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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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