Human Gene RPP40 (uc003mwl.3)
  Description: Homo sapiens ribonuclease P/MRP 40kDa subunit (RPP40), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr6:4,995,280-5,004,271 Size: 8,992 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr6:4,995,312-5,004,236 Size: 8,925 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:4,995,280-5,004,271)mRNA (may differ from genome)Protein (363 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RPP40_HUMAN
DESCRIPTION: RecName: Full=Ribonuclease P protein subunit p40; Short=RNaseP protein p40; EC=3.1.26.5; AltName: Full=RNase P subunit 1;
FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.
CATALYTIC ACTIVITY: Endonucleolytic cleavage of RNA, removing 5'- extranucleotides from tRNA precursor.
SUBUNIT: RNase P consists of a RNA moiety and at least 8 protein subunits; POP1, RPP14, RPP20/POP7, RPP25, RPP29/POP4, RPP30, RPP38 and RPP40.
SUBCELLULAR LOCATION: Nucleus, nucleolus (Potential).
SEQUENCE CAUTION: Sequence=AAC24114.1; Type=Erroneous initiation; Sequence=AAH17871.1; Type=Frameshift; Positions=327; Sequence=CAH73740.1; Type=Erroneous initiation;

-  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): RPP40
CDC HuGE Published Literature: RPP40
Positive Disease Associations: Myocardial Infarction
Related Studies:
  1. Myocardial Infarction
    , , . [PubMed 0]
  2. Myocardial Infarction
    , , . [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.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.32 RPKM in Adrenal Gland
Total median expression: 106.84 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 -6.4035-0.183 Picture PostScript Text
3' UTR -0.9032-0.028 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
IPR013893 - RNase_P_Rpp40

Pfam Domains:
PF08584 - Ribonuclease P 40kDa (Rpp40) subunit

ModBase Predicted Comparative 3D Structure on O75818
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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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004526 ribonuclease P activity
GO:0016787 hydrolase activity

Biological Process:
GO:0008033 tRNA processing
GO:0090501 RNA phosphodiester bond hydrolysis
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005655 nucleolar ribonuclease P complex
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  BC017871 - Homo sapiens ribonuclease P/MRP 40kDa subunit, mRNA (cDNA clone MGC:22670 IMAGE:4278825), complete cds.
CU676094 - Synthetic construct Homo sapiens gateway clone IMAGE:100022148 5' read RPP40 mRNA.
KJ902159 - Synthetic construct Homo sapiens clone ccsbBroadEn_11553 RPP40 gene, encodes complete protein.

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

Protein O75818 (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: NM_006638, NP_006629, O75818, Q5VX97, Q8WVK8, RNASEP1, RPP40_HUMAN
UCSC ID: uc003mwl.3
RefSeq Accession: NM_006638
Protein: O75818 (aka RPP40_HUMAN)
CCDS: CCDS34333.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006638.2
exon count: 8CDS single in 3' UTR: no RNA size: 1174
ORF size: 1092CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2384.00frame shift in genome: no % Coverage: 98.72
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.