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] See more...

Aliases for NCL Gene

Aliases for NCL Gene

  • Nucleolin 2 3 4 5
  • Protein C23 4
  • Nsr1 3
  • C23 3

External Ids for NCL Gene

Previous GeneCards Identifiers for NCL Gene

  • GC02M230377
  • GC02M231051
  • GC02M232283
  • GC02M232521
  • GC02M232522
  • GC02M232144
  • GC02M232027
  • GC02M232318
  • GC02M224160

Summaries for NCL Gene

Entrez Gene Summary for NCL Gene

  • 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]

GeneCards Summary for NCL Gene

NCL (Nucleolin) is a Protein Coding gene. Diseases associated with NCL include Noonan Syndrome 6 and Alzheimer Disease 6. Among its related pathways are Aurora B signaling and Regulation of lipid metabolism Insulin signaling-generic cascades. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and identical protein binding. An important paralog of this gene is RBM19.

UniProtKB/Swiss-Prot Summary for NCL Gene

  • Nucleolin is the major nucleolar protein of growing eukaryotic cells. It is found associated with intranucleolar chromatin and pre-ribosomal particles. It induces chromatin decondensation by binding to histone H1. It is thought to play a role in pre-rRNA transcription and ribosome assembly. May play a role in the process of transcriptional elongation. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats.

Gene Wiki entry for NCL Gene

Additional gene information for NCL Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NCL Gene

Genomics for NCL Gene

GeneHancer (GH) Regulatory Elements for NCL Gene

Promoters and enhancers for NCL Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NCL on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NCL

Top Transcription factor binding sites by QIAGEN in the NCL gene promoter:
  • AML1a
  • TBP

Genomic Locations for NCL Gene

Genomic Locations for NCL Gene
chr2:231,453,531-231,483,641
(GRCh38/hg38)
Size:
30,111 bases
Orientation:
Minus strand
chr2:232,318,242-232,348,352
(GRCh37/hg19)
Size:
30,111 bases
Orientation:
Minus strand

Genomic View for NCL Gene

Genes around NCL on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NCL Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NCL Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NCL Gene

Proteins for NCL Gene

  • Protein details for NCL Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P19338-NUCL_HUMAN
    Recommended name:
    Nucleolin
    Protein Accession:
    P19338
    Secondary Accessions:
    • Q53SK1
    • Q8NB06
    • Q9UCF0
    • Q9UDG1

    Protein attributes for NCL Gene

    Size:
    710 amino acids
    Molecular mass:
    76614 Da
    Quaternary structure:
    • Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs (PubMed:17289661). Component of the SWAP complex that consists of NPM1, NCL/nucleolin, PARP1 and SWAP70 (By similarity). Component of a complex which is at least composed of HTATSF1/Tat-SF1, the P-TEFb complex components CDK9 and CCNT1, RNA polymerase II, SUPT5H, and NCL/nucleolin (PubMed:10393184). Interacts with AICDA (By similarity). Interacts with APTX (PubMed:15044383). Interacts with C1QBP (PubMed:21536856). Interacts with ERBB4 (PubMed:20858735). Interacts (via C-terminus) with FMR1 isoform 6 (via N-terminus) (PubMed:24658146). Interacts with GZF1; this interaction is important for nucleolar localization of GZF1 (PubMed:17674968). Interacts with NSUN2 (PubMed:17215513). Interacts with NVL (PubMed:21474449). Interacts (via N-terminus domain) with SETX (PubMed:21700224). Interacts (via RRM1 and C-terminal RRM4/Arg/Gly-rich domains) with TERT; the interaction is important for nucleolar localization of TERT (PubMed:15371412). Interacts with WDR46 (PubMed:23848194). Interacts with ZFP36 (PubMed:20221403). Interacts with LRRC34 (By similarity). Interacts with RRP1B (PubMed:19710015). Interacts with HNRNPU; this interaction occurs during mitosis (PubMed:21242313). Interacts with RIOK1; RIOK1 recruits NCL to PRMT5 for symmetrically methylation (PubMed:21081503). Interacts with ZBTB7B (By similarity). Interacts with MDK; this interaction promotes NCL clustering and lateral movements of this complex into lipid rafts leading to MDK internalization (PubMed:12147681). Interacts with HDGF (isoform 1) (PubMed:26845719).
    SequenceCaution:
    • Sequence=BAC03738.1; Type=Miscellaneous discrepancy; Note=Unlikely isoform. Aberrant splice sites.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NCL Gene

neXtProt entry for NCL Gene

Post-translational modifications for NCL Gene

  • Some glutamate residues are glycylated by TTLL8. This modification occurs exclusively on glutamate residues and results in a glycine chain on the gamma-carboxyl group (By similarity).
  • Symmetrically methylated by PRMT5.
  • Ubiquitination at Lys324, Lys333, Lys348, Lys370, Lys398, Lys403, Lys467, Lys513, Lys572, Lys577, and Lys610
  • Modification sites at PhosphoSitePlus

