Human Gene POP4 (ENST00000585603.6_4) from GENCODE V47lift37
  Description: POP4 homolog, ribonuclease P/MRP subunit, transcript variant 1 (from RefSeq NM_006627.3)
Gencode Transcript: ENST00000585603.6_4
Gencode Gene: ENSG00000105171.10_10
Transcript (Including UTRs)
   Position: hg19 chr19:30,097,190-30,108,144 Size: 10,955 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr19:30,097,226-30,106,287 Size: 9,062 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:30,097,190-30,108,144)mRNA (may differ from genome)Protein (220 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RPP29_HUMAN
DESCRIPTION: RecName: Full=Ribonuclease P protein subunit p29; Short=hPOP4; EC=3.1.26.5;
FUNCTION: Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. May function with RPP38 to coordinate the nucleolar targeting and/or assembly of RNase P.
CATALYTIC ACTIVITY: Endonucleolytic cleavage of RNA, removing 5'- extranucleotides from tRNA precursor.
SUBUNIT: Component of nuclear RNase P and RNase MRP ribonucleoproteins. RNase P consists of a RNA moiety and at least 8 protein subunits; POP1, RPP14, RPP20/POP7, RPP25, RPP29/POP4, RPP30, RPP38 and RPP40. RNase MRP consists of a RNA moiety and at least 9 protein subunits; POP1, RPP14, RPP20/POP7, RPP25, RPP29/POP4, RPP30, RPP38, RPP40, POP5 and RPP21. Interacts with RPP25 and POP5.
INTERACTION: Q99575:POP1; NbExp=2; IntAct=EBI-366477, EBI-366741; Q969H6:POP5; NbExp=2; IntAct=EBI-366477, EBI-366525; Q9BUL9:RPP25; NbExp=2; IntAct=EBI-366477, EBI-366570; P78345:RPP38; NbExp=2; IntAct=EBI-366477, EBI-366493;
SUBCELLULAR LOCATION: Nucleus, nucleolus.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the eukaryotic/archaeal RNase P protein component 1 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           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: 7.01 RPKM in Testis
Total median expression: 208.85 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 -9.3036-0.258 Picture PostScript Text
3' UTR -672.401857-0.362 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
IPR002730 - RNase_P/MRP_p29
IPR016848 - RNase_P/MRP_p29-subunit
IPR023534 - Rof/RNase_P-like

Pfam Domains:
PF01868 - Ribonuclease P/MRP, subunit p29

SCOP Domains:
101744 - Rof/RNase P subunit-like

ModBase Predicted Comparative 3D Structure on O95707
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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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0004526 ribonuclease P activity
GO:0004540 ribonuclease activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0033204 ribonuclease P RNA binding
GO:0000171 ribonuclease MRP activity

Biological Process:
GO:0001682 tRNA 5'-leader removal
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0008033 tRNA processing
GO:0090501 RNA phosphodiester bond hydrolysis
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic

Cellular Component:
GO:0000172 ribonuclease MRP complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0030677 ribonuclease P complex
GO:0030681 multimeric ribonuclease P complex


-  Descriptions from all associated GenBank mRNAs
  AK314790 - Homo sapiens cDNA, FLJ95660, Homo sapiens POP4 (processing of precursor, S. cerevisiae) homolog(POP4), mRNA.
AF001176 - Homo sapiens ribonuclease P protein subunit p29 (Rpp29) mRNA, complete cds.
BC013686 - Homo sapiens processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae), mRNA (cDNA clone IMAGE:3856962), containing frame-shift errors.
Y18863 - Homo sapiens mRNA for ribonuclease MRP protein subunit Pop4.
CR936714 - Homo sapiens mRNA; cDNA DKFZp781F17163 (from clone DKFZp781F17163).
BC006098 - Homo sapiens processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae), mRNA (cDNA clone MGC:12747 IMAGE:2989197), complete cds.
AK303791 - Homo sapiens cDNA FLJ57473 complete cds, highly similar to Ribonuclease P protein subunit p29 (EC 3.1.26.5).
BC004438 - Homo sapiens processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae), mRNA (cDNA clone MGC:3998 IMAGE:2820501), complete cds.
DQ893057 - Synthetic construct clone IMAGE:100005687; FLH193142.01X; RZPDo839D0278D processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae) (POP4) gene, encodes complete protein.
DQ896307 - Synthetic construct Homo sapiens clone IMAGE:100010767; FLH193138.01L; RZPDo839D0268D processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae) (POP4) gene, encodes complete protein.
CU675243 - Synthetic construct Homo sapiens gateway clone IMAGE:100018043 5' read POP4 mRNA.
KJ893132 - Synthetic construct Homo sapiens clone ccsbBroadEn_02526 POP4 gene, encodes complete protein.
KJ898283 - Synthetic construct Homo sapiens clone ccsbBroadEn_07677 POP4 gene, encodes complete protein.
CR536569 - Homo sapiens full open reading frame cDNA clone RZPDo834F0622D for gene POP4, POP4 (processing of precursor, S. cerevisiae) homolog; complete cds, incl. stopcodon.
JD554430 - Sequence 535454 from Patent EP1572962.
JD093533 - Sequence 74557 from Patent EP1572962.
JD278788 - Sequence 259812 from Patent EP1572962.
JD174638 - Sequence 155662 from Patent EP1572962.
JD239157 - Sequence 220181 from Patent EP1572962.

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

Protein O95707 (Reactome details) participates in the following event(s):

R-HSA-5696810 RNase P cleaves the 5' end of pre-tRNA
R-HSA-6784531 tRNA processing in the nucleus
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000585603.1, ENST00000585603.2, ENST00000585603.3, ENST00000585603.4, ENST00000585603.5, NM_006627, O95707, Q5XKL7, Q6FHW9, Q9UQQ3, RPP29, RPP29_HUMAN, uc326ozn.1, uc326ozn.2
UCSC ID: ENST00000585603.6_4
RefSeq Accession: NM_006627.3
Protein: O95707 (aka RPP29_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.