Human Gene NOP16 (uc003mee.4) Description and Page Index
  Description: Homo sapiens NOP16 nucleolar protein (NOP16), transcript variant 1, mRNA.
RefSeq Summary (NM_001256539): This gene encodes a protein that is localized to the nucleolus. Expression of this gene is induced by estrogens and Myc protein and is a marker of poor patient survival in breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015].
Transcript (Including UTRs)
   Position: hg19 chr5:175,810,940-175,815,763 Size: 4,824 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr5:175,810,967-175,815,540 Size: 4,574 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:175,810,940-175,815,763)mRNA (may differ from genome)Protein (237 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: D6RGD3_HUMAN
DESCRIPTION: SubName: Full=Nucleolar protein 16;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D000082 Acetaminophen
  • D001564 Benzo(a)pyrene
  • D016572 Cyclosporine
  • D003907 Dexamethasone
  • D006861 Hydrogen Peroxide
  • D015474 Isotretinoin
  • D008070 Lipopolysaccharides
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.53 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 357.36 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -81.50223-0.365 Picture PostScript Text
3' UTR 0.00270.000 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
IPR019002 - Ribosome_biogenesis_Nop16

Pfam Domains:
PF09420 - Ribosome biogenesis protein Nop16

ModBase Predicted Comparative 3D Structure on D6RGD3
FrontTopSide
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  KJ893921 - Synthetic construct Homo sapiens clone ccsbBroadEn_03315 NOP16 gene, encodes complete protein.
KJ902598 - Synthetic construct Homo sapiens clone ccsbBroadEn_11992 NOP16 gene, encodes complete protein.
BC040106 - Homo sapiens NOP16 nucleolar protein homolog (yeast), mRNA (cDNA clone MGC:48665 IMAGE:6066208), complete cds.
BC032424 - Homo sapiens NOP16 nucleolar protein homolog (yeast), mRNA (cDNA clone MGC:40298 IMAGE:5416724), complete cds.
AF161460 - Homo sapiens HSPC111 mRNA, complete cds.
BC019331 - Homo sapiens NOP16 nucleolar protein homolog (yeast), mRNA (cDNA clone MGC:892 IMAGE:3534019), complete cds.
AF151019 - Homo sapiens HSPC185 mRNA, complete cds.
AF151875 - Homo sapiens CGI-117 protein mRNA, complete cds.
AK300883 - Homo sapiens cDNA FLJ51327 complete cds, highly similar to Protein CGI-117.
JD306958 - Sequence 287982 from Patent EP1572962.
JD341603 - Sequence 322627 from Patent EP1572962.
JD140568 - Sequence 121592 from Patent EP1572962.
JD020589 - Sequence 1613 from Patent EP1572962.
JD385143 - Sequence 366167 from Patent EP1572962.
JD389338 - Sequence 370362 from Patent EP1572962.
JD031339 - Sequence 12363 from Patent EP1572962.
JD235249 - Sequence 216273 from Patent EP1572962.
JD224769 - Sequence 205793 from Patent EP1572962.
JD062275 - Sequence 43299 from Patent EP1572962.
AY561704 - Homo sapiens HBV pre-S2 trans-regulated protein 3 mRNA, complete cds.
HQ257929 - Synthetic construct Homo sapiens clone IMAGE:100072238 NOP16 nucleolar protein homolog (yeast) (NOP16) (NOP16) gene, encodes complete protein.
CR457169 - Homo sapiens full open reading frame cDNA clone RZPDo834H118D for gene HSPC111, hypothetical protein HSPC111; complete cds, incl. stopcodon.
AK303281 - Homo sapiens cDNA FLJ57864 complete cds, moderately similar to Protein CGI-117.
JD446595 - Sequence 427619 from Patent EP1572962.
JD411064 - Sequence 392088 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: D6RGD3, D6RGD3_HUMAN, NM_001256539, NP_001243468, uc003mee.3
UCSC ID: uc003mee.4
RefSeq Accession: NM_001256539
Protein: D6RGD3 CCDS: CCDS58991.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001256539.1
exon count: 5CDS single in 3' UTR: no RNA size: 981
ORF size: 714CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1518.50frame shift in genome: no % Coverage: 98.27
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.