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    nop56 NOP56 ribonucleoprotein homolog [ Danio rerio (zebrafish) ]

    Gene ID: 394196, updated on 9-Dec-2024

    Summary

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    Official Symbol
    nop56provided by ZNC
    Official Full Name
    NOP56 ribonucleoprotein homologprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040109-1
    See related
    Ensembl:ENSDARG00000012820 AllianceGenome:ZFIN:ZDB-GENE-040109-1
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    nol5a
    Summary
    Predicted to enable snoRNA binding activity. Acts upstream of or within several processes, including central nervous system development; swimming behavior; and thigmotaxis. Predicted to be located in nucleolus. Predicted to be part of box C/D methylation guide snoRNP complex and small-subunit processome. Is expressed in head and midbrain. 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]
    Orthologs
    human mouse all
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    Genomic context

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    See nop56 in Genome Data Viewer
    Location:
    chromosome: 21
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 21 NC_007132.7 (11958581..11970242, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 21 NC_007132.6 (11865953..11877614, complement)

    Chromosome 21 - NC_007132.7Genomic Context describing neighboring genes Neighboring gene DDB1 and CUL4 associated factor 12 Neighboring gene ubiquitin associated protein 2a Neighboring gene small nucleolar RNA SNORD57 Neighboring gene motilin-like Neighboring gene zgc:64106 Neighboring gene aquaporin 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. CRISPR/Cas9-mediated precise genome modification by a long ssDNA template in zebrafish. Bai H, et al. BMC Genomics, 2020 Jan 21. PMID 31964350, Free PMC Article
    2. A nop56 Zebrafish Loss-of-Function Model Exhibits a Severe Neurodegenerative Phenotype. Quelle-Regaldie A, et al. Biomedicines, 2022 Jul 28. PMID 36009362, Free PMC Article
    3. Drug-sensitized zebrafish screen identifies multiple genes, including GINS3, as regulators of myocardial repolarization. Milan DJ, et al. Circulation, 2009 Aug 18. PMID 19652097, Free PMC Article
    4. Nucleolar Protein 56 Deficiency in Zebrafish Leads to Developmental Abnormalities and Anemia via p53 and JAK2-STAT3 Signaling. Liang F, et al. Biology (Basel), 2023 Mar 31. PMID 37106740, Free PMC Article
    5. Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis. Recher G, et al. Development, 2013 Dec. PMID 24198278

    See all (14) 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 ZFIN

    Function Evidence Code Pubs
    enables snoRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables snoRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within central nervous system formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cerebellum development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within rRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of motor neuron axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of neuromuscular junction development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within swimming behavior IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within thigmotaxis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus 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 IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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

    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_001309383.1 → NP_001296312.1  nucleolar protein 56 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses two alternate splice sites and lacks an alternate exon in the 5' coding region, compared to variant 1. These differences result in translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      CT027620, EH447336, EH473181
      UniProtKB/TrEMBL
      A0A8M1P758
      Conserved Domains (1) summary
      pfam01798
      Location:52 → 224
      Nop; snoRNA binding domain, fibrillarin

    2. NM_201217.2 → NP_957511.2  nucleolar protein 56 isoform 1

      See identical proteins and their annotated locations for NP_957511.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      CT027620, EH447336, EH473181
      UniProtKB/TrEMBL
      A0A8M1PCD0, Q6DRE5
      Related
      ENSDARP00000099474.3, ENSDART00000114524.5
      Conserved Domains (3) summary
      smart00931
      Location:169 → 220
      NOSIC; NOSIC (NUC001) domain
      COG1498
      Location:47 → 414
      SIK1; RNA processing factor Prp31, contains Nop domain [Translation, ribosomal structure and biogenesis]
      pfam08156
      Location:5 → 70
      NOP5NT; NOP5NT (NUC127) domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007132.7 Reference GRCz11 Primary Assembly

      Range
      11958581..11970242 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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