Other Protein References for NCL Gene

No data available for DME Specific Peptides for NCL Gene

Domains & Families for NCL Gene

Gene Families for NCL Gene

Protein Domains for NCL Gene

Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NCL Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ10452 fis, clone NT2RP1000966, highly similar to NUCLEOLIN (B3KM80_HUMAN)
  • Protein C23 (NUCL_HUMAN)
genes like me logo Genes that share domains with NCL: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for NCL Gene

Function for NCL Gene

Molecular function for NCL Gene

UniProtKB/Swiss-Prot Function:
Nucleolin is the major nucleolar protein of growing eukaryotic cells. It is found associated with intranucleolar chromatin and pre-ribosomal particles. It induces chromatin decondensation by binding to histone H1. It is thought to play a role in pre-rRNA transcription and ribosome assembly. May play a role in the process of transcriptional elongation. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats.
GENATLAS Biochemistry:
nucleolin,major multifunctional nucleolar protein of exponentially growing cells,characterized by unique tripartite function within each domain,performing activities i.e. a specific DNA helicase and DNA-dependent ATPase,also acting as a sequence-specific RNA binding protein an autoantigen,a component of B cell specific transcription factor,involved in ribosome biogenesis,cytokinesis,nucleogenesis,cell proliferation and growth,chromatin remodeling etc...

Phenotypes From GWAS Catalog for NCL Gene

Gene Ontology (GO) - Molecular Function for NCL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA,IDA 8321232
GO:0005515 protein binding IPI 12147681
GO:0008022 protein C-terminus binding IPI 16403913
genes like me logo Genes that share ontologies with NCL: view
genes like me logo Genes that share phenotypes with NCL: view

Animal Model Products

CRISPR Products

Clone Products

  • Addgene plasmids for NCL

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NCL Gene

Localization for NCL Gene

Subcellular locations from UniProtKB/Swiss-Prot for NCL Gene

Nucleus, nucleolus. Cytoplasm. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NCL gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
endosome 2
lysosome 2
peroxisome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (4)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NCL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 15121898
GO:0005654 nucleoplasm IDA 23353999
GO:0005681 spliceosomal complex IBA 21873635
GO:0005730 nucleolus IDA 12944467
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with NCL: view

Pathways & Interactions for NCL Gene

genes like me logo Genes that share pathways with NCL: view

Pathways by source for NCL Gene

1 GeneGo (Thomson Reuters) pathway for NCL Gene
  • Cell adhesion PLAU signaling
2 Cell Signaling Technology pathways for NCL Gene

SIGNOR curated interactions for NCL Gene

Activates:
Inactivates:

Gene Ontology (GO) - Biological Process for NCL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IDA 16403913
GO:0017148 negative regulation of translation IMP 16213212
GO:0045944 positive regulation of transcription by RNA polymerase II IEA --
GO:0048026 positive regulation of mRNA splicing, via spliceosome IBA 21873635
GO:0071364 cellular response to epidermal growth factor stimulus IEA --
genes like me logo Genes that share ontologies with NCL: view

Drugs & Compounds for NCL Gene

(20) Drugs for NCL Gene - From: DGIdb and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
AS1411 Pharma 0
IPP-204106 Pharma 0

(13) Additional Compounds for NCL Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with NCL: view

Transcripts for NCL Gene

mRNA/cDNA for NCL Gene

1 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for NCL

Alternative Splicing Database (ASD) splice patterns (SP) for NCL Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c · 8d · 8e ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b · 13c ^
SP1: - - - - - - -
SP2: - - - - - - - - - - - - - -
SP3:
SP4: -
SP5: - - - - - - - - - - - - - - - - -
SP6: - - - - - - - - - - -
SP7:
SP8:
SP9:
SP10:
SP11: - - - - -
SP12: - -
SP13: - - -
SP14: -
SP15:
SP16: - - - - - - - - -

ExUns: 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18a · 18b ^ 19a · 19b · 19c · 19d ^ 20a · 20b · 20c
SP1: - -
SP2:
SP3: -
SP4: - - - - - - - -
SP5:
SP6:
SP7: - - -
SP8: -
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:

Relevant External Links for NCL Gene

GeneLoc Exon Structure for
NCL

Expression for NCL Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NCL Gene

Protein differential expression in normal tissues from HIPED for NCL Gene

This gene is overexpressed in Tlymphocyte (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NCL Gene



Protein tissue co-expression partners for NCL Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NCL

SOURCE GeneReport for Unigene cluster for NCL Gene:

Hs.79110

Evidence on tissue expression from TISSUES for NCL Gene

  • Skin(4.9)
  • Liver(4.8)
  • Nervous system(4.8)
  • Eye(4.4)
  • Intestine(4.4)
  • Heart(3.6)
  • Lung(3.6)
  • Kidney(3.5)
  • Muscle(3.4)
  • Adrenal gland(3)
  • Blood(3)
  • Bone marrow(3)
  • Gall bladder(3)
  • Lymph node(3)
  • Pancreas(3)
  • Spleen(3)
  • Stomach(3)
  • Thyroid gland(3)
genes like me logo Genes that share expression patterns with NCL: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NCL Gene

Orthologs for NCL Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NCL Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NCL 31 30
  • 99.54 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NCL 31 30
  • 90.4 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NCL 31 31 30
  • 88.41 (n)
OneToMany
rat
(Rattus norvegicus)
Mammalia Ncl 30
  • 88.2 (n)
mouse
(Mus musculus)
Mammalia Ncl 17 31 30
  • 87.67 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NCL 31
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NCL 31
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves NCL 31
  • 59 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NCL 31
  • 58 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia LOC397919 30
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10165 30
zebrafish
(Danio rerio)
Actinopterygii ncl 31
  • 50 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NSR1 31
  • 32 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8423 31
  • 36 (a)
OneToOne
Species where no ortholog for NCL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NCL Gene

ENSEMBL:
Gene Tree for NCL (if available)
TreeFam:
Gene Tree for NCL (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NCL: view image

Paralogs for NCL Gene

(4) SIMAP similar genes for NCL Gene using alignment to 8 proteins:

  • NUCL_HUMAN
  • B3KM80_HUMAN
  • C9J1H7_HUMAN
  • C9JLB1_HUMAN
  • C9JWL1_HUMAN
  • C9JYW2_HUMAN
  • H7BY16_HUMAN
  • L8EAF1_HUMAN

Pseudogenes.org Pseudogenes for NCL Gene

genes like me logo Genes that share paralogs with NCL: view

Variants for NCL Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NCL Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
712368 Benign: not provided 231,456,731(-) G/A SYNONYMOUS_VARIANT
718933 Likely Benign: not provided 231,460,208(-) G/A SYNONYMOUS_VARIANT
720026 Benign: not provided 231,460,685(-) TTCC/T INFRAME_DELETION
723973 Benign: not provided 231,461,565(-) C/G MISSENSE_VARIANT
726319 Likely Benign: not provided 231,461,559(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for NCL Gene

Structural Variations from Database of Genomic Variants (DGV) for NCL Gene

Variant ID Type Subtype PubMed ID
esv3306627 CNV mobile element insertion 20981092
esv3423511 CNV insertion 20981092
nsv819681 CNV loss 19587683
nsv834567 CNV gain 17160897

Variation tolerance for NCL Gene

Residual Variation Intolerance Score: 12.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.31; 41.24% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NCL Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NCL

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NCL Gene

Disorders for NCL Gene

MalaCards: The human disease database

(4) MalaCards diseases for NCL Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
noonan syndrome 6
  • ns6
alzheimer disease 6
  • ad6
cervical cancer
  • cervical cancer, somatic
leukemia, acute myeloid
  • aml
- elite association - COSMIC cancer census association via MalaCards
Search NCL in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with NCL: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NCL Gene

Publications for NCL Gene

  1. Nucleolin modulates the subcellular localization of GDNF-inducible zinc finger protein 1 and its roles in transcription and cell proliferation. (PMID: 17674968) Dambara A … Takahashi M (Experimental cell research 2007) 3 4 23 54
  2. Nucleolin interacts with telomerase. (PMID: 15371412) Khurts S … Murakami S (The Journal of biological chemistry 2004) 3 4 23 54
  3. The anti-HIV cytokine midkine binds the cell surface-expressed nucleolin as a low affinity receptor. (PMID: 12147681) Said EA … Hovanessian AG (The Journal of biological chemistry 2002) 3 4 23 54
  4. Genomic organization and chromosomal localization of the human nucleolin gene. (PMID: 2394707) Srivastava M … Burns AL (The Journal of biological chemistry 1990) 2 3 4 54
  5. Two new isoforms of the human hepatoma-derived growth factor interact with components of the cytoskeleton. (PMID: 26845719) Nüße J … Dietz F (Biological chemistry 2016) 3 4 54

Products for NCL Gene

  • Addgene plasmids for NCL