Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	51602
Gene name	NOP58 ribonucleoprotein
Gene symbol	NOP58
Synonyms (NCBI Gene)	HSPC120NOP5NOP5/NOP58
Chromosome	2
Chromosome location	2q33.1
Summary	The protein encoded by this gene is a core component of box C/D small nucleolar ribonucleoproteins. Some box C/D small nucleolar RNAs (snoRNAs), such as U3, U8, and U14, are dependent upon the encoded protein for their synthesis. This protein is SUMOylate

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miRTarBase ID	miRNA	Experiments	Reference
MIRT046864	hsa-miR-221-3p	CLASH	23622248
MIRT1189348	hsa-miR-1303	CLIP-seq
MIRT1189349	hsa-miR-204	CLIP-seq
MIRT1189350	hsa-miR-211	CLIP-seq
MIRT1189351	hsa-miR-324-5p	CLIP-seq
MIRT1189352	hsa-miR-4292	CLIP-seq
MIRT1189353	hsa-miR-4308	CLIP-seq
MIRT1189354	hsa-miR-4724-5p	CLIP-seq
MIRT1189355	hsa-miR-4755-5p	CLIP-seq
MIRT1189356	hsa-miR-4774-5p	CLIP-seq
MIRT1189357	hsa-miR-4780	CLIP-seq
MIRT1189358	hsa-miR-550b	CLIP-seq
MIRT1189359	hsa-miR-623	CLIP-seq
MIRT2054831	hsa-miR-34b	CLIP-seq
MIRT2054832	hsa-miR-3616-5p	CLIP-seq
MIRT2054833	hsa-miR-3647-5p	CLIP-seq
MIRT2054834	hsa-miR-3682-3p	CLIP-seq
MIRT2054835	hsa-miR-4670-3p	CLIP-seq
MIRT1189356	hsa-miR-4774-5p	CLIP-seq
MIRT2054836	hsa-miR-573	CLIP-seq
MIRT2283862	hsa-miR-3657	CLIP-seq
MIRT2283863	hsa-miR-3689a-5p	CLIP-seq
MIRT2283864	hsa-miR-3689b	CLIP-seq
MIRT2283865	hsa-miR-3689e	CLIP-seq
MIRT2283866	hsa-miR-3689f	CLIP-seq
MIRT2283867	hsa-miR-4503	CLIP-seq
MIRT2283868	hsa-miR-4669	CLIP-seq
MIRT1189348	hsa-miR-1303	CLIP-seq
MIRT1189349	hsa-miR-204	CLIP-seq
MIRT1189350	hsa-miR-211	CLIP-seq
MIRT2582049	hsa-miR-219-1-3p	CLIP-seq
MIRT2582050	hsa-miR-2964a-5p	CLIP-seq
MIRT1189351	hsa-miR-324-5p	CLIP-seq
MIRT2054832	hsa-miR-3616-5p	CLIP-seq
MIRT2054833	hsa-miR-3647-5p	CLIP-seq
MIRT2283862	hsa-miR-3657	CLIP-seq
MIRT1189352	hsa-miR-4292	CLIP-seq
MIRT1189353	hsa-miR-4308	CLIP-seq
MIRT2582051	hsa-miR-4464	CLIP-seq
MIRT2283867	hsa-miR-4503	CLIP-seq
MIRT2283868	hsa-miR-4669	CLIP-seq
MIRT2054835	hsa-miR-4670-3p	CLIP-seq
MIRT2582052	hsa-miR-4748	CLIP-seq
MIRT1189355	hsa-miR-4755-5p	CLIP-seq
MIRT1189356	hsa-miR-4774-5p	CLIP-seq
MIRT1189357	hsa-miR-4780	CLIP-seq
MIRT2582053	hsa-miR-4797-5p	CLIP-seq
MIRT2054836	hsa-miR-573	CLIP-seq
MIRT1189359	hsa-miR-623	CLIP-seq
MIRT1189348	hsa-miR-1303	CLIP-seq
MIRT1189349	hsa-miR-204	CLIP-seq
MIRT1189350	hsa-miR-211	CLIP-seq
MIRT1189351	hsa-miR-324-5p	CLIP-seq
MIRT2054832	hsa-miR-3616-5p	CLIP-seq
MIRT2054833	hsa-miR-3647-5p	CLIP-seq
MIRT2283862	hsa-miR-3657	CLIP-seq
MIRT1189352	hsa-miR-4292	CLIP-seq
MIRT1189353	hsa-miR-4308	CLIP-seq
MIRT2582051	hsa-miR-4464	CLIP-seq
MIRT2283867	hsa-miR-4503	CLIP-seq
MIRT2283868	hsa-miR-4669	CLIP-seq
MIRT2054835	hsa-miR-4670-3p	CLIP-seq
MIRT2582052	hsa-miR-4748	CLIP-seq
MIRT1189355	hsa-miR-4755-5p	CLIP-seq
MIRT1189356	hsa-miR-4774-5p	CLIP-seq
MIRT1189357	hsa-miR-4780	CLIP-seq
MIRT2054836	hsa-miR-573	CLIP-seq
MIRT1189359	hsa-miR-623	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0001094	Function	TFIID-class transcription factor complex binding	IPI	17636026
GO:0001650	Component	Fibrillar center	IDA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	17636026, 21522132, 30021884, 33367824, 33961781, 35271311
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IDA	16687569, 33367824
GO:0005730	Component	Nucleolus	IEA
GO:0005730	Component	Nucleolus	TAS	10925205
GO:0005732	Component	Sno(s)RNA-containing ribonucleoprotein complex	IDA	17636026
GO:0005829	Component	Cytosol	IDA
GO:0006364	Process	RRNA processing	TAS	10925205
GO:0015030	Component	Cajal body	IDA	16687569
GO:0016020	Component	Membrane	HDA	19946888
GO:0030515	Function	SnoRNA binding	IBA
GO:0030515	Function	SnoRNA binding	IDA	17636026
GO:0030515	Function	SnoRNA binding	IEA
GO:0031428	Component	Box C/D methylation guide snoRNP complex	IBA
GO:0031428	Component	Box C/D methylation guide snoRNP complex	IDA	33367824, 39570315
GO:0031428	Component	Box C/D methylation guide snoRNP complex	IEA
GO:0031428	Component	Box C/D methylation guide snoRNP complex	NAS	17636026
GO:0032040	Component	Small-subunit processome	IBA
GO:0032040	Component	Small-subunit processome	IDA	34516797
GO:0032040	Component	Small-subunit processome	IEA
GO:0042254	Process	Ribosome biogenesis	IEA
GO:0042274	Process	Ribosomal small subunit biogenesis	IDA	34516797
GO:0048254	Process	SnoRNA localization	IMP	17636026
GO:0051117	Function	ATPase binding	IPI	17636026
GO:0070761	Component	Pre-snoRNP complex	IDA	17636026
GO:1990904	Component	Ribonucleoprotein complex	IEA

MIM	HGNC	e!Ensembl
616742	29926	ENSG00000055044

Q9Y2X3

Protein name

Nucleolar protein 58 (Nucleolar protein 5)

Protein function

Required for the biogenesis of box C/D snoRNAs such as U3, U8 and U14 snoRNAs (PubMed:15574333, PubMed:17636026, PubMed:19620283, PubMed:34516797). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal sub

PDB

7MQ8 , 7MQ9 , 7MQA

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF08156	NOP5NT	2 → 66	NOP5NT (NUC127) domain	Domain
PF01798	Nop	168 → 397	snoRNA binding domain, fibrillarin	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous.

Sequence

MLVLFETSVGYAIFKVLNEKKLQEVDSLWKEFETPEKANKIVKLKHFEKFQDTAEALAAF
TALMEGKINKQLKKVLKKIVKEAHEPLAVADAKLGGVIKEKLNLSCIHSPVVNELMRGIR
SQMDGLIPGVEPREMAAMCLGLAHSLSRYRLKFSADKVDTMIVQAISLLDDLDKELNNYI
MRCREWYGWHFPELGKIISDNLTYCKCLQKVGDRKNYASAKLSELLPEEVEAEVKAAAEI
SMGTEVSEEDICNILHLCTQVIEISEYRTQLYEYLQNRMMAIAPNVTVMVGELVGARLIA
HAGSLLNLAKHAASTVQILGAEKALFRALKSRRDTPKYGLIYHASLVGQTSPKHKGKISR
MLAAKTVLAIRYDAFGEDSSSAMGVENRAKLEARLRTLEDRGIRKISGTGKALAKTEKYE
HKSEVKTYDPSGDSTLPTCSKKRKIEQVDKEDEITEKKAKKAKIKVKVEEEEEEKVAEEE
ETSVKKKKKRGKKKHIKEEPLSEEEPCTSTAIASPEKKKKKKKKRENED

Sequence length

529

Interactions

View interactions

	KEGG		Reactome
	Ribosome biogenesis in eukaryotes		SUMOylation of RNA binding proteins Major pathway of rRNA processing in the nucleolus and cytosol

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CORONARY ARTERY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (2)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Carcinoma Hepatocellular	Associate	33750838, 37891494	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	35088879	★★★★★ ★☆☆☆☆ Found in Text Mining only

NOP58 (NOP58 ribonucleoprotein)