Human Gene RPP21 (uc003nqf.2)
  Description: Homo sapiens ribonuclease P/MRP 21kDa subunit (RPP21), transcript variant 3, mRNA.
RefSeq Summary (NM_001199121): RPP21 is a protein subunit of nuclear ribonuclease P, which processes the 5-prime leader sequence of precursor tRNAs (Jarrous et al., 2001 [PubMed 11497433]).[supplied by OMIM, Jan 2009].
Transcript (Including UTRs)
   Position: hg19 chr6:30,312,906-30,314,635 Size: 1,730 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr6:30,312,949-30,314,550 Size: 1,602 Coding Exon Count: 5 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:30,312,906-30,314,635)mRNA (may differ from genome)Protein (144 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
ReactomeUniProtKBBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RPP21
CDC HuGE Published Literature: RPP21
Positive Disease Associations: Body Height
Related Studies:
  1. Body Height
    , , . [PubMed 0]

-  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.

+  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 -16.1043-0.374 Picture PostScript Text
3' UTR -13.4085-0.158 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
  Pfam Domains:
PF04032 - RNAse P Rpr2/Rpp21/SNM1 subunit domain

ModBase Predicted Comparative 3D Structure on Q9H633-3
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
  EU012025 - Homo sapiens TRIM39-like protein (TRIM39R) mRNA, partial cds.
LF210820 - JP 2014500723-A/18323: Polycomb-Associated Non-Coding RNAs.
AF212152 - Homo sapiens ribonuclease P subunit (RPP21) mRNA, complete cds.
AJ504714 - Homo sapiens mRNA for ribonucleoprotein V2 (CAT60-V2 gene).
AK026291 - Homo sapiens cDNA: FLJ22638 fis, clone HSI06727.
BC011730 - Homo sapiens ribonuclease P/MRP 21kDa subunit, mRNA (cDNA clone MGC:19462 IMAGE:4422871), complete cds.
AJ504715 - Homo sapiens mRNA for ribonucleoprotein V3 (CAT60-V3 gene).
AJ504713 - Homo sapiens mRNA for ribonucleoprotein V1 (CAT60-V1 gene).
AJ504716 - Homo sapiens mRNA for ribonucleoprotein V4 (CAT60-V4 gene).
CU680032 - Synthetic construct Homo sapiens gateway clone IMAGE:100020626 5' read RPP21 mRNA.
HQ448318 - Synthetic construct Homo sapiens clone IMAGE:100071734; CCSB006968_01 ribonuclease P/MRP 21kDa subunit (RPP21) gene, encodes complete protein.
KJ899585 - Synthetic construct Homo sapiens clone ccsbBroadEn_08979 RPP21 gene, encodes complete protein.
LF341369 - JP 2014500723-A/148872: Polycomb-Associated Non-Coding RNAs.
LF341368 - JP 2014500723-A/148871: Polycomb-Associated Non-Coding RNAs.
JD282687 - Sequence 263711 from Patent EP1572962.
MA446397 - JP 2018138019-A/18323: Polycomb-Associated Non-Coding RNAs.
MA576946 - JP 2018138019-A/148872: Polycomb-Associated Non-Coding RNAs.
MA576945 - JP 2018138019-A/148871: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9H633 (Reactome details) participates in the following event(s):

R-HSA-5696810 RNase P cleaves the 5' end of pre-tRNA
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6784531 tRNA processing in the nucleus
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72306 tRNA processing
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: C6orf135, CAT60, NM_001199121, NP_001186050, Q9H633-3
UCSC ID: uc003nqf.2
RefSeq Accession: NM_001199121
Protein: Q9H633-3, splice isoform of Q9H633 CCDS: CCDS56410.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001199121.1
exon count: 5CDS single in 3' UTR: no RNA size: 568
ORF size: 435CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1070.00frame shift in genome: no % Coverage: 99.12
has start codon: yes stop codon in genome: no # of Alignments: 7
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.