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Nop56 NOP56 ribonucleoprotein [ Mus musculus (house mouse) ]

Gene ID: 67134, updated on 11-Apr-2024

Summary

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 act upstream of or within ribosome biogenesis. Predicted to be located in fibrillar center. Predicted to be part of box C/D RNP 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, Apr 2022]
Expression
Broad expression in CNS E11.5 (RPKM 75.9), liver E14 (RPKM 61.1) and 23 other tissues See more
Orthologs
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Genomic context

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

Expression

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

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

General protein information

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_024193.2NP_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:168219
    NOSIC; NOSIC (NUC001) domain
    COG1498
    Location:48416
    SIK1; RNA processing factor Prp31, contains Nop domain [Translation, ribosomal structure and biogenesis]
    pfam08156
    Location:570
    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_006500062.2XP_006500125.1  nucleolar protein 56 isoform X1

    UniProtKB/TrEMBL
    Q3USZ5
    Conserved Domains (2) summary
    COG1498
    Location:48416
    SIK1; RNA processing factor Prp31, contains Nop domain [Translation, ribosomal structure and biogenesis]
    pfam08156
    Location:570
    NOP5NT; NOP5NT (NUC127) domain

RNA

  1. XR_374509.3 RNA Sequence

  2. XR_866335.3 RNA Sequence