URB1

Summary

URB1 (URB1 ribosome biogenesis factor, HGNC:17344) is a protein-coding gene on chromosome 21q22.11, encoding Nucleolar pre-ribosomal-associated protein 1 (O60287). It is a common-essential gene (DepMap: required in 98.4% of cancer cell lines).

Enables RNA binding activity. Predicted to be involved in maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in fibrillar center.

Source: NCBI Gene 9875 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 439 total
• Cancer dependency (DepMap): dependent in 98.4% of screened cell lines (common-essential)
• MANE Select transcript: NM_014825

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17344
Approved symbol	URB1
Name	URB1 ribosome biogenesis factor
Location	21q22.11
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0539, NPA1
Ensembl gene	ENSG00000142207
Ensembl biotype	protein_coding
OMIM	608865
Entrez	9875

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000382751, ENST00000480196, ENST00000492603, ENST00000864001, ENST00000913255, ENST00000947585

RefSeq mRNA: 1 — MANE Select: NM_014825 NM_014825

CCDS: CCDS46645

Canonical transcript exons

ENST00000382751 — 39 exons

Exon	Start	End
ENSE00000952905	32333317	32333419
ENSE00001042861	32345374	32345575
ENSE00001042862	32357537	32357656
ENSE00001042866	32373647	32373772
ENSE00001042868	32341466	32341524
ENSE00001042870	32322478	32322584
ENSE00001042871	32346956	32347811
ENSE00001042875	32350704	32350922
ENSE00001042879	32363156	32363329
ENSE00001042882	32317676	32317917
ENSE00001042885	32349304	32349483
ENSE00001042891	32366618	32366755
ENSE00001042896	32375398	32375483
ENSE00001042904	32378445	32378541
ENSE00001042917	32361892	32362021
ENSE00001042926	32337404	32337514
ENSE00001042928	32354859	32354997
ENSE00001042932	32344570	32344756
ENSE00001042937	32372507	32372631
ENSE00001042940	32384313	32384464
ENSE00001042942	32368403	32368598
ENSE00001042944	32324491	32324602
ENSE00001042947	32361007	32361123
ENSE00001042951	32316466	32317065
ENSE00001042954	32353933	32354103
ENSE00001042957	32325229	32325389
ENSE00001042963	32355449	32355565
ENSE00001042969	32319217	32319414
ENSE00001042971	32359796	32359908
ENSE00001042973	32320531	32320640
ENSE00001042974	32383422	32383554
ENSE00001042983	32385545	32385684
ENSE00001042988	32338707	32338900
ENSE00001042993	32321801	32321944
ENSE00001042998	32352710	32352906
ENSE00001178996	32337094	32337157
ENSE00001493247	32311018	32315099
ENSE00001493352	32392769	32393012
ENSE00003525489	32334163	32334334

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 92.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.5152 / max 357.5144, expressed in 1812 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
190182	28.8888	1809
190181	5.3508	1519
209295	0.1925	104
190179	0.0831	50

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	92.35	gold quality
stromal cell of endometrium	CL:0002255	83.16	gold quality
Brodmann (1909) area 23	UBERON:0013554	82.31	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.87	gold quality
body of uterus	UBERON:0009853	81.23	gold quality
sural nerve	UBERON:0015488	81.10	gold quality
adrenal tissue	UBERON:0018303	80.99	gold quality
cortical plate	UBERON:0005343	80.39	gold quality
thoracic aorta	UBERON:0001515	80.22	gold quality
ascending aorta	UBERON:0001496	80.21	gold quality
ventricular zone	UBERON:0003053	80.07	gold quality
gastrocnemius	UBERON:0001388	79.75	gold quality
middle temporal gyrus	UBERON:0002771	79.69	gold quality
right uterine tube	UBERON:0001302	79.58	gold quality
left adrenal gland	UBERON:0001234	78.83	gold quality
muscle of leg	UBERON:0001383	78.82	gold quality
prostate gland	UBERON:0002367	78.82	gold quality
left ovary	UBERON:0002119	78.57	gold quality
descending thoracic aorta	UBERON:0002345	78.54	gold quality
choroid plexus epithelium	UBERON:0003911	78.54	gold quality
left adrenal gland cortex	UBERON:0035825	78.47	gold quality
lower esophagus muscularis layer	UBERON:0035833	78.31	gold quality
lower esophagus	UBERON:0013473	78.29	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	78.09	gold quality
right ovary	UBERON:0002118	78.07	gold quality
ovary	UBERON:0000992	77.88	gold quality
vagina	UBERON:0000996	77.83	gold quality
right adrenal gland	UBERON:0001233	77.79	gold quality
adrenal gland	UBERON:0002369	77.69	gold quality
tibial nerve	UBERON:0001323	77.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	6.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting URB1, 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-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-3934-5P	99.67	64.04	846
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-186-3P	99.51	66.24	1685

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.4% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

• RAPTOR promotes colorectal cancer proliferation by inducing mTORC1 and upregulating ribosome assembly factor URB1. (PMID:31886628)
• Ribosome assembly factor URB1 contributes to colorectal cancer proliferation through transcriptional activation of ATF4. (PMID:32888357)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	urb1	ENSDARG00000060308
mus_musculus	Urb1	ENSMUSG00000039929
rattus_norvegicus	Urb1	ENSRNOG00000002080
drosophila_melanogaster	CG12499	FBGN0038968
caenorhabditis_elegans		WBGENE00020273

Protein

Protein identifiers

Nucleolar pre-ribosomal-associated protein 1 — O60287 (reviewed: O60287)

Alternative names: Nucleolar protein 254 kDa, URB1 ribosome biogenesis 1 homolog

All UniProt accessions (1): O60287

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus. Nucleolus.

