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    NOP56 NOP56 ribonucleoprotein [ Homo sapiens (human) ]

    Gene ID: 10528, updated on 4-Feb-2024

    Summary

    Official Symbol
    NOP56provided by HGNC
    Official Full Name
    NOP56 ribonucleoproteinprovided by HGNC
    Primary source
    HGNC:HGNC:15911
    See related
    Ensembl:ENSG00000101361 MIM:614154; AllianceGenome:HGNC:15911
    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
    NEW
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    Genomic context

    See NOP56 in Genome Data Viewer
    Location:
    20p13
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (2652632..2658393)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (2683093..2688860)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (2633278..2639039)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372504 Neighboring gene transmembrane channel like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2538685-2539395 Neighboring gene uncharacterized LOC105372505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12604 Neighboring gene NOP56 ribonucleoprotein repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2636106-2636623 Neighboring gene MPRA-validated peak4124 silencer Neighboring gene small nucleolar RNA, C/D box 110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2643139-2643926 Neighboring gene microRNA 1292 Neighboring gene small nucleolar RNA, H/ACA box 51 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2645500-2646285 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 (NAD(+)) 3 non-catalytic subunit beta Neighboring gene IDH3B divergent transcript

    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 Apr 4 07:08:55 2018

    Bibliography

    Related articles in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

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

    NEW Try the new Transcript table

    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
      5101..10862
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_006392.4NP_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, BC104793, DA805367
      Consensus CDS
      CCDS13030.1
      UniProtKB/Swiss-Prot
      O00567, Q2M3T6, Q9NQ05
      UniProtKB/TrEMBL
      A8K9K6
      Related
      ENSP00000370589.3, ENST00000329276.10
      Conserved Domains (2) summary
      COG1498
      Location:48412
      SIK1; RNA processing factor Prp31, contains Nop domain [Translation, ribosomal structure and biogenesis]
      pfam08156
      Location:570
      NOP5NT; NOP5NT (NUC127) domain

    RNA

    1. NR_027700.3 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
    2. NR_145428.2 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, BC104793, CN371696, DA805367

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      2652632..2658393
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      2683093..2688860
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)