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nup54 nucleoporin 54 [ Danio rerio (zebrafish) ]

Gene ID: 335750, updated on 4-Jan-2025

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, Jan 2025]
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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