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    NCL nucleolin [ Homo sapiens (human) ]

    Gene ID: 4691, updated on 9-Jun-2024

    Summary

    Official Symbol
    NCLprovided by HGNC
    Official Full Name
    nucleolinprovided by HGNC
    Primary source
    HGNC:HGNC:7667
    See related
    Ensembl:ENSG00000115053 MIM:164035; AllianceGenome:HGNC:7667
    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
    Also known as
    C23; Nsr1
    Summary
    Nucleolin (NCL), a eukaryotic nucleolar phosphoprotein, is involved in the synthesis and maturation of ribosomes. It is located mainly in dense fibrillar regions of the nucleolus. Human NCL gene consists of 14 exons with 13 introns and spans approximately 11kb. The intron 11 of the NCL gene encodes a small nucleolar RNA, termed U20. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in lymph node (RPKM 147.8), appendix (RPKM 146.7) and 25 other tissues See more
    Orthologs
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    Genomic context

    See NCL in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (231453531..231464484, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231937970..231948923, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (232318242..232329195, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene zinc finger and BTB domain containing 8 opposite strand pseudogene 2 Neighboring gene HIGD2A pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 5541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17284 Neighboring gene Sharpr-MPRA regulatory region 11632 Neighboring gene small nucleolar RNA, H/ACA box 75 Neighboring gene small nucleolar RNA, C/D box 20 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232328263-232328934 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232328935-232329604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17287 Neighboring gene small nucleolar RNA, C/D box 82 Neighboring gene NANOG hESC enhancer GRCh37_chr2:232340658-232341163 Neighboring gene uncharacterized LOC107985998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232345298-232345810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232345811-232346321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17289 Neighboring gene RNA, U2 small nuclear 22, pseudogene

    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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genetic variants associated with disordered eating.
    EBI GWAS Catalog
    Polygenic transmission and complex neuro developmental network for attention deficit hyperactivity disorder: genome-wide association study of both common and rare variants.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 downregulates the expression of nucleolin and modulates the expression of LC3, leading to autophage and cell death of uninfected CD4 T cells PubMed
    env Tandem affinity purification and mass spectrometry analysis identify nucleolin (NCL), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify nucleolin (NCL), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify nucleolin (NCL), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag The presence of HIV-1 Gag protein upregulates the levels of cytoplasmic nucleolin in Gag expression 293T cells PubMed
    gag Tandem affinity purification and mass spectrometry analysis identify nucleolin (NCL), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    gag Nucleolin binds HIV-1 Gag and enhances the release of HIV-1 virions containing viral genomic RNA with the RNA packaging signal, psi PubMed
    gag Nucleolin is incorporated into HIV-1 particles during budding of HIV-1 from lipid rafts and following virus entry into cells is recovered in fractions containing HIV-1 DNA, the Matrix protein of HIV-1 Gag and HIV-1 Reverse Transcriptase PubMed
    Tat tat Nucleolin is downregulated in HIV-1 Tat and NC cotransfection of HEK 293T cells PubMed
    matrix gag Nucleolin is incorporated into HIV-1 particles during budding of HIV-1 from lipid rafts and following virus entry into cells is recovered in fractions containing HIV-1 DNA, Matrix and Reverse Transcriptase proteins PubMed
    nucleocapsid gag Nucleolin is downregulated in HIV-1 Tat and NC cotransfection of HEK 293T cells PubMed
    reverse transcriptase gag-pol After HIV entry into cells, equilibrium density fractionation of cellular extracts revealed cell surface nucleolin is recovered in fractions containing actin, HIV DNA, viral matrix, and reverse transcriptase, suggesting nucleolin accompanies viral entry 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

    Clone Names

    • FLJ45706, FLJ59041

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA topoisomerase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables PH domain binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables insulin receptor substrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables mRNA 5'-UTR binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables telomeric DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell cortex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromosome IDA
    Inferred from Direct Assay
    more info
     
    located_in cornified envelope IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasmic ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in macropinosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in membrane HDA PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    part_of ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    NCBI Reference Sequences (RefSeq)

    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_005381.3NP_005372.2  nucleolin

      See identical proteins and their annotated locations for NP_005372.2

      Status: REVIEWED

      Source sequence(s)
      AC017104, AK000221, AK001314, BM761058, BQ001029
      Consensus CDS
      CCDS33397.1
      UniProtKB/Swiss-Prot
      P19338, Q53SK1, Q8NB06, Q9UCF0, Q9UDG1
      UniProtKB/TrEMBL
      A0A7I2V3F3
      Related
      ENSP00000318195.4, ENST00000322723.9
      Conserved Domains (5) summary
      COG0724
      Location:379628
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12403
      Location:307381
      RRM1_NCL; RNA recognition motif 1 in vertebrate nucleolin
      cd12404
      Location:390465
      RRM2_NCL; RNA recognition motif 2 in vertebrate nucleolin
      cd12405
      Location:485557
      RRM3_NCL; RNA recognition motif 3 in vertebrate nucleolin
      cd12406
      Location:572649
      RRM4_NCL; RNA recognition motif 4 in vertebrate nucleolin

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      231453531..231464484 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      231937970..231948923 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)