RefSeq proteins (1): NP_055640* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016024	ARM-type_fold	Homologous_superfamily
IPR021714	URB1_N	Domain
IPR032436	URB1_C	Domain
IPR039844	URB1	Family
IPR059018	HEAT_URB1	Domain

Pfam: PF11707, PF16201, PF26140

UniProt features (8 total): region of interest 2, modified residue 2, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60287-F1	75.57	0.07

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): 17, 1143

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 80 (showing top): GOBP_RIBOSOME_BIOGENESIS, ONKEN_UVEAL_MELANOMA_UP, GOBP_MATURATION_OF_5_8S_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, GOBP_MATURATION_OF_LSU_RRNA, GOBP_MATURATION_OF_5_8S_RRNA, chr21q22, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, GOCC_NUCLEOLUS, MANALO_HYPOXIA_DN, GOBP_MATURATION_OF_LSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, LEE_BMP2_TARGETS_DN, GOCC_FIBRILLAR_CENTER, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, E2F3_UP.V1_DN

GO Biological Process (2): maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000463), maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000466)

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (3): fibrillar center (GO:0001650), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
maturation of LSU-rRNA	1
maturation of 5.8S rRNA	1
nucleic acid binding	1
nucleolus	1
cellular anatomical structure	1
nuclear lumen	1
intracellular membraneless organelle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1664 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
URB1	URB2	Q14146	860
URB1	PDCD11	Q14690	718
URB1	NOL9	Q5SY16	646
URB1	RBM34	P42696	618
URB1	EVA1C	P58658	587
URB1	TMEM242	Q9NWH2	562
URB1	GNL2	Q13823	554
URB1	CRYZL1	O95825	551
URB1	HUNK	P57058	549
URB1	CEBPZ	Q03701	541
URB1	LTV1	Q96GA3	534
URB1	MIS18A	Q9NYP9	518
URB1	DDX51	Q8N8A6	505
URB1	UTP14A	Q9BVJ6	498
URB1	DHX15	O43143	493

IntAct

158 interactions, top by confidence:

A	B	Type	Score
MECP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
NPM1	NVL	psi-mi:“MI:0914”(association)	0.610
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
PLEKHO1	UBA6	psi-mi:“MI:0914”(association)	0.530
FGF3	GTPBP10	psi-mi:“MI:0914”(association)	0.530
MECP2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
ZNF512	ZNF724	psi-mi:“MI:0914”(association)	0.530
RBM34	NVL	psi-mi:“MI:0914”(association)	0.530
RRP8	NVL	psi-mi:“MI:0914”(association)	0.530
RPL18	NOP56	psi-mi:“MI:0914”(association)	0.530
MACROH2A2	PPM1G	psi-mi:“MI:0914”(association)	0.530
RPL18A	RRP8	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
CCDC59	GAPDHS	psi-mi:“MI:0914”(association)	0.530
RBM4	NVL	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RRP8	MAGEB2	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
ILVBL	SLC33A1	psi-mi:“MI:0914”(association)	0.530
RPLP0	GTPBP10	psi-mi:“MI:0914”(association)	0.530
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480

BioGRID (183): URB1 (Affinity Capture-RNA), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS), URB1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0B4K859, A1Z7L1, A1ZBE8, A8WTE8, F4JC97, F4KBW6, F6S215, F6WXT2, O13665, O60287, O75691, P34343, P40090, P42173, P48322, P49815, P49816, P78527, P78847, Q03280, Q09716, Q21106, Q571H0, Q5SRE5, Q5WNI9, Q61037, Q6ZQH8, Q750S2, Q8BH53, Q8IQV9, Q8MYL1, Q8QGX4, Q8WN22, Q93903, Q95YE9, Q9C8Z4, Q9DEI1, Q9FIN7, Q9HDV6, Q9P7M6

Diamond homologs: O60287, Q571H0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 176 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:

Pathway	Partners	Fold	FDR
rRNA modification in the nucleus and cytosol	8	14.0×	3e-06
Peptide chain elongation	11	13.0×	1e-07
Viral mRNA Translation	11	13.0×	1e-07
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	11	12.9×	1e-07
Selenocysteine synthesis	11	12.4×	1e-07
Eukaryotic Translation Termination	11	12.4×	1e-07
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	11	12.1×	1e-07
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	11	12.1×	1e-07

GO biological processes:

