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RPP40 ribonuclease P/MRP subunit p40 [ Homo sapiens (human) ]

Gene ID: 10799, updated on 2-Nov-2024

Summary

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Official Symbol
RPP40provided by HGNC
Official Full Name
ribonuclease P/MRP subunit p40provided by HGNC
Primary source
HGNC:HGNC:20992
See related
Ensembl:ENSG00000124787 MIM:606117; AllianceGenome:HGNC:20992
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RNASEP1; bA428J1.3
Summary
Enables ribonuclease P RNA binding activity. Contributes to ribonuclease P activity. Involved in tRNA 5'-leader removal. Part of multimeric ribonuclease P complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in adrenal (RPKM 3.2), testis (RPKM 2.4) and 25 other tissues See more
Orthologs
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Genomic context

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See RPP40 in Genome Data Viewer
Location:
6p25.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (4988426..5004037, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (4855789..4873023, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (4994951..5004271, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene chromodomain Y like Neighboring gene uncharacterized LOC105374897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4903364-4903864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16863 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:4922310-4922536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4922523-4923034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4923035-4923546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4924846-4925614 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4925615-4926383 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4932371-4933089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4947173-4947916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4971812-4972338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4972339-4972863 Neighboring gene MPRA-validated peak5629 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16865 Neighboring gene MPRA-validated peak5630 silencer Neighboring gene uncharacterized LOC124901248 Neighboring gene ribosomal protein S18 pseudogene 8 Neighboring gene LYRM4 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5027971-5028470 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:5031032-5031192 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:5044856-5046055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5063575-5064076 Neighboring gene LYR motif containing 4 Neighboring gene TFB2M pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Viperin mRNA is a novel target for the human RNase MRP/RNase P endoribonuclease. Mattijssen S, et al. Cell Mol Life Sci, 2011 Jul. PMID 21053045, Free PMC Article
  2. Autoantigenic properties of some protein subunits of catalytically active complexes of human ribonuclease P. Jarrous N, et al. RNA, 1998 Apr. PMID 9630247, Free PMC Article
  3. Identification and characterization of essential genes in the human genome. Wang T, et al. Science, 2015 Nov 27. PMID 26472758, Free PMC Article
  4. Mutual interactions between subunits of the human RNase MRP ribonucleoprotein complex. Welting TJ, et al. Nucleic Acids Res, 2004. PMID 15096576, Free PMC Article
  5. Cryo-EM Structure of the Human Ribonuclease P Holoenzyme. Wu J, et al. Cell, 2018 Nov 15. PMID 30454648

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Data idenified two cleavage sites for RNase MRP/RNase P in the coding sequence of viperin mRNA.
    Title: Viperin mRNA is a novel target for the human RNase MRP/RNase P endoribonuclease.
Submit: New GeneRIF Correction

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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Replication interactions

Interaction Pubs
Knockdown of ribonuclease P/MRP 40kDa subunit (RPP40) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to ribonuclease MRP activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ribonuclease P RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to ribonuclease P activity IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to ribonuclease P activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA 5'-leader removal IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA 5'-leader removal IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of multimeric ribonuclease P complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of multimeric ribonuclease P complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of nucleolar ribonuclease P complex TAS
Traceable Author Statement
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 
part_of ribonuclease MRP complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ribonuclease P protein subunit p40
Names
RNase P subunit 1
RNaseP protein p40
ribonuclease P (40 kD)
ribonuclease P, 40kD subunit
ribonuclease P/MRP 40kDa subunit
ribonuclease P1
NP_001273061.1
NP_001273062.1
NP_006629.2
XP_011512555.1
XP_024302077.1
XP_047274051.1
XP_047274052.1
XP_054210037.1
XP_054210038.1
XP_054210039.1
XP_054210040.1

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)

  1. NM_001286132.2 → NP_001273061.1  ribonuclease P protein subunit p40 isoform b

    See identical proteins and their annotated locations for NP_001273061.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AL359643, BC017871, BM015573, BU607286, BX951376
    Consensus CDS
    CCDS69040.1
    UniProtKB/TrEMBL
    X6RLL4
    Related
    ENSP00000317998.5, ENST00000319533.9
    Conserved Domains (1) summary
    pfam08584
    Location:75 → 320
    Ribonuc_P_40; Ribonuclease P 40kDa (Rpp40) subunit

  2. NM_001286133.2 → NP_001273062.1  ribonuclease P protein subunit p40 isoform c

    See identical proteins and their annotated locations for NP_001273062.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform a.
    Source sequence(s)
    AL359643, BC017871, BM827175, BU607286, BX951376
    Consensus CDS
    CCDS75391.1
    UniProtKB/TrEMBL
    A0A087X1N3, X6RLL4
    Related
    ENSP00000484334.1, ENST00000618533.4
    Conserved Domains (1) summary
    pfam08584
    Location:75 → 301
    Ribonuc_P_40; Ribonuclease P 40kDa (Rpp40) subunit

  3. NM_006638.4 → NP_006629.2  ribonuclease P protein subunit p40 isoform a

    See identical proteins and their annotated locations for NP_006629.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AL359643, BC017871, BQ220155, BU607286, BX951376
    Consensus CDS
    CCDS34333.1
    UniProtKB/Swiss-Prot
    O75818, Q5VX97, Q8WVK8
    UniProtKB/TrEMBL
    X6RLL4
    Related
    ENSP00000369391.2, ENST00000380051.7
    Conserved Domains (1) summary
    pfam08584
    Location:75 → 343
    Ribonuc_P_40; Ribonuclease P 40kDa (Rpp40) subunit

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    4988426..5004037 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418096.1 → XP_047274052.1  ribonuclease P protein subunit p40 isoform X3

  2. XM_024446309.2 → XP_024302077.1  ribonuclease P protein subunit p40 isoform X4

    Conserved Domains (1) summary
    pfam08584
    Location:75 → 255
    Ribonuc_P_40; Ribonuclease P 40kDa (Rpp40) subunit

  3. XM_011514253.3 → XP_011512555.1  ribonuclease P protein subunit p40 isoform X1

    Conserved Domains (1) summary
    pfam08584
    Location:75 → 297
    Ribonuc_P_40; Ribonuclease P 40kDa (Rpp40) subunit

  4. XM_047418095.1 → XP_047274051.1  ribonuclease P protein subunit p40 isoform X2

RNA

  1. XR_007059200.1 RNA Sequence

  2. XR_926031.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    4855789..4873023 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354064.1 → XP_054210039.1  ribonuclease P protein subunit p40 isoform X3

  2. XM_054354065.1 → XP_054210040.1  ribonuclease P protein subunit p40 isoform X4

  3. XM_054354062.1 → XP_054210037.1  ribonuclease P protein subunit p40 isoform X1

  4. XM_054354063.1 → XP_054210038.1  ribonuclease P protein subunit p40 isoform X2

RNA

  1. XR_008487243.1 RNA Sequence

  2. XR_008487242.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75818.3 GenPept UniProtKB/Swiss-Prot:O75818

Gene LinkOut

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