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

    Gene ID: 10799, updated on 9-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in adrenal (RPKM 3.2), testis (RPKM 2.4) and 25 other tissues See more
    Orthologs
    mouse all
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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
    • 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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