NCL nucleolin [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TLR4 TIR domain and nucleolin GAR domain synergistically mediate RSV infection and induce neuronal inflammatory damage in SH-SY5Y cells.
Title: TLR4 TIR domain and nucleolin GAR domain synergistically mediate RSV infection and induce neuronal inflammatory damage in SH-SY5Y cells.
RGS6 drives cardiomyocyte death following nucleolar stress by suppressing Nucleolin/miRNA-21.
Title: RGS6 drives cardiomyocyte death following nucleolar stress by suppressing Nucleolin/miRNA-21.
Structural Integrity of Nucleolin Is Required to Suppress TDP-43-Mediated Cytotoxicity in Yeast and Human Cell Models.
Title: Structural Integrity of Nucleolin Is Required to Suppress TDP-43-Mediated Cytotoxicity in Yeast and Human Cell Models.
Nucleolin; A tumor associated antigen as a potential lung cancer biomarker.
Title: Nucleolin; A tumor associated antigen as a potential lung cancer biomarker.
Nucleolin expression has prognostic value in neuroblastoma patients.
Title: Nucleolin expression has prognostic value in neuroblastoma patients.
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA.
Title: The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA.
Overexpression of Nucleolin and Associated Genes in Prostate Cancer.
Title: Overexpression of Nucleolin and Associated Genes in Prostate Cancer.
Downregulation of NCL attenuates tumor formation and growth in HeLa cells by targeting the PI3K/AKT pathway.
Title: Downregulation of NCL attenuates tumor formation and growth in HeLa cells by targeting the PI3K/AKT pathway.
Nucleolin as activator of TCF7L2 in human hematopoietic stem/progenitor cells.
Title: Nucleolin as activator of TCF7L2 in human hematopoietic stem/progenitor cells.
CRYbetaB2 enhances tumorigenesis through upregulation of nucleolin in triple negative breast cancer.
Title: CRYβB2 enhances tumorigenesis through upregulation of nucleolin in triple negative breast cancer.

Submit: New GeneRIF Correction See all GeneRIFs (204)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic variants associated with disordered eating. EBI GWAS Catalog EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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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

RH65048 (e-PCR)
- UniSTS:86085

RH120232 (e-PCR)
- UniSTS:132690

PMC207647P1 (e-PCR)
- UniSTS:271973

D2S2594 (e-PCR)
- UniSTS:57191

D2S1557E (e-PCR)
- UniSTS:150642

NCL (e-PCR)
- UniSTS:503929

RH11536 (e-PCR)
- UniSTS:23228

Ncl (e-PCR), detects polymorphism
- UniSTS:479178

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 more info	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

Process	Evidence Code	Pubs
involved_in angiogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to epidermal growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of insulin receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of translation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of peptidyl-tyrosine phosphorylation	IEA Inferred from Electronic Annotation more info

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 more info	PubMed
located_in macropinosome membrane	TAS Traceable Author Statement more info
located_in membrane	HDA more info	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

General protein information

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Preferred Names: nucleolin

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)

NM_005381.3 → NP_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:379 → 628

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12403
Location:307 → 381

RRM1_NCL; RNA recognition motif 1 in vertebrate nucleolin

cd12404
Location:390 → 465

RRM2_NCL; RNA recognition motif 2 in vertebrate nucleolin

cd12405
Location:485 → 557

RRM3_NCL; RNA recognition motif 3 in vertebrate nucleolin

cd12406
Location:572 → 649

RRM4_NCL; RNA recognition motif 4 in vertebrate nucleolin