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    nup54 nucleoporin 54 [ Danio rerio (zebrafish) ]

    Gene ID: 335750, updated on 9-Dec-2024

    Summary

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    Official Symbol
    nup54provided by ZNC
    Official Full Name
    nucleoporin 54provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-2263
    See related
    AllianceGenome:ZFIN:ZDB-GENE-040426-2263
    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
    zgc:77551; wu:fp63g06
    Summary
    Acts upstream of or within several processes, including digestive system development; dorsal/ventral pattern formation; and liver development. Predicted to be located in nucleus. Predicted to be part of nuclear pore. Is expressed in ovary. Human ortholog(s) of this gene implicated in dystonia 37, early-onset with striatal lesions. Orthologous to human NUP54 (nucleoporin 54). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See nup54 in Genome Data Viewer
    Location:
    chromosome: 21
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 21 NC_007132.7 (214575..226080, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 21 NC_007132.6 (193569..204619, complement)

    Chromosome 21 - NC_007132.7Genomic Context describing neighboring genes Neighboring gene gonadal somatic cell derived factor Neighboring gene serine/threonine-protein phosphatase with EF-hands 2 Neighboring gene brix domain containing 2 Neighboring gene DTW domain containing 2 Neighboring gene StAR related lipid transfer domain containing 4

    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. The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes. Gautier A, et al. Gene, 2011 Feb 1. PMID 21047546
    2. Nucleoporin 62-like protein activates canonical Wnt signaling through facilitating the nuclear import of β-catenin in zebrafish. Yang X, et al. Mol Cell Biol, 2015 Apr. PMID 25605329, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    acts_upstream_of_or_within digestive tract development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within dorsal/ventral pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within exocrine pancreas 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 liver development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of nuclear pore IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    nucleoporin p54

    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_001430811.1 → NP_001417740.1  nucleoporin p54

      Status: VALIDATED

      Source sequence(s)
      CU856510, CZQB01146713
      UniProtKB/TrEMBL
      A0A8M9PCH4

    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
      214575..226080 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021468770.2 → XP_021324445.1  nucleoporin p54 isoform X12

      UniProtKB/TrEMBL
      A0A8M9PTQ0
      Conserved Domains (2) summary
      pfam13634
      Location:5 → 113
      Nucleoporin_FG; Nucleoporin FG repeat region
      pfam13874
      Location:308 → 443
      Nup54; Nucleoporin complex subunit 54

    2. XM_021468769.2 → XP_021324444.1  nucleoporin p54 isoform X11

      UniProtKB/TrEMBL
      A0A8M9PI50
      Conserved Domains (2) summary
      pfam13634
      Location:5 → 114
      Nucleoporin_FG; Nucleoporin FG repeat region
      pfam13874
      Location:309 → 444
      Nup54; Nucleoporin complex subunit 54

    3. XM_021468762.2 → XP_021324437.1  nucleoporin p54 isoform X5

      UniProtKB/TrEMBL
      A0A8M9P371
      Conserved Domains (2) summary
      pfam13874
      Location:352 → 487
      Nup54; Nucleoporin complex subunit 54
      cl25599
      Location:3 → 131
      Nucleoporin_FG2; Nucleoporin FG repeated region

    4. XM_021468768.2 → XP_021324443.1  nucleoporin p54 isoform X10

      UniProtKB/TrEMBL
      A0A8M9PCH8
      Conserved Domains (2) summary
      pfam13634
      Location:5 → 116
      Nucleoporin_FG; Nucleoporin FG repeat region
      pfam13874
      Location:311 → 446
      Nup54; Nucleoporin complex subunit 54

    5. XM_021468767.2 → XP_021324442.1  nucleoporin p54 isoform X9

      UniProtKB/TrEMBL
      A0A8M9P373
      Conserved Domains (2) summary
      pfam13634
      Location:5 → 117
      Nucleoporin_FG; Nucleoporin FG repeat region
      pfam13874
      Location:312 → 447
      Nup54; Nucleoporin complex subunit 54

    6. XM_021468761.2 → XP_021324436.1  nucleoporin p54 isoform X4

      UniProtKB/TrEMBL
      A0A8M9PQ95
      Conserved Domains (2) summary
      pfam13874
      Location:355 → 490
      Nup54; Nucleoporin complex subunit 54
      cl25599
      Location:3 → 134
      Nucleoporin_FG2; Nucleoporin FG repeated region

    7. XM_021468766.2 → XP_021324441.1  nucleoporin p54 isoform X8

      UniProtKB/TrEMBL
      A0A8M9PQA0
      Conserved Domains (1) summary
      pfam13874
      Location:339 → 474
      Nup54; Nucleoporin complex subunit 54

    8. XM_021468765.2 → XP_021324440.1  nucleoporin p54 isoform X7

      UniProtKB/TrEMBL
      A0A8M9PTP5
      Conserved Domains (1) summary
      pfam13874
      Location:340 → 475
      Nup54; Nucleoporin complex subunit 54

    9. XM_021468760.2 → XP_021324435.1  nucleoporin p54 isoform X3

      UniProtKB/TrEMBL
      A0A8M9PTP0
      Conserved Domains (1) summary
      pfam13874
      Location:383 → 518
      Nup54; Nucleoporin complex subunit 54

    10. XM_021468764.2 → XP_021324439.1  nucleoporin p54 isoform X6

      UniProtKB/TrEMBL
      A0A8M9PI46
      Conserved Domains (1) summary
      pfam13874
      Location:342 → 477
      Nup54; Nucleoporin complex subunit 54

    11. XM_021468759.2 → XP_021324434.1  nucleoporin p54 isoform X2

      UniProtKB/TrEMBL
      A0A8M9PI41
      Conserved Domains (1) summary
      pfam13874
      Location:385 → 520
      Nup54; Nucleoporin complex subunit 54

    12. XM_021468758.2 → XP_021324433.1  nucleoporin p54 isoform X1

      UniProtKB/TrEMBL
      A0A8M9PCH0
      Conserved Domains (1) summary
      pfam13874
      Location:386 → 521
      Nup54; Nucleoporin complex subunit 54

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001001948.1: Suppressed sequence

      Description
      NM_001001948.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein Strain
    Heading Accession and Version

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