U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Nup54 nucleoporin 54 [ Mus musculus (house mouse) ]

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

    Summary

    Go to the top of the page Help
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Alleles

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

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    nuclear pore complex protein Nup54
    Names
    54 kDa nucleoporin
    nucleoporin 54kDa
    nucleoporin Nup54

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous