17:67719669:A:AGacceptor_gain1.0000
17:67719669:ATTAG:Aacceptor_gain1.0000
17:67719670:T:Gacceptor_gain1.0000
17:67719670:TTA:Tacceptor_loss1.0000
17:67719671:TA:Tacceptor_loss1.0000
17:67719672:A:AGacceptor_gain1.0000
17:67719673:G:GGacceptor_gain1.0000
17:67719673:GGTTT:Gacceptor_gain1.0000
17:67719784:TAAG:Tdonor_gain1.0000
17:67719786:AG:Adonor_gain1.0000
17:67719787:GG:Gdonor_gain1.0000
17:67719788:G:GGdonor_gain1.0000
17:67719963:G:GGdonor_gain1.0000
17:67721376:A:AGacceptor_gain1.0000
17:67721376:AGTT:Aacceptor_gain1.0000
17:67721377:G:GTacceptor_gain1.0000
17:67721377:GT:Gacceptor_gain1.0000
17:67721377:GTT:Gacceptor_gain1.0000
17:67721377:GTTG:Gacceptor_gain1.0000
17:67721377:GTTGT:Gacceptor_gain1.0000
17:67721526:AG:Adonor_loss1.0000
17:67721527:G:GGdonor_gain1.0000
17:67721529:AA:Adonor_loss1.0000
17:67721543:G:GGdonor_gain1.0000
17:67722574:TTGTA:Tacceptor_loss1.0000
17:67722575:TGTAG:Tacceptor_loss1.0000
17:67722576:GTAG:Gacceptor_loss1.0000
17:67722577:TA:Tacceptor_loss1.0000
17:67722578:A:ACacceptor_loss1.0000

AlphaMissense

4710 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:67719918:T:AW90R0.995
17:67719918:T:CW90R0.995
17:67734389:T:CF294L0.994
17:67734391:T:AF294L0.994
17:67734391:T:GF294L0.994
17:67743488:T:AW649R0.994
17:67743488:T:CW649R0.994
17:67719701:T:AW57R0.991
17:67719701:T:CW57R0.991
17:67743762:T:CL688P0.990
17:67719951:T:CF101L0.987
17:67719953:T:AF101L0.987
17:67719953:T:GF101L0.987
17:67719956:A:CK102N0.987
17:67719956:A:TK102N0.987
17:67743509:G:CA656P0.987
17:67734377:T:AW290R0.985
17:67734377:T:CW290R0.985
17:67739523:T:CL617P0.984
17:67718075:T:AV43D0.983
17:67719957:G:CA103P0.983
17:67743504:T:CL654P0.983
17:67743515:T:CF658L0.983
17:67743517:T:AF658L0.983
17:67743517:T:GF658L0.983
17:67734382:C:AN291K0.982
17:67734382:C:GN291K0.982
17:67721430:T:AV122E0.981
17:67719910:T:CL87S0.979
17:67734390:T:CF294S0.979

dbSNP variants (sampled 300 via entrez): RS1000004451 (17:67739332 C>A,T), RS1000037729 (17:67735196 G>A), RS1000120857 (17:67724258 T>C), RS1000138067 (17:67729276 C>G), RS1000254915 (17:67724488 C>A,G), RS1000325421 (17:67734932 T>C), RS1000326720 (17:67742105 A>G), RS1000620948 (17:67718455 G>A), RS1000779525 (17:67718853 A>G), RS1001027074 (17:67718784 G>A,C), RS1001036089 (17:67724645 T>C), RS1001061069 (17:67740884 A>G,T), RS1001092770 (17:67730169 A>G), RS1001371064 (17:67743103 A>G), RS1001477965 (17:67719105 T>A)

Disease associations

OMIM: gene MIM:615366 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002875_91Diisocyanate-induced asthma6.000000e-07
GCST005392_1Tooth agenesis (maxillary second premolars)3.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0006995response to diisocyanate

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
bisphenol Adecreases expression2
Valproic Aciddecreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
afuresertibdecreases expression1
bisphenol Faffects cotreatment, decreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
kojic aciddecreases expression1
trichostatin Aaffects expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumdecreases expression1
jinfukangdecreases expression1
LDN 193189affects cotreatment, decreases expression1
Temozolomideincreases expression1
Sunitinibincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Indomethacinaffects cotreatment, decreases expression1
Ivermectindecreases expression1
Manganeseaffects cotreatment, increases abundance, increases 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): tooth agenesis

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
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Sources 75

This page pulls from 75 datasets indexed by BioBTree:

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