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NUP54 nucleoporin 54 [ Homo sapiens (human) ]

Gene ID: 53371, updated on 6-Nov-2022

Summary

Official Symbol
NUP54provided by HGNC
Official Full Name
nucleoporin 54provided by HGNC
Primary source
HGNC:HGNC:17359
See related
Ensembl:ENSG00000138750 MIM:607607; AllianceGenome:HGNC:17359
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013]
Expression
Ubiquitous expression in bone marrow (RPKM 12.3), testis (RPKM 11.6) and 25 other tissues See more
Orthologs
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Genomic context

See NUP54 in Genome Data Viewer
Location:
4q21.1
Exon count:
14
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (76114664..76148397, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (79455330..79489069, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (77035817..77069550, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ADP-ribosyltransferase 3 (inactive) Neighboring gene ribosomal protein L36 pseudogene 8 Neighboring gene C-X-C motif chemokine ligand 11 Neighboring gene uncharacterized LOC124900718 Neighboring gene scavenger receptor class B member 2 Neighboring gene family with sequence similarity 47 member E Neighboring gene uncharacterized LOC105377286

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr binds to nucleoporin p54 in vitro during docking of the HIV-1 preintegration complex at the nuclear envelope PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC13407

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
enables structural constituent of nuclear pore IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in NLS-bearing protein import into nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in mRNA transport IEA
Inferred from Electronic Annotation
more info
 
involved_in nuclear pore organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in nucleocytoplasmic transport IC
Inferred by Curator
more info
PubMed 
involved_in protein localization to nuclear inner membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in protein targeting IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of protein import into nucleus IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in nuclear envelope IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear envelope TAS
Traceable Author Statement
more info
 
located_in nuclear membrane IEA
Inferred from Electronic Annotation
more info
 
part_of nuclear pore IC
Inferred by Curator
more info
PubMed 
part_of nuclear pore central transport channel IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
nucleoporin p54
Names
54 kDa nucleoporin
nucleoporin 54kD
nucleoporin 54kDa

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_001278603.2NP_001265532.1  nucleoporin p54 isoform 2

    See identical proteins and their annotated locations for NP_001265532.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AI580839, AK300036, BP420577
    Consensus CDS
    CCDS63998.1
    UniProtKB/Swiss-Prot
    Q7Z3B4
    Related
    ENSP00000421304.1, ENST00000514987.6
    Conserved Domains (1) summary
    pfam13874
    Location:254389
    Nup54; Nucleoporin complex subunit 54
  2. NM_017426.4NP_059122.2  nucleoporin p54 isoform 1

    See identical proteins and their annotated locations for NP_059122.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AF157322, AI580839, BC012559, DA577078
    Consensus CDS
    CCDS3576.1
    UniProtKB/Swiss-Prot
    Q7Z3B4, Q9P0I1
    Related
    ENSP00000264883.3, ENST00000264883.8
    Conserved Domains (2) summary
    pfam13874
    Location:300437
    Nup54; Nucleoporin complex subunit 54
    pfam18437
    Location:453491
    Nup54_C; Nup54 C-terminal interacting domain

RNA

  1. NR_103780.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI580839, AK299442, BC012559, BC034226
    Related
    ENST00000695550.2
  2. NR_103781.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF157322, AI580839, BC012559, BX538002
    Related
    ENST00000507257.6
  3. NR_103782.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has two additional exons in the 5' region and lacks two exons in a downstream region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI580839, AK307571, BC012559, BC034226

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    76114664..76148397 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047415783.1XP_047271739.1  nucleoporin p54 isoform X2

  2. XM_011532033.4XP_011530335.1  nucleoporin p54 isoform X1

    Related
    ENST00000695557.2
    Conserved Domains (1) summary
    pfam13874
    Location:302401
    Nup54; Nucleoporin complex subunit 54
  3. XM_047415785.1XP_047271741.1  nucleoporin p54 isoform X3

    UniProtKB/TrEMBL
    A0A8Q3WLP2
    Related
    ENSP00000512009.1, ENST00000515460.6
  4. XM_047415784.1XP_047271740.1  nucleoporin p54 isoform X3

    UniProtKB/TrEMBL
    A0A8Q3WLP2
  5. XM_047415786.1XP_047271742.1  nucleoporin p54 isoform X4

    UniProtKB/TrEMBL
    A0A8Q3SHX2
    Related
    ENSP00000512014.1, ENST00000695556.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    79455330..79489069 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)