POP4 POP4 homolog, ribonuclease P/MRP subunit [Homo sapiens (human)] - Gene

Summary

Official Symbol: POP4provided by HGNC
Official Full Name: POP4 homolog, ribonuclease P/MRP subunitprovided by HGNC
Primary source: HGNC:HGNC:30081
See related: Ensembl:ENSG00000105171 MIM:606114; AllianceGenome:HGNC:30081
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RPP29
Summary: 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]
Expression: Ubiquitous expression in testis (RPKM 7.0), lymph node (RPKM 6.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q12

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (29606283..29617237)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (32131858..32142812)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (30097190..30108144)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rpp29 regulates H3.3-mediated epigenetic mechanisms by processing a transcribed signal that recruits H3.3 to its incorporation sites
Title: Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms.
Results demonstrate that Rpp29 promotes homology-directed repair of double-strand breaks. It is rapidly and transiently recruited to laser-microirradiated DNA sites.
Title: A role of human RNase P subunits, Rpp29 and Rpp21, in homology directed-repair of double-strand breaks.
Collectively, the present results suggest that PhoRpp21 binds the loop between P11 and P12 helices through overall positively charged clusters on the surface of the complex and serves as a scaffold for PhoRpp29 to optimize structural conformation of its N-terminal helix (alpha2) in PhoRpp21, as well as C-terminal residues in PhoRpp29, for RNase P activity.
Title: Functional characterization of archaeal homologs of human nuclear RNase P proteins Rpp21 and Rpp29 provides insights into the molecular basis of their cooperativity in catalysis.
Rpp29 represses H3.3 nucleosome deposition, a finding with implications for epigenetic regulation.
Title: RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	HIV-1 Vpr downregulates POP4 in HeLa cells within 12 hours of exposure	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-W74757 (e-PCR)
- UniSTS:46903

WI-11914 (e-PCR)
- UniSTS:41531

RH104441 (e-PCR)
- UniSTS:98766

Homology

Homologs of the POP4 gene: The POP4 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, and frog.
Orthologs from Annotation Pipeline: 482 organisms have orthologs with human gene POP4
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribonuclease P RNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables ribonuclease P RNA binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to ribonuclease P activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA phosphodiester bond hydrolysis, endonucleolytic	IEA Inferred from Electronic Annotation more info
involved_in rRNA processing	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in tRNA 5'-leader removal	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of multimeric ribonuclease P complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
part_of ribonuclease MRP complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of ribonuclease P complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed

General protein information

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Preferred Names: ribonuclease P protein subunit p29

Names: hPOP4

NP_006618.1

EC 3.1.26.5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_006627.3 → NP_006618.1 ribonuclease P protein subunit p29

See identical proteins and their annotated locations for NP_006618.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes processing of precursor 4.

Source sequence(s)

AC010505, BU727144, Y18863

Consensus CDS

CCDS12416.1

UniProtKB/Swiss-Prot

O95707, Q9UQQ3

Related

ENSP00000465213.1, ENST00000585603.6

Conserved Domains (1) summary

pfam01868
Location:128 → 210

UPF0086; Domain of unknown function UPF0086

RNA

NR_027368.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC010505, AK303791, BU727144

Related

ENST00000221770.7