Human Gene NOL9 (ENST00000377705.6) from GENCODE V44
  Description: Homo sapiens nucleolar protein 9 (NOL9), mRNA. (from RefSeq NM_024654)
Gencode Transcript: ENST00000377705.6
Gencode Gene: ENSG00000162408.11
Transcript (Including UTRs)
   Position: hg38 chr1:6,521,347-6,554,513 Size: 33,167 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg38 chr1:6,525,854-6,554,502 Size: 28,649 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:6,521,347-6,554,513)mRNA (may differ from genome)Protein (702 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Polynucleotide 5'-hydroxyl-kinase NOL9; EC=2.7.1.-; AltName: Full=Nucleolar protein 9;
FUNCTION: Polynucleotide 5'-kinase involved in rRNA processing. The kinase activity is required for the processing of the 32S precursor into 5.8S and 28S rRNAs, more specifically for the generation of the major 5.8S(S) form. In vitro, has both DNA and RNA 5'-kinase activities. Probably binds RNA.
SUBCELLULAR LOCATION: Nucleus, nucleolus. Note=Colocalizes with pre-60S rRNPs particles.
SIMILARITY: Belongs to the Clp1 family. NOL9/GRC3 subfamily.
SEQUENCE CAUTION: Sequence=BAB15611.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Primer design for this transcript

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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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.91 RPKM in Spleen
Total median expression: 175.17 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
3' UTR -1921.604507-0.426 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
IPR010655 - Pre-mRNA_cleavage_cplxII_Clp1

Pfam Domains:
PF06807 - Pre-mRNA cleavage complex II protein Clp1

ModBase Predicted Comparative 3D Structure on Q5SY16
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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0051731 polynucleotide 5'-hydroxyl-kinase activity

Biological Process:
GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000460 maturation of 5.8S rRNA
GO:0006364 rRNA processing
GO:0016310 phosphorylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0016020 membrane
GO:0045111 intermediate filament cytoskeleton

