Human Gene NCL (ENST00000322723.9_10) from GENCODE V47lift37
  Description: nucleolin (from RefSeq NM_005381.3)
Gencode Transcript: ENST00000322723.9_10
Gencode Gene: ENSG00000115053.17_16
Transcript (Including UTRs)
   Position: hg19 chr2:232,318,242-232,329,195 Size: 10,954 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr2:232,319,902-232,329,064 Size: 9,163 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:232,318,242-232,329,195)mRNA (may differ from genome)Protein (710 aa)
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-  Comments and Description Text from UniProtKB
  ID: NUCL_HUMAN
DESCRIPTION: RecName: Full=Nucleolin; AltName: Full=Protein C23;
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.
SUBUNIT: Identified in a mRNP granule complex, at least composed of ACTB, ACTN4, DHX9, ERG, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPD, HNRNPL, HNRNPR, HNRNPU, HSPA1, HSPA8, IGF2BP1, ILF2, ILF3, NCBP1, NCL, PABPC1, PABPC4, PABPN1, RPLP0, RPS3, RPS3A, RPS4X, RPS8, RPS9, SYNCRIP, TROVE2, YBX1 and untranslated mRNAs. Interacts with APTX and NSUN2. Component of the SWAP complex that consists of NPM1, NCL/nucleolin, PARP1 and SWAP70. 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. Interacts (via RRM1 and C-terminal RRM4/Arg/Gly- rich domains) with TERT; the interaction is important for nucleolar localization of TERT. Interacts with ERBB4. Interacts with GZF1; this interaction is important for nucleolar localization of GZF1. Interacts with NVL.
INTERACTION: P49407:ARRB1; NbExp=3; IntAct=EBI-346967, EBI-743313; P32121:ARRB2; NbExp=3; IntAct=EBI-346967, EBI-714559; P39060:COL18A1; NbExp=5; IntAct=EBI-346967, EBI-2566375; Q00987:MDM2; NbExp=2; IntAct=EBI-346967, EBI-389668; P35579:MYH9; NbExp=3; IntAct=EBI-346967, EBI-350338; Q9UQ80:PA2G4; NbExp=2; IntAct=EBI-346967, EBI-924893; Q06710:PAX8; NbExp=2; IntAct=EBI-346967, EBI-2683132;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Cytoplasm. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs.
PTM: 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).
SIMILARITY: Contains 4 RRM (RNA recognition motif) domains.
SEQUENCE CAUTION: Sequence=BAC03738.1; Type=Miscellaneous discrepancy; Note=Unlikely isoform. Aberrant splice sites;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 219.27 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 4036.60 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -34.90131-0.266 Picture PostScript Text
3' UTR -527.901660-0.318 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
50249 - Nucleic acid-binding proteins
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2FC8 - NMR MuPIT 2FC9 - NMR MuPIT 2KRR - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P19338
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0042162 telomeric DNA binding
GO:0042802 identical protein binding
GO:0044547 DNA topoisomerase binding
GO:0048027 mRNA 5'-UTR binding

Biological Process:
GO:0001525 angiogenesis
GO:0017148 negative regulation of translation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0071364 cellular response to epidermal growth factor stimulus
GO:1901838 positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter
GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005938 cell cortex
GO:0016020 membrane
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  JD340936 - Sequence 321960 from Patent EP1572962.
JD340935 - Sequence 321959 from Patent EP1572962.
JD045861 - Sequence 26885 from Patent EP1572962.
JD446397 - Sequence 427421 from Patent EP1572962.
JD410778 - Sequence 391802 from Patent EP1572962.
JD128078 - Sequence 109102 from Patent EP1572962.
JD446396 - Sequence 427420 from Patent EP1572962.
AK091742 - Homo sapiens cDNA FLJ34423 fis, clone HHDPC2008123, highly similar to NUCLEOLIN.
AX747156 - Sequence 681 from Patent EP1308459.
AK095897 - Homo sapiens cDNA FLJ38578 fis, clone HCHON2007674, highly similar to NUCLEOLIN.
AK122805 - Homo sapiens cDNA FLJ16383 fis, clone TLIVE2007016, highly similar to NUCLEOLIN.
AK127608 - Homo sapiens cDNA FLJ45706 fis, clone FEBRA2028457, highly similar to Nucleolin.
AK000250 - Homo sapiens cDNA FLJ20243 fis, clone COLF6418, highly similar to NUCL_HUMAN NUCLEOLIN.
AK000221 - Homo sapiens cDNA FLJ20214 fis, clone COLF2014, highly similar to NUCL_HUMAN NUCLEOLIN.
BC002343 - Homo sapiens nucleolin, mRNA (cDNA clone MGC:8580 IMAGE:2960982), complete cds.
BC006494 - Homo sapiens nucleolin, mRNA (cDNA clone MGC:1440 IMAGE:2960982), complete cds.
BC006516 - Homo sapiens nucleolin, mRNA (cDNA clone MGC:3588 IMAGE:2960982), complete cds.
AY320411 - Homo sapiens nasopharyngeal carcinoma-associated antigen mRNA sequence.
AK128584 - Homo sapiens cDNA FLJ46743 fis, clone TRACH3021778, moderately similar to Nucleolin.
AK001314 - Homo sapiens cDNA FLJ10452 fis, clone NT2RP1000966, highly similar to NUCLEOLIN.
JD152797 - Sequence 133821 from Patent EP1572962.
JD133142 - Sequence 114166 from Patent EP1572962.
KJ901595 - Synthetic construct Homo sapiens clone ccsbBroadEn_10989 NCL gene, encodes complete protein.
AB385068 - Synthetic construct DNA, clone: pF1KB5231, Homo sapiens NCL gene for nucleolin, complete cds, without stop codon, in Flexi system.
DQ586566 - Homo sapiens piRNA piR-53678, complete sequence.
CU677918 - Synthetic construct Homo sapiens gateway clone IMAGE:100019610 5' read NCL mRNA.
JD471146 - Sequence 452170 from Patent EP1572962.
JD065593 - Sequence 46617 from Patent EP1572962.
DQ583080 - Homo sapiens piRNA piR-50192, complete sequence.
JD261114 - Sequence 242138 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000322723.1, ENST00000322723.2, ENST00000322723.3, ENST00000322723.4, ENST00000322723.5, ENST00000322723.6, ENST00000322723.7, ENST00000322723.8, NM_005381, NUCL_HUMAN, P19338, Q53SK1, Q8NB06, Q9UCF0, Q9UDG1, uc317rif.1, uc317rif.2
UCSC ID: ENST00000322723.9_10
RefSeq Accession: NM_005381.3
Protein: P19338 (aka NUCL_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.