Human Gene RRP1 (ENST00000497547.2_4) from GENCODE V47lift37
  Description: ribosomal RNA processing 1 (from RefSeq NM_003683.6)
Gencode Transcript: ENST00000497547.2_4
Gencode Gene: ENSG00000160214.13_7
Transcript (Including UTRs)
   Position: hg19 chr21:45,209,458-45,225,174 Size: 15,717 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr21:45,209,511-45,223,655 Size: 14,145 Coding Exon Count: 13 

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 (chr21:45,209,458-45,225,174)mRNA (may differ from genome)Protein (461 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RRP1_HUMAN
DESCRIPTION: RecName: Full=Ribosomal RNA processing protein 1 homolog A; AltName: Full=Novel nuclear protein 1; Short=NNP-1; AltName: Full=Nucleolar protein Nop52; AltName: Full=RRP1-like protein;
FUNCTION: Plays a critical role in the generation of 28S rRNA.
SUBCELLULAR LOCATION: Nucleus, nucleolus.
TISSUE SPECIFICITY: Ubiquitously expressed in fetal and adult tissues.
SIMILARITY: Belongs to the RRP1 family.

-  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

+  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: 18.46 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 397.86 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 -19.4053-0.366 Picture PostScript Text
3' UTR -671.101519-0.442 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
IPR010301 - Nop52

Pfam Domains:
PF05997 - Nucleolar protein,Nop52

ModBase Predicted Comparative 3D Structure on P56182
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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 Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding

Biological Process:
GO:0006364 rRNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0030687 preribosome, large subunit precursor
GO:0030688 preribosome, small subunit precursor


-  Descriptions from all associated GenBank mRNAs
  LF208801 - JP 2014500723-A/16304: Polycomb-Associated Non-Coding RNAs.
AK223185 - Homo sapiens mRNA for nucleolar protein NOP52 variant, clone: PNC05509.
AK303000 - Homo sapiens cDNA FLJ61500 complete cds, highly similar to NNP-1 protein.
AK313116 - Homo sapiens cDNA, FLJ93601.
AK223215 - Homo sapiens mRNA for nucleolar protein NOP52 variant, clone: SPL07557.
BC000380 - Homo sapiens ribosomal RNA processing 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:8387 IMAGE:2820455), complete cds.
U79775 - Homo sapiens NNP-1/Nop52 (NNP-1) mRNA, complete cds.
DQ894567 - Synthetic construct Homo sapiens clone IMAGE:100009027; FLH176472.01L; RZPDo839D09121D DNA segment on chromosome 21 (unique) 2056 expressed sequence (D21S2056E) gene, encodes complete protein.
DQ891391 - Synthetic construct clone IMAGE:100004021; FLH176476.01X; RZPDo839D09122D DNA segment on chromosome 21 (unique) 2056 expressed sequence (D21S2056E) gene, encodes complete protein.
KJ897872 - Synthetic construct Homo sapiens clone ccsbBroadEn_07266 RRP1 gene, encodes complete protein.
BC014787 - Homo sapiens ribosomal RNA processing 1 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4178914), partial cds.
AL137757 - Homo sapiens mRNA; cDNA DKFZp434C085 (from clone DKFZp434C085); partial cds.
KJ901886 - Synthetic construct Homo sapiens clone ccsbBroadEn_11280 RRP1 gene, encodes complete protein.
AY033999 - Homo sapiens NNP3 mRNA, complete cds.
MA444378 - JP 2018138019-A/16304: Polycomb-Associated Non-Coding RNAs.
CU674182 - Synthetic construct Homo sapiens gateway clone IMAGE:100017317 5' read RRP1 mRNA.
LF323028 - JP 2014500723-A/130531: Polycomb-Associated Non-Coding RNAs.
LF323022 - JP 2014500723-A/130525: Polycomb-Associated Non-Coding RNAs.
MA558605 - JP 2018138019-A/130531: Polycomb-Associated Non-Coding RNAs.
MA558599 - JP 2018138019-A/130525: Polycomb-Associated Non-Coding RNAs.
LF323018 - JP 2014500723-A/130521: Polycomb-Associated Non-Coding RNAs.
AK026354 - Homo sapiens cDNA: FLJ22701 fis, clone HSI12115.
LF323014 - JP 2014500723-A/130517: Polycomb-Associated Non-Coding RNAs.
JD022045 - Sequence 3069 from Patent EP1572962.
JD033750 - Sequence 14774 from Patent EP1572962.
JD459057 - Sequence 440081 from Patent EP1572962.
JD408361 - Sequence 389385 from Patent EP1572962.
JD044255 - Sequence 25279 from Patent EP1572962.
JD144366 - Sequence 125390 from Patent EP1572962.
JD462894 - Sequence 443918 from Patent EP1572962.
JD045521 - Sequence 26545 from Patent EP1572962.
JD064495 - Sequence 45519 from Patent EP1572962.
JD387035 - Sequence 368059 from Patent EP1572962.
JD563795 - Sequence 544819 from Patent EP1572962.
JD261798 - Sequence 242822 from Patent EP1572962.
JD378761 - Sequence 359785 from Patent EP1572962.
JD102538 - Sequence 83562 from Patent EP1572962.
JD227067 - Sequence 208091 from Patent EP1572962.
JD519685 - Sequence 500709 from Patent EP1572962.
JD071283 - Sequence 52307 from Patent EP1572962.
JD137803 - Sequence 118827 from Patent EP1572962.
JD098329 - Sequence 79353 from Patent EP1572962.
JD501552 - Sequence 482576 from Patent EP1572962.
JD270897 - Sequence 251921 from Patent EP1572962.
JD339201 - Sequence 320225 from Patent EP1572962.
JD099922 - Sequence 80946 from Patent EP1572962.
JD476335 - Sequence 457359 from Patent EP1572962.
JD347953 - Sequence 328977 from Patent EP1572962.
JD179776 - Sequence 160800 from Patent EP1572962.
JD128089 - Sequence 109113 from Patent EP1572962.
JD340982 - Sequence 322006 from Patent EP1572962.
JD329010 - Sequence 310034 from Patent EP1572962.
JD319015 - Sequence 300039 from Patent EP1572962.
JD447382 - Sequence 428406 from Patent EP1572962.
JD366423 - Sequence 347447 from Patent EP1572962.
JD149362 - Sequence 130386 from Patent EP1572962.
JD517560 - Sequence 498584 from Patent EP1572962.
JD517559 - Sequence 498583 from Patent EP1572962.
JD117198 - Sequence 98222 from Patent EP1572962.
MA558595 - JP 2018138019-A/130521: Polycomb-Associated Non-Coding RNAs.
MA558591 - JP 2018138019-A/130517: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: D21S2056E, ENST00000497547.1, NM_003683, NNP1, NOP52, P56182, Q9NST5, RRP1A, RRP1_HUMAN, uc322tox.1, uc322tox.2
UCSC ID: ENST00000497547.2_4
RefSeq Accession: NM_003683.6
Protein: P56182 (aka RRP1_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.