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Nup54 nucleoporin 54 [ Mus musculus (house mouse) ]

Gene ID: 269113, updated on 5-Mar-2024

Summary

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Official Symbol
Nup54provided by MGI
Official Full Name
nucleoporin 54provided by MGI
Primary source
MGI:MGI:1920460
See related
Ensembl:ENSMUSG00000034826 AllianceGenome:MGI:1920460
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
54kDa; 3110079L04Rik
Summary
Predicted to enable identical protein binding activity. Predicted to be a structural constituent of nuclear pore. Predicted to be involved in several processes, including nuclear pore organization; protein localization to nucleus; and regulation of protein import into nucleus. Predicted to act upstream of or within mRNA transport and protein transport. Predicted to be located in nuclear envelope. Predicted to be part of nuclear pore central transport channel. Is expressed in pancreas epithelium. Orthologous to human NUP54 (nucleoporin 54). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 10.3), CNS E14 (RPKM 9.8) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
5 E2; 5 46.75 cM
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (92563399..92583117, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (92415540..92435259, complement)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene ADP-ribosyltransferase 3 Neighboring gene STARR-positive B cell enhancer ABC_E6346 Neighboring gene chemokine (C-X-C motif) ligand 11 Neighboring gene STARR-positive B cell enhancer ABC_E4766 Neighboring gene CWF19-like 1, cell cycle control pseudogene Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:92864208-92864361 Neighboring gene predicted gene, 42114 Neighboring gene scavenger receptor class B, member 2 Neighboring gene microRNA 6415 Neighboring gene STARR-seq mESC enhancer starr_13641 Neighboring gene STARR-seq mESC enhancer starr_13643 Neighboring gene STARR-positive B cell enhancer ABC_E10330 Neighboring gene family with sequence similarity 47, member E Neighboring gene STARR-seq mESC enhancer starr_13648

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

Bibliography

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Related articles in PubMed

  1. Peering through the pore: nuclear pore complex structure, assembly, and function. Suntharalingam M, et al. Dev Cell, 2003 Jun. PMID 12791264
  2. The sperm-associated antigen 6 interactome and its role in spermatogenesis. Liu Y, et al. Reproduction, 2019 Aug. PMID 31146259, Free PMC Article
  3. Identification of transcripts with enriched expression in the developing and adult pancreas. Hoffman BG, et al. Genome Biol, 2008. PMID 18554416, Free PMC Article
  4. A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Hansen J, et al. Proc Natl Acad Sci U S A, 2003 Aug 19. PMID 12904583, Free PMC Article
  5. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Stryke D, et al. Nucleic Acids Res, 2003 Jan 1. PMID 12520002, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

Pathways from PubChem

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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 MGI

Function Evidence Code Pubs
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
  
enables structural constituent of nuclear pore IBA
Inferred from Biological aspect of Ancestor
more info
  
enables structural constituent of nuclear pore ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in NLS-bearing protein import into nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within mRNA transport IEA
Inferred from Electronic Annotation
more info
  
involved_in nuclear pore organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nucleocytoplasmic transport ISO
Inferred from Sequence Orthology
more info
  
involved_in nucleocytoplasmic transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in protein localization to nuclear inner membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein targeting ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of protein import into nucleus ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear envelope ISO
Inferred from Sequence Orthology
more info
  
part_of nuclear pore ISO
Inferred from Sequence Orthology
more info
  
part_of nuclear pore NAS
Non-traceable Author Statement
more info
 PubMed 
part_of nuclear pore central transport channel IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of protein-containing complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
nuclear pore complex protein Nup54
Names
54 kDa nucleoporin
nucleoporin 54kDa
nucleoporin Nup54

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_001359995.1 → NP_001346924.1  nuclear pore complex protein Nup54 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC122365
    Conserved Domains (1) summary
    pfam13874
    Location:359 → 494
    Nup54; Nucleoporin complex subunit 54

  2. NM_183392.2 → NP_899248.1  nuclear pore complex protein Nup54 isoform 2

    See identical proteins and their annotated locations for NP_899248.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AK133841, BQ032638, CJ049542
    Consensus CDS
    CCDS19430.1
    UniProtKB/Swiss-Prot
    Q3TSI2, Q8BTS4, Q8BU42
    Related
    ENSMUSP00000046540.9, ENSMUST00000038514.15
    Conserved Domains (1) summary
    pfam13874
    Location:305 → 440
    Nup54; Nucleoporin complex subunit 54

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_000071.7 Reference GRCm39 C57BL/6J

    Range
    92563399..92583117 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006534959.5 → XP_006535022.1  nuclear pore complex protein Nup54 isoform X2

    Conserved Domains (2) summary
    pfam13874
    Location:106 → 243
    Nup54; Nucleoporin complex subunit 54
    pfam18437
    Location:259 → 297
    Nup54_C; Nup54 C-terminal interacting domain

  2. XM_017320895.3 → XP_017176384.1  nuclear pore complex protein Nup54 isoform X2

    Conserved Domains (2) summary
    pfam13874
    Location:106 → 243
    Nup54; Nucleoporin complex subunit 54
    pfam18437
    Location:259 → 297
    Nup54_C; Nup54 C-terminal interacting domain

  3. XM_006534958.5 → XP_006535021.1  nuclear pore complex protein Nup54 isoform X1

    Conserved Domains (2) summary
    pfam13874
    Location:120 → 257
    Nup54; Nucleoporin complex subunit 54
    pfam18437
    Location:273 → 311
    Nup54_C; Nup54 C-terminal interacting domain

  4. XM_030254531.2 → XP_030110391.1  nuclear pore complex protein Nup54 isoform X1

    Conserved Domains (2) summary
    pfam13874
    Location:120 → 257
    Nup54; Nucleoporin complex subunit 54
    pfam18437
    Location:273 → 311
    Nup54_C; Nup54 C-terminal interacting domain

RNA

  1. XR_004942520.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8BTS4.1 GenPept UniProtKB/Swiss-Prot:Q8BTS4

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