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    Nop56 NOP56 ribonucleoprotein [ Mus musculus (house mouse) ]

    Gene ID: 67134, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Nop56provided by MGI
    Official Full Name
    NOP56 ribonucleoproteinprovided by MGI
    Primary source
    MGI:MGI:1914384
    See related
    Ensembl:ENSMUSG00000027405 AllianceGenome:MGI:1914384
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Nol5a; 2310044F10Rik
    Summary
    Enables RNA binding activity. Predicted to be involved in ribosomal small subunit biogenesis. Predicted to be located in fibrillar center. Predicted to be part of box C/D methylation guide snoRNP complex; pre-snoRNP complex; and small-subunit processome. Is expressed in alimentary system; central nervous system; liver; metanephros; and retina nuclear layer. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 36. Orthologous to human NOP56 (NOP56 ribonucleoprotein). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in CNS E11.5 (RPKM 75.9), liver E14 (RPKM 61.1) and 23 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Nop56 in Genome Data Viewer
    Location:
    2 F1; 2 63.2 cM
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (130112904..130121233)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (130274367..130279313)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E2047 Neighboring gene small nuclear ribonucleoprotein B Neighboring gene transmembrane channel-like gene family 2 Neighboring gene STARR-seq mESC enhancer starr_05689 Neighboring gene STARR-seq mESC enhancer starr_05690 Neighboring gene STARR-positive B cell enhancer ABC_E643 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:130100530-130100713 Neighboring gene STARR-positive B cell enhancer ABC_E3405 Neighboring gene small nucleolar RNA, C/D box 110 Neighboring gene STARR-seq mESC enhancer starr_05691 Neighboring gene predicted gene, 24451 Neighboring gene predicted gene, 23187 Neighboring gene predicted gene, 23650 Neighboring gene small nucleolar RNA, C/D box 57 Neighboring gene isocitrate dehydrogenase 3 (NAD+) beta Neighboring gene early B cell factor 4 Neighboring gene predicted gene, 39936 Neighboring gene ribosomal protein L27A pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Early and selective reduction of NOP56 (Asidan) and RNA processing proteins in the motor neuron of ALS model mice. Miyazaki K, et al. Neurol Res, 2013 Sep. PMID 23582672
    2. Box C/D small nucleolar RNA (snoRNA) U60 regulates intracellular cholesterol trafficking. Brandis KA, et al. J Biol Chem, 2013 Dec 13. PMID 24174535, Free PMC Article
    3. Friend of Prmt1, a novel chromatin target of protein arginine methyltransferases. van Dijk TB, et al. Mol Cell Biol, 2010 Jan. PMID 19858291, Free PMC Article
    4. LARP7-Mediated U6 snRNA Modification Ensures Splicing Fidelity and Spermatogenesis in Mice. Wang X, et al. Mol Cell, 2020 Mar 5. PMID 32017896
    5. Nmyc plays an essential role during lung development as a dosage-sensitive regulator of progenitor cell proliferation and differentiation. Okubo T, et al. Development, 2005 Mar. PMID 15716345

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables histone methyltransferase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone methyltransferase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables snoRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables snoRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables snoRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in ribosomal small subunit biogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ribosomal small subunit biogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of box C/D methylation guide snoRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of box C/D methylation guide snoRNP complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of pre-snoRNP complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of pre-snoRNP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of small-subunit processome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of small-subunit processome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of small-subunit processome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of sno(s)RNA-containing ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_024193.2 → NP_077155.2  nucleolar protein 56

      See identical proteins and their annotated locations for NP_077155.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the protein-coding transcript.
      Source sequence(s)
      AI115137, AK150258, CJ162437
      Consensus CDS
      CCDS16737.1
      UniProtKB/Swiss-Prot
      Q3UD45, Q8BVL1, Q8VDT2, Q99LT8, Q9CT15, Q9D6Z1
      UniProtKB/TrEMBL
      Q3USZ5
      Related
      ENSMUSP00000099487.5, ENSMUST00000103198.11
      Conserved Domains (3) summary
      smart00931
      Location:168 → 219
      NOSIC; NOSIC (NUC001) domain
      COG1498
      Location:48 → 416
      SIK1; RNA processing factor Prp31, contains Nop domain [Translation, ribosomal structure and biogenesis]
      pfam08156
      Location:5 → 70
      NOP5NT; NOP5NT (NUC127) domain

    RNA

    1. NR_149733.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL833804

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      130112904..130121233
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006500062.2 → XP_006500125.1  nucleolar protein 56 isoform X1

      UniProtKB/TrEMBL
      Q3USZ5
      Conserved Domains (2) summary
      COG1498
      Location:48 → 416
      SIK1; RNA processing factor Prp31, contains Nop domain [Translation, ribosomal structure and biogenesis]
      pfam08156
      Location:5 → 70
      NOP5NT; NOP5NT (NUC127) domain

    RNA

    1. XR_374509.3 RNA Sequence

    2. XR_866335.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9D6Z1.2 GenPept UniProtKB/Swiss-Prot:Q9D6Z1

    Gene LinkOut

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