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    RPF2 ribosome production factor 2 homolog [ Homo sapiens (human) ]

    Gene ID: 84154, updated on 27-Nov-2024

    Summary

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    Official Symbol
    RPF2provided by HGNC
    Official Full Name
    ribosome production factor 2 homologprovided by HGNC
    Primary source
    HGNC:HGNC:20870
    See related
    Ensembl:ENSG00000197498 MIM:618471; AllianceGenome:HGNC:20870
    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
    BXDC1; bA397G5.4
    Summary
    Enables 5S rRNA binding activity. Involved in protein localization to nucleolus; regulation of signal transduction by p53 class mediator; and ribosomal large subunit biogenesis. Located in chromosome; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 6.1), testis (RPKM 4.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RPF2 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (110982038..111028263)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (112160651..112206881)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (111303241..111349466)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene PDGFA associated protein 1 pseudogene Neighboring gene MPRA-validated peak6032 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24939 Neighboring gene Sharpr-MPRA regulatory region 5639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24940 Neighboring gene small nucleolar RNA U13 Neighboring gene general transcription factor IIIC subunit 6 Neighboring gene uncharacterized LOC124901375 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:111337799-111338443 Neighboring gene RNA, U6 small nuclear 906, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17472 Neighboring gene glutathione S-transferase mu 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17473 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:111409089-111409589 Neighboring gene solute carrier family 16 member 10 Neighboring gene RNA, U6 small nuclear 960, pseudogene

    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. Clinical significance of ribosome production factor 2 homolog in hepatocellular carcinoma. An Y, et al. Clin Res Hepatol Gastroenterol, 2024 Mar. PMID 38307254
    2. Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus. Hirano Y, et al. Genes Cells, 2009 Feb. PMID 19170763
    3. Rpf2p, an evolutionarily conserved protein, interacts with ribosomal protein L11 and is essential for the processing of 27 SB Pre-rRNA to 25 S rRNA and the 60 S ribosomal subunit assembly in Saccharomyces cerevisiae. Morita D, et al. J Biol Chem, 2002 Aug 9. PMID 12048200
    4. The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress. Sloan KE, et al. Cell Rep, 2013 Oct 17. PMID 24120868, Free PMC Article
    5. DSSylation, a novel protein modification targets proteins