This gene encodes one of the protein subunits of the small nucleolar ribonucleoprotein complexes: the endoribonuclease for mitochondrial RNA processing complex and the ribonuclease P complex. The encoded protein is localized to the nucleus and associates directly with the RNA component of these complexes. This protein is involved in processing of precursor RNAs. Alternative spl... See more...

Aliases for POP4 Gene

Aliases for POP4 Gene

  • POP4 Homolog, Ribonuclease P/MRP Subunit 2 3 5
  • RPP29 2 3 4
  • Ribonuclease P Protein Subunit P29 3 4
  • EC 3.1.26.5 4 51
  • HPOP4 3 4
  • Processing Of Precursor 4, Ribonuclease P/MRP Subunit (S. Cerevisiae) 2
  • POP4 5

External Ids for POP4 Gene

Previous GeneCards Identifiers for POP4 Gene

  • GC19P030719
  • GC19P030546
  • GC19P034773
  • GC19P034789
  • GC19P030097
  • GC19P026609

Summaries for POP4 Gene

Entrez Gene Summary for POP4 Gene

  • This gene encodes one of the protein subunits of the small nucleolar ribonucleoprotein complexes: the endoribonuclease for mitochondrial RNA processing complex and the ribonuclease P complex. The encoded protein is localized to the nucleus and associates directly with the RNA component of these complexes. This protein is involved in processing of precursor RNAs. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]

GeneCards Summary for POP4 Gene

POP4 (POP4 Homolog, Ribonuclease P/MRP Subunit) is a Protein Coding gene. Diseases associated with POP4 include Intracystic Papillary Adenoma. Among its related pathways are tRNA processing and Gene Expression. Gene Ontology (GO) annotations related to this gene include RNA binding and ribonuclease P activity.

UniProtKB/Swiss-Prot Summary for POP4 Gene

  • Component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5'-ends.

Gene Wiki entry for POP4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for POP4 Gene

Genomics for POP4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for POP4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around POP4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for POP4

Top Transcription factor binding sites by QIAGEN in the POP4 gene promoter:
  • AREB6
  • Bach1
  • Bach2
  • HOXA9
  • HOXA9B
  • ITF-2
  • Meis-1
  • Meis-1a
  • NF-AT
  • Tal-1beta

Genomic Locations for POP4 Gene

Genomic Locations for POP4 Gene
chr19:29,606,283-29,617,237
(GRCh38/hg38)
Size:
10,955 bases
Orientation:
Plus strand
chr19:30,094,924-30,108,162
(GRCh37/hg19)
Size:
13,239 bases
Orientation:
Plus strand

Genomic View for POP4 Gene

Genes around POP4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
POP4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for POP4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for POP4 Gene

Proteins for POP4 Gene

  • Protein details for POP4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95707-RPP29_HUMAN
    Recommended name:
    Ribonuclease P protein subunit p29
    Protein Accession:
    O95707
    Secondary Accessions:
    • Q5XKL7
    • Q6FHW9
    • Q9UQQ3

    Protein attributes for POP4 Gene

    Size:
    220 amino acids
    Molecular mass:
    25425 Da
    Quaternary structure:
    • Component of nuclear RNase P and RNase MRP ribonucleoproteins (PubMed:10024167, PubMed:10352175, PubMed:30454648). RNase P consists of a catalytic RNA moiety and 10 different protein chains; POP1, POP4, POP5, POP7, RPP14, RPP21, RPP25, RPP30, RPP38 and RPP40 (PubMed:16723659, PubMed:30454648). Within the RNase P complex, POP1, POP7 and RPP25 form the 'finger' subcomplex, POP5, RPP14, RPP40 and homodimeric RPP30 form the 'palm' subcomplex, and RPP21, POP4 and RPP38 form the 'wrist' subcomplex. All subunits of the RNase P complex interact with the catalytic RNA (PubMed:30454648). Several subunits of RNase P are also part of the RNase MRP complex. RNase MRP consists of a catalytic RNA moiety and about 8 protein subunits; POP1, POP7, RPP25, RPP30, RPP38, RPP40 and possibly also POP4 and POP5 (PubMed:15096576).

    Three dimensional structures from OCA and Proteopedia for POP4 Gene

neXtProt entry for POP4 Gene

Selected DME Specific Peptides for POP4 Gene

O95707:
  • QRAEAFVRAFLK
  • FISYIYGSKFQLR
  • TGILLQETKH
  • LKVIPKLNCVFT
  • SERSAKKFKAKG

Post-translational modifications for POP4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for POP4 Gene

Domains & Families for POP4 Gene

Gene Families for POP4 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for POP4 Gene

InterPro:
Blocks:
  • Protein of unknown function UPF0086
ProtoNet:

Suggested Antigen Peptide Sequences for POP4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57473, highly similar to Ribonuclease P protein subunit p29 (EC 3.1.26.5) (A8MYC1_HUMAN)
  • Ribonuclease P protein subunit p29 (RPP29_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O95707

UniProtKB/Swiss-Prot:

RPP29_HUMAN :
  • Belongs to the eukaryotic/archaeal RNase P protein component 1 family.
Family:
  • Belongs to the eukaryotic/archaeal RNase P protein component 1 family.
genes like me logo Genes that share domains with POP4: view

Function for POP4 Gene

Molecular function for POP4 Gene

UniProtKB/Swiss-Prot Function:
Component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5'-ends.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor.; EC=3.1.26.5; Evidence={ECO:0000269|PubMed:10352175, ECO:0000269|PubMed:30454648};.

Enzyme Numbers (IUBMB) for POP4 Gene

Phenotypes From GWAS Catalog for POP4 Gene

Gene Ontology (GO) - Molecular Function for POP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000171 contributes_to ribonuclease MRP activity IBA 21873635
GO:0003723 RNA binding IEA --
GO:0004526 contributes_to ribonuclease P activity IBA,IDA 16723659
GO:0004540 ribonuclease activity IEA --
GO:0005515 protein binding IPI 15096576
genes like me logo Genes that share ontologies with POP4: view
genes like me logo Genes that share phenotypes with POP4: view

Animal Models for POP4 Gene

MGI Knock Outs for POP4:
  • Pop4 Pop4<tm1a(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for POP4

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for POP4 Gene

Localization for POP4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for POP4 Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for POP4 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for POP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000172 ribonuclease MRP complex IBA 21873635
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA,IDA 10444065
GO:0030677 ribonuclease P complex IEA,IBA 21873635
genes like me logo Genes that share ontologies with POP4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for POP4 Gene

Pathways & Interactions for POP4 Gene

genes like me logo Genes that share pathways with POP4: view

Pathways by source for POP4 Gene

Gene Ontology (GO) - Biological Process for POP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001682 tRNA 5'-leader removal TAS --
GO:0006364 rRNA processing IBA 21873635
GO:0006396 RNA processing IEA --
GO:0008033 tRNA processing IEA --
GO:0090501 RNA phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with POP4: view

No data available for SIGNOR curated interactions for POP4 Gene

Drugs & Compounds for POP4 Gene

No Compound Related Data Available

Transcripts for POP4 Gene

mRNA/cDNA for POP4 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
13 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for POP4

Alternative Splicing Database (ASD) splice patterns (SP) for POP4 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c · 10d · 10e · 10f
SP1: - - - - - - - - -
SP2: - - - -
SP3: - - - - - - - - - - -
SP4: - - - - - - - - -
SP5: - - - -
SP6: - - - - - - -
SP7: - - - - - - - - - -
SP8: - - - - - - -
SP9: - - - - - -
SP10:
SP11: -
SP12: - - - - -

Relevant External Links for POP4 Gene

GeneLoc Exon Structure for
POP4

Expression for POP4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for POP4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Colon (Gastrointestinal Tract)
  • Ovary (Reproductive System)

Protein differential expression in normal tissues from HIPED for POP4 Gene

This gene is overexpressed in Lavage (51.9) and Lung (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for POP4 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for POP4

SOURCE GeneReport for Unigene cluster for POP4 Gene:

Hs.412870

Evidence on tissue expression from TISSUES for POP4 Gene

  • Nervous system(4.8)
  • Lung(4.6)
  • Skin(2.5)
  • Intestine(2.2)
  • Blood(2.1)
  • Kidney(2.1)
  • Muscle(2.1)
  • Bone marrow(2)
genes like me logo Genes that share expression patterns with POP4: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for POP4 Gene

Orthologs for POP4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for POP4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia POP4 30 31
  • 99.55 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia POP4 30 31
  • 88.18 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia POP4 30 31
  • 87.29 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia POP4 31
  • 84 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pop4 30
  • 83.48 (n)
Mouse
(Mus musculus)
Mammalia Pop4 30 17 31
  • 82.58 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia POP4 31
  • 73 (a)
OneToOne
Chicken
(Gallus gallus)
Aves POP4 30 31
  • 70.61 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia POP4 31
  • 70 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pop4 30
  • 63.62 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.3040 30
Zebrafish
(Danio rerio)
Actinopterygii pop4 30 31
  • 63.17 (n)
OneToOne
Dr.6289 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011713 30
  • 50.88 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG8038 30 31
  • 48.07 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea C15C6.4 31
  • 24 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes POP4 31 33
  • 20 (a)
OneToOne
Species where no ortholog for POP4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for POP4 Gene

ENSEMBL:
Gene Tree for POP4 (if available)
TreeFam:
Gene Tree for POP4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for POP4: view image

Paralogs for POP4 Gene

No data available for Paralogs for POP4 Gene

Variants for POP4 Gene

Additional dbSNP identifiers (rs#s) for POP4 Gene

Structural Variations from Database of Genomic Variants (DGV) for POP4 Gene

Variant ID Type Subtype PubMed ID
nsv1061604 CNV loss 25217958
nsv833799 CNV gain 17160897

Variation tolerance for POP4 Gene

Residual Variation Intolerance Score: 86.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.26; 40.54% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for POP4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
POP4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for POP4 Gene

Disorders for POP4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for POP4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
intracystic papillary adenoma
  • intracystic papilloma
- elite association - COSMIC cancer census association via MalaCards
Search POP4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for POP4

genes like me logo Genes that share disorders with POP4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for POP4 Gene

Publications for POP4 Gene

  1. Rpp14 and Rpp29, two protein subunits of human ribonuclease P. (PMID: 10024167) Jarrous N … Altman S (RNA (New York, N.Y.) 1999) 2 3 4 23
  2. hPop4: a new protein subunit of the human RNase MRP and RNase P ribonucleoprotein complexes. (PMID: 10352175) van Eenennaam H … van Venrooij WJ (Nucleic acids research 1999) 2 3 4 23
  3. Localization in the nucleolus and coiled bodies of protein subunits of the ribonucleoprotein ribonuclease P. (PMID: 10444065) Jarrous N … Altman S (The Journal of cell biology 1999) 3 4 23
  4. Cryo-EM Structure of the Human Ribonuclease P Holoenzyme. (PMID: 30454648) Wu J … Lei M (Cell 2018) 3 4
  5. Differential association of protein subunits with the human RNase MRP and RNase P complexes. (PMID: 16723659) Welting TJ … Pruijn GJ (RNA (New York, N.Y.) 2006) 3 4

Products for POP4 Gene

Sources for POP4 Gene