GO term	Partners	Fold	FDR
ribosomal large subunit biogenesis	7	20.7×	9e-06
cytoplasmic translation	12	14.8×	2e-08
ribosomal small subunit biogenesis	8	12.2×	5e-05
rRNA processing	12	11.3×	3e-07
negative regulation of translation	7	9.1×	2e-03
translation	13	8.9×	8e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	354
Likely benign	46
Benign	7

Top pathogenic / likely-pathogenic (0)

SpliceAI

6123 predictions. Top by Δscore:

Variant	Effect	Δscore
21:32314946:T:TA	donor_gain	1.0000
21:32316460:CCTTA:C	donor_loss	1.0000
21:32316461:CTTAC:C	donor_loss	1.0000
21:32316462:TTA:T	donor_loss	1.0000
21:32316463:TA:T	donor_loss	1.0000
21:32317674:A:AC	donor_gain	1.0000
21:32317674:ACT:A	donor_gain	1.0000
21:32317675:C:CA	donor_gain	1.0000
21:32317675:CT:C	donor_gain	1.0000
21:32317675:CTC:C	donor_gain	1.0000
21:32319212:CTCA:C	donor_loss	1.0000
21:32319213:TCA:T	donor_loss	1.0000
21:32319214:CA:C	donor_loss	1.0000
21:32319215:A:AC	donor_gain	1.0000
21:32319216:C:CC	donor_gain	1.0000
21:32319216:C:T	donor_loss	1.0000
21:32319216:CCT:C	donor_gain	1.0000
21:32319361:CACAG:C	acceptor_gain	1.0000
21:32319412:AACC:A	acceptor_loss	1.0000
21:32319415:C:CA	acceptor_loss	1.0000
21:32320529:A:AC	donor_gain	1.0000
21:32320530:C:CA	donor_gain	1.0000
21:32320530:CT:C	donor_gain	1.0000
21:32320530:CTT:C	donor_gain	1.0000
21:32320530:CTTG:C	donor_gain	1.0000
21:32320636:CAATT:C	acceptor_gain	1.0000
21:32320639:TT:T	acceptor_gain	1.0000
21:32320639:TTCTG:T	acceptor_loss	1.0000
21:32320640:TC:T	acceptor_loss	1.0000
21:32320641:C:CC	acceptor_gain	1.0000

AlphaMissense

14820 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:32353997:A:C	S784R	0.996
21:32353997:A:T	S784R	0.996
21:32353999:T:G	S784R	0.996
21:32368432:A:G	W390R	0.996
21:32368432:A:T	W390R	0.996
21:32372536:A:C	F324L	0.996
21:32372536:A:T	F324L	0.996
21:32372538:A:G	F324L	0.996
21:32355514:A:G	W681R	0.995
21:32355514:A:T	W681R	0.995
21:32368524:A:G	L359P	0.995
21:32375408:A:G	L247P	0.994
21:32372546:C:T	G321E	0.993
21:32372576:A:G	L311P	0.993
21:32373747:T:A	K259I	0.993
21:32334324:A:G	W1566R	0.992
21:32334324:A:T	W1566R	0.992
21:32359810:A:G	W619R	0.991
21:32359810:A:T	W619R	0.991
21:32373685:A:G	W280R	0.991
21:32373685:A:T	W280R	0.991
21:32373746:T:A	K259N	0.991
21:32373746:T:G	K259N	0.991
21:32384424:C:G	R108P	0.991
21:32368589:G:C	N337K	0.990
21:32368589:G:T	N337K	0.990
21:32384433:A:T	I105K	0.990
21:32372567:A:G	L314P	0.989
21:32383531:A:G	L153P	0.989
21:32383537:A:G	L151P	0.989

dbSNP variants (sampled 300 via entrez): RS1000089116 (21:32383281 G>A), RS1000180123 (21:32312570 G>A), RS1000185628 (21:32334861 C>T), RS1000214938 (21:32388466 C>T), RS1000259601 (21:32350904 T>A,C), RS1000268913 (21:32388672 C>A), RS1000297595 (21:32339831 C>G,T), RS1000312073 (21:32391300 A>G), RS1000334838 (21:32362037 A>C), RS1000405376 (21:32378766 T>G), RS1000411239 (21:32327726 G>C), RS1000416407 (21:32318380 G>A), RS1000434787 (21:32383035 C>A,T), RS1000471032 (21:32361773 G>A,C), RS1000509944 (21:32329978 A>C)

Disease associations

OMIM: gene MIM:608865 | disease phenotypes: MIM:607398

GenCC curated gene-disease

Mondo (1): glucocorticoid deficiency 2 (MONDO:0011826)

Orphanet (1): Familial glucocorticoid deficiency (Orphanet:361)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C564577	Glucocorticoid Deficiency 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol S	increases methylation, affects cotreatment, decreases expression	2
Estradiol	increases expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	decreases methylation	1
potassium chromate(VI)	increases expression	1
pentabromodiphenyl ether	increases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Dinitrochlorobenzene	affects binding	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1
Methapyrilene	decreases methylation	1
Ribonucleotides	affects binding	1
Tretinoin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Fatty Acids, Omega-3	increases expression	1
Cadmium Chloride	decreases expression	1
Fatty Acids, Omega-6	decreases expression	1

Clinical trials (associated diseases)

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