NOP56 (NOP56 ribonucleoprotein)

Gene

• Entrez ID: 10528
• Gene name: NOP56 ribonucleoprotein
• Gene symbol: NOP56
• Synonyms (NCBI Gene): NOL5A, SCA36
• Chromosome: 20
• Chromosome location: 20p13
• Summary: Nop56p is a yeast nucleolar protein that is part of a complex with the nucleolar proteins Nop58p and fibrillarin. Nop56p is required for assembly of the 60S ribosomal subunit and is involved in pre-rRNA processing. The protein encoded by this gene is simi

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT030362	hsa-miR-24-3p	Microarray	19748357
MIRT049889	hsa-miR-31-5p	CLASH	23622248
MIRT1189335	hsa-miR-1257	CLIP-seq
MIRT1189336	hsa-miR-1587	CLIP-seq
MIRT1189337	hsa-miR-2110	CLIP-seq
MIRT1189338	hsa-miR-3150a-3p	CLIP-seq
MIRT1189339	hsa-miR-3153	CLIP-seq
MIRT1189340	hsa-miR-3189-3p	CLIP-seq
MIRT1189341	hsa-miR-3611	CLIP-seq
MIRT1189342	hsa-miR-4271	CLIP-seq
MIRT1189343	hsa-miR-4668-5p	CLIP-seq
MIRT1189344	hsa-miR-4674	CLIP-seq
MIRT1189345	hsa-miR-4725-3p	CLIP-seq
MIRT1189346	hsa-miR-581	CLIP-seq
MIRT1189347	hsa-miR-635	CLIP-seq
MIRT2283857	hsa-miR-1224-3p	CLIP-seq
MIRT1189336	hsa-miR-1587	CLIP-seq
MIRT2283858	hsa-miR-3123	CLIP-seq
MIRT1189340	hsa-miR-3189-3p	CLIP-seq
MIRT2283859	hsa-miR-3189-5p	CLIP-seq
MIRT2283860	hsa-miR-3919	CLIP-seq
MIRT1189344	hsa-miR-4674	CLIP-seq
MIRT2283861	hsa-miR-4758-3p	CLIP-seq
MIRT1189347	hsa-miR-635	CLIP-seq
MIRT2283857	hsa-miR-1224-3p	CLIP-seq
MIRT1189336	hsa-miR-1587	CLIP-seq
MIRT2283858	hsa-miR-3123	CLIP-seq
MIRT1189340	hsa-miR-3189-3p	CLIP-seq
MIRT2283859	hsa-miR-3189-5p	CLIP-seq
MIRT2283860	hsa-miR-3919	CLIP-seq
MIRT1189344	hsa-miR-4674	CLIP-seq
MIRT2283861	hsa-miR-4758-3p	CLIP-seq
MIRT1189347	hsa-miR-635	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001650	Component	Fibrillar center	IDA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0003723	Function	RNA binding	TAS	9372940
GO:0005515	Function	Protein binding	IPI	17636026, 30021884, 32296183, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IEA
GO:0005730	Component	Nucleolus	TAS	9372940
GO:0005732	Component	Sno(s)RNA-containing ribonucleoprotein complex	IDA	17636026
GO:0005737	Component	Cytoplasm	IEA
GO:0006364	Process	RRNA processing	TAS	9372940
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	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:0045296	Function	Cadherin binding	HDA	25468996
GO:0070761	Component	Pre-snoRNP complex	IDA	17636026
GO:1990226	Function	Histone methyltransferase binding	IPI	17636026
GO:1990904	Component	Ribonucleoprotein complex	IEA

Other IDs

• MIM: 614154
• HGNC: 15911
• e!Ensembl: ENSG00000101361

Protein

• UniProt ID: O00567
• Protein name: Nucleolar protein 56 (Nucleolar protein 5A)
• Protein function: Involved in the early to middle stages of 60S ribosomal subunit biogenesis. Required for the biogenesis of box C/D snoRNAs such U3, U8 and U14 snoRNAs (PubMed:12777385, PubMed:15574333). Part of the small subunit (SSU) processome, first precurso
• PDB: 7MQ8, 7MQ9, 7MQA
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08156	NOP5NT	5 → 70	NOP5NT (NUC127) domain	Domain
  PF01798	Nop	174 → 407	snoRNA binding domain, fibrillarin	Family

• Sequence:

  MVLLHVLFEHAVGYALLALKEVEEISLLQPQVEESVLNLGKFHSIVRLVAFCPFASSQVA
  LENANAVSEGVVHEDLRLLLETHLPSKKKKVLLGVGDPKIGAAIQEELGYNCQTGGVIAE
  ILRGVRLHFHNLVKGLTDLSACKAQLGLGHSYSRAKVKFNVNRVDNMIIQSISLLDQLDK
  DINTFSMRVREWYGYHFPELVKIINDNATYCRLAQFIGNRRELNEDKLEKLEELTMDGAK
  AKAILDASRSSMGMDISAIDLINIESFSSRVVSLSEYRQSLHTYLRSKMSQVAPSLSALI
  GEAVGARLIAHAGSLTNLAKYPASTVQILGAEKALFRALKTRGNTPKYGLIFHSTFIGRA
  AAKNKGRISRYLANKCSIASRIDCFSEVPTSVFGEKLREQVEERLSFYETGEIPRKNLDV
  MKEAMVQAEEAAAEITRKLEKQEKKRLKKEKKRLAALALASSENSSSTPEECEEMSEKPK
  KKKKQKPQEVPQENGMEDPSISFSKPKKKKSFSKEELMSSDLEETAGSTSIPKRKKSTPK
  EETVNDPEEAGHRSGSKKKRKFSKEEPVSSGPEEAVGKSSSKKKKKFHKASQED

• Sequence length: 594

Pathways

KEGG:

Ribosome biogenesis in eukaryotes
Spinocerebellar ataxia

Reactome:

Major pathway of rRNA processing in the nucleolus and cytosol

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Spinocerebellar ataxia type 36	Likely pathogenic; Pathogenic	rs1295942947, rs1555779353	RCV001849220 RCV000024102

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Cerebellar ataxia	Uncertain significance	rs1360494485	RCV000626898
Mild global developmental delay	Uncertain significance	rs1360494485	RCV000626898
NOP56-related disorder	Uncertain significance; Likely benign; Benign	rs2514743642, rs200308757, rs542648737, rs547494052, rs34450120, rs61739391, rs140030798, rs144743768, rs745419060, rs74685243, rs151080095	RCV003399984 RCV003904551 RCV003942029 RCV003934581 RCV003917240 RCV003919411 RCV003941510 RCV003943826 RCV003947222 RCV003932182 RCV003936772
Uveal melanoma	Benign	rs542648737	RCV005871413

Associations from Text Mining
Disease Name	Relationship Type	References
Ataxia	Associate	22492559
Atherosclerosis	Associate	29685964
Carcinoma Hepatocellular	Associate	33750838, 34257558
Carcinoma Renal Cell	Associate	29099775
Colorectal Neoplasms	Associate	20473941
Macular Degeneration	Associate	30946360
Mandibulofacial Dysostosis	Associate	12777385
Neoplasms	Associate	34257558
Neuromuscular Diseases	Associate	24269018
Precursor B Cell Lymphoblastic Leukemia Lymphoma	Associate	32011831
Spinocerebellar Ataxias	Stimulate	21683323, 40004498
Spinocerebellar Ataxias	Associate	22492559