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NOP56 NOP56 ribonucleoprotein [ Homo sapiens (human) ]

Gene ID: 10528, updated on 12-Aug-2018

Summary

Official Symbol
NOP56provided by HGNC
Official Full Name
NOP56 ribonucleoproteinprovided by HGNC
Primary source
HGNC:HGNC:15911
See related
Ensembl:ENSG00000101361 MIM:614154; Vega:OTTHUMG00000031703
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NOL5A; SCA36
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 similar in sequence to Nop56p and is also found in the nucleolus. Expansion of a GGCCTG repeat from 3-8 copies to 1500-2500 copies in an intron of this gene results in spinocerebellar ataxia 36. Multiple transcript variants encoding several different isoforms have been found for this gene, but the full-length nature of most of them has not been determined. [provided by RefSeq, Jul 2016]
Expression
Ubiquitous expression in lymph node (RPKM 34.3), appendix (RPKM 31.9) and 25 other tissues See more
Orthologs

Genomic context

See NOP56 in Genome Data Viewer
Location:
20p13
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 20 NC_000020.11 (2652532..2658393)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (2633178..2639039)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372504 Neighboring gene transmembrane channel like 2 Neighboring gene uncharacterized LOC105372505 Neighboring gene NOP56 ribonucleoprotein repeat instability region Neighboring gene small nucleolar RNA, C/D box 110 Neighboring gene uncharacterized LOC105372507 Neighboring gene microRNA 1292 Neighboring gene small nucleolar RNA, H/ACA box 51 Neighboring gene small nucleolar RNA, C/D box 86 Neighboring gene small nucleolar RNA, C/D box 56 Neighboring gene small nucleolar RNA, C/D box 57 Neighboring gene isocitrate dehydrogenase 3 (NAD(+)) beta Neighboring gene uncharacterized LOC105372506 Neighboring gene early B cell factor 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Association of TriC/CCT with target proteins during biosynthesis, organism-specific biosystem (from REACTOME)
    Association of TriC/CCT with target proteins during biosynthesis, organism-specific biosystemTRiC has broad recognition specificities, but in the cell it interacts with only a defined set of substrates (Yam et al. 2008). Many of its substrates that are targeted during biosynthesis are conse...
  • Chaperonin-mediated protein folding, organism-specific biosystem (from REACTOME)
    Chaperonin-mediated protein folding, organism-specific biosystemThe eukaryotic chaperonin TCP-1 ring complex (TRiC/ CCT) plays an essential role in the folding of a subset of proteins prominent among which are the actins and tubulins (reviewed in Altschuler and...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystem (from REACTOME)
    Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystemIn humans, a 47S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I from rRNA-encoding genes (rDNA) at the boundary of the fibrillar center and the dense fibrillar components of the nucleol...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Protein folding, organism-specific biosystem (from REACTOME)
    Protein folding, organism-specific biosystemDue to the crowded envirnoment within the cell, many proteins must interact with molecular chaperones to attain their native conformation (reviewed in Young et al., 2004). Chaperones recognize and...
  • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • rRNA modification in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA modification in the nucleus and cytosol, organism-specific biosystemHuman ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Herna...
  • rRNA processing, organism-specific biosystem (from REACTOME)
    rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
  • rRNA processing in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA processing in the nucleus and cytosol, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
cadherin binding HDA PubMed 
histone methyltransferase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
snoRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
snoRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
rRNA processing TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
box C/D snoRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
box C/D snoRNP complex NAS
Non-traceable Author Statement
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
fibrillar center IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
nucleolus TAS
Traceable Author Statement
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
pre-snoRNP complex IDA
Inferred from Direct Assay
more info
PubMed 
small nucleolar ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
small-subunit processome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
nucleolar protein 56
Names
NOP56 ribonucleoprotein homolog
nucleolar protein 5A (56kDa with KKE/D repeat)

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_032136.1 RefSeqGene

    Range
    5001..10862
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_006392.3NP_006383.2  nucleolar protein 56

    See identical proteins and their annotated locations for NP_006383.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the protein-coding transcript.
    Source sequence(s)
    BC035369, BC104791, BC104793, DA805367
    Consensus CDS
    CCDS13030.1
    UniProtKB/Swiss-Prot
    O00567
    Related
    ENSP00000370589.3, OTTHUMP00000030035, ENST00000329276.9, OTTHUMT00000077631
    Conserved Domains (3) summary
    smart00931
    Location:168219
    NOSIC; NOSIC (NUC001) domain
    pfam01798
    Location:174405
    Nop; snoRNA binding domain, fibrillarin
    pfam08156
    Location:570
    NOP5NT; NOP5NT (NUC127) domain

RNA

  1. NR_027700.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice junction compared to variant 1. The extra sequence introduces an in-frame stop codon that makes this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK292721, BC004937, BC104791, CV338938, DA805367
  2. NR_145428.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate internal exon compared to variant 1. The extra sequence introduces an in-frame stop codon that makes this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC035369, BC104791, BC104793, CN371696, DA805367

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p12 Primary Assembly

    Range
    2652532..2658393
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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