-  Descriptions from all associated GenBank mRNAs
  LF383933 - JP 2014500723-A/191436: Polycomb-Associated Non-Coding RNAs.
MA619510 - JP 2018138019-A/191436: Polycomb-Associated Non-Coding RNAs.
AK091284 - Homo sapiens cDNA FLJ33965 fis, clone CTONG2019063.
AX746895 - Sequence 420 from Patent EP1308459.
AK289653 - Homo sapiens cDNA FLJ75381 complete cds, highly similar to Homo sapiens nucleolar protein 9 (NOL9), mRNA.
BC110849 - Homo sapiens nucleolar protein 9, mRNA (cDNA clone MGC:131821 IMAGE:6167575), complete cds.
BC105095 - Homo sapiens nucleolar protein 9, mRNA (cDNA clone MGC:132755 IMAGE:8144098), complete cds.
BC112278 - Homo sapiens nucleolar protein 9, mRNA (cDNA clone MGC:138483 IMAGE:8327746), complete cds.
BC143646 - Homo sapiens cDNA clone IMAGE:9052160.
HQ258631 - Synthetic construct Homo sapiens clone IMAGE:100073186 nucleolar protein 9 (NOL9) gene, encodes complete protein.
KJ899555 - Synthetic construct Homo sapiens clone ccsbBroadEn_08949 NOL9 gene, encodes complete protein.
KJ901072 - Synthetic construct Homo sapiens clone ccsbBroadEn_10466 NOL9 gene, encodes complete protein.
AK026976 - Homo sapiens cDNA: FLJ23323 fis, clone HEP12456.
BC073860 - Homo sapiens nucleolar protein 9, mRNA (cDNA clone IMAGE:3852937).
JD490265 - Sequence 471289 from Patent EP1572962.
JD235769 - Sequence 216793 from Patent EP1572962.
JD168023 - Sequence 149047 from Patent EP1572962.
JD394186 - Sequence 375210 from Patent EP1572962.
JD085436 - Sequence 66460 from Patent EP1572962.
JD058592 - Sequence 39616 from Patent EP1572962.
JD247160 - Sequence 228184 from Patent EP1572962.
JD547523 - Sequence 528547 from Patent EP1572962.
JD436600 - Sequence 417624 from Patent EP1572962.
JD492808 - Sequence 473832 from Patent EP1572962.
JD300998 - Sequence 282022 from Patent EP1572962.
JD415173 - Sequence 396197 from Patent EP1572962.
JD147744 - Sequence 128768 from Patent EP1572962.
JD524878 - Sequence 505902 from Patent EP1572962.
JD352628 - Sequence 333652 from Patent EP1572962.
JD352627 - Sequence 333651 from Patent EP1572962.
JD227532 - Sequence 208556 from Patent EP1572962.
JD140621 - Sequence 121645 from Patent EP1572962.
JD153209 - Sequence 134233 from Patent EP1572962.
JD198429 - Sequence 179453 from Patent EP1572962.
JD547570 - Sequence 528594 from Patent EP1572962.
JD547569 - Sequence 528593 from Patent EP1572962.
JD161501 - Sequence 142525 from Patent EP1572962.
JD153208 - Sequence 134232 from Patent EP1572962.
JD476982 - Sequence 458006 from Patent EP1572962.
JD256641 - Sequence 237665 from Patent EP1572962.
JD560776 - Sequence 541800 from Patent EP1572962.
JD457556 - Sequence 438580 from Patent EP1572962.
JD541875 - Sequence 522899 from Patent EP1572962.
JD443445 - Sequence 424469 from Patent EP1572962.
JD517258 - Sequence 498282 from Patent EP1572962.
JD105399 - Sequence 86423 from Patent EP1572962.
JD518172 - Sequence 499196 from Patent EP1572962.
JD076882 - Sequence 57906 from Patent EP1572962.
BC009257 - Homo sapiens nucleolar protein 9, mRNA (cDNA clone IMAGE:3948222), partial cds.
LF357505 - JP 2014500723-A/165008: Polycomb-Associated Non-Coding RNAs.
MA593082 - JP 2018138019-A/165008: Polycomb-Associated Non-Coding RNAs.
BC012439 - Homo sapiens nucleolar protein 9, mRNA (cDNA clone IMAGE:3859950), partial cds.
BC063639 - Homo sapiens nucleolar protein 9, mRNA (cDNA clone IMAGE:4452792), partial cds.
BC094836 - Homo sapiens nucleolar protein 9, mRNA (cDNA clone IMAGE:5094034), partial cds.
JD456058 - Sequence 437082 from Patent EP1572962.
LF357504 - JP 2014500723-A/165007: Polycomb-Associated Non-Coding RNAs.
MA593081 - JP 2018138019-A/165007: Polycomb-Associated Non-Coding RNAs.
LF357502 - JP 2014500723-A/165005: Polycomb-Associated Non-Coding RNAs.
MA593079 - JP 2018138019-A/165005: Polycomb-Associated Non-Coding RNAs.
LF357498 - JP 2014500723-A/165001: Polycomb-Associated Non-Coding RNAs.
MA593075 - JP 2018138019-A/165001: Polycomb-Associated Non-Coding RNAs.
LF357496 - JP 2014500723-A/164999: Polycomb-Associated Non-Coding RNAs.
MA593073 - JP 2018138019-A/164999: Polycomb-Associated Non-Coding RNAs.
LF357495 - JP 2014500723-A/164998: Polycomb-Associated Non-Coding RNAs.
MA593072 - JP 2018138019-A/164998: Polycomb-Associated Non-Coding RNAs.
LF357494 - JP 2014500723-A/164997: Polycomb-Associated Non-Coding RNAs.
MA593071 - JP 2018138019-A/164997: Polycomb-Associated Non-Coding RNAs.
JD393620 - Sequence 374644 from Patent EP1572962.
LF357489 - JP 2014500723-A/164992: Polycomb-Associated Non-Coding RNAs.
MA593066 - JP 2018138019-A/164992: Polycomb-Associated Non-Coding RNAs.
LF357487 - JP 2014500723-A/164990: Polycomb-Associated Non-Coding RNAs.
MA593064 - JP 2018138019-A/164990: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q5SY16 (Reactome details) participates in the following event(s):

R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000377705.1, ENST00000377705.2, ENST00000377705.3, ENST00000377705.4, ENST00000377705.5, NM_024654, NOL9_HUMAN, Q2NL84, Q4VBY3, Q5SY16, Q6P472, Q7L4D6, Q96EE0, Q9H5L4, uc001ans.1, uc001ans.2, uc001ans.3, uc001ans.4, uc001ans.5
UCSC ID: ENST00000377705.6
RefSeq Accession: NM_024654
Protein: Q5SY16 (aka NOL9_HUMAN)

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