Mouse Gene Ncl (ENSMUST00000027438.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus nucleolin (Ncl), mRNA. (from RefSeq NM_010880)
Gencode Transcript: ENSMUST00000027438.7
Gencode Gene: ENSMUSG00000026234.12
Transcript (Including UTRs)
   Position: mm10 chr1:86,344,719-86,359,400 Size: 14,682 Total Exon Count: 14 Strand: -
Coding Region
   Position: mm10 chr1:86,350,620-86,359,223 Size: 8,604 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:86,344,719-86,359,400)mRNA (may differ from genome)Protein (707 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
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-  Comments and Description Text from UniProtKB
  ID: NUCL_MOUSE
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 (By similarity).
SUBUNIT: Interacts with APTX and NSUN2. Component of the SWAP complex that consists of NPM1, NCL/nucleolin, PARP1 and SWAP70. 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 (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. 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 (By similarity). Interacts with ERBB4. Interacts with GZF1; this interaction is important for nucleolar localization of GZF1 (By similarity). Interacts with NVL.
INTERACTION: Q9DC51:Gnai3; NbExp=4; IntAct=EBI-641864, EBI-641852;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Cytoplasm (By similarity). Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs (By similarity).
TISSUE SPECIFICITY: Expressed in B-cells that have been induced to switch to various Ig isotypes.
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.
SIMILARITY: Contains 4 RRM (RNA recognition motif) domains.

-  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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -66.00177-0.373 Picture PostScript Text
3' UTR -1867.405901-0.316 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

ModBase Predicted Comparative 3D Structure on P09405
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-  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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
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Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003697 single-stranded DNA binding
GO:0003723 RNA binding
GO:0005102 receptor binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0035368 selenocysteine insertion sequence binding
GO:0042134 rRNA primary transcript binding
GO:0042162 telomeric DNA binding
GO:0042393 histone binding
GO:0042802 identical protein binding
GO:0043236 laminin binding
GO:0043565 sequence-specific DNA binding
GO:0044547 DNA topoisomerase binding
GO:0048027 mRNA 5'-UTR binding
GO:1990631 ErbB-4 class receptor binding

Biological Process:
GO:0001525 angiogenesis
GO:0006897 endocytosis
GO:0017148 negative regulation of translation
GO:0032760 positive regulation of tumor necrosis factor production
GO:0043066 negative regulation of apoptotic process
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0071222 cellular response to lipopolysaccharide
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
GO:2000232 regulation of rRNA processing
GO:2000778 positive regulation of interleukin-6 secretion

Cellular Component:
GO:0001650 fibrillar center
GO:0001651 dense fibrillar component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005938 cell cortex
GO:0009986 cell surface
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:1990904 ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  AK046732 - Mus musculus adult male cortex cDNA, RIKEN full-length enriched library, clone:B530004O11 product:unclassifiable, full insert sequence.
AK136427 - Mus musculus adult male colon cDNA, RIKEN full-length enriched library, clone:9030023E15 product:unclassifiable, full insert sequence.
AK079553 - Mus musculus adult male hypothalamus cDNA, RIKEN full-length enriched library, clone:A230061K20 product:unclassifiable, full insert sequence.
AK050703 - Mus musculus 9 days embryo whole body cDNA, RIKEN full-length enriched library, clone:D030005O06 product:unclassifiable, full insert sequence.
AK144894 - Mus musculus lung RCB-0558 LLC cDNA, RIKEN full-length enriched library, clone:G730049H03 product:nucleolin, full insert sequence.
AK029128 - Mus musculus 10 days neonate skin cDNA, RIKEN full-length enriched library, clone:4732495B18 product:nucleolin, full insert sequence.
AK031606 - Mus musculus 13 days embryo male testis cDNA, RIKEN full-length enriched library, clone:6030459G24 product:nucleolin, full insert sequence.
BC005460 - Mus musculus nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665), complete cds.
AK050958 - Mus musculus 9 days embryo whole body cDNA, RIKEN full-length enriched library, clone:D030044N17 product:nucleolin, full insert sequence.
AK161706 - Mus musculus 8 days embryo whole body cDNA, RIKEN full-length enriched library, clone:5730589I21 product:nucleolin, full insert sequence.
AK163275 - Mus musculus 2 cells egg cDNA, RIKEN full-length enriched library, clone:B020008K19 product:nucleolin, full insert sequence.
AK166681 - Mus musculus blastocyst blastocyst cDNA, RIKEN full-length enriched library, clone:I1C0002A07 product:nucleolin, full insert sequence.
AK165167 - Mus musculus 8 cells embryo 8 cells cDNA, RIKEN full-length enriched library, clone:E860016D17 product:nucleolin, full insert sequence.
AK168579 - Mus musculus 17 days embryo heart cDNA, RIKEN full-length enriched library, clone:I920036J10 product:nucleolin, full insert sequence.
AK161597 - Mus musculus 6 days neonate head cDNA, RIKEN full-length enriched library, clone:5430406C13 product:nucleolin, full insert sequence.
AK168623 - Mus musculus 13 days embryo liver cDNA, RIKEN full-length enriched library, clone:I920039B08 product:nucleolin, full insert sequence.
AF318184 - Mus musculus nucleolin mRNA, complete cds.
AK088402 - Mus musculus 2 days neonate thymus thymic cells cDNA, RIKEN full-length enriched library, clone:E430014O05 product:nucleolin, full insert sequence.
AK083307 - Mus musculus 2 days neonate thymus thymic cells cDNA, RIKEN full-length enriched library, clone:C920001J17 product:nucleolin, full insert sequence.
AK028681 - Mus musculus 10 days neonate skin cDNA, RIKEN full-length enriched library, clone:4732433L19 product:nucleolin, full insert sequence.
AK011201 - Mus musculus 10 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2600013M03 product:nucleolin, full insert sequence.
BC012657 - Mus musculus nucleolin, mRNA (cDNA clone IMAGE:3983668), with apparent retained intron.
BC014285 - Mus musculus nucleolin, mRNA (cDNA clone IMAGE:3667173), with apparent retained intron.
AK181817 - Mus musculus cDNA, clone:Y0G0119I21, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000027438, based on BLAT search.
AK215976 - Mus musculus cDNA, clone:Y2G0136M16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000027438, based on BLAT search.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_010880, Nuc, NUCL_MOUSE, P09405, Q548M9, Q61991, Q8BQD8, Q99K50, uc007bvl.1, uc007bvl.2
UCSC ID: uc007bvl.2
RefSeq Accession: NM_010880
Protein: P09405 (aka NUCL_MOUSE)
CCDS: CCDS35646.1

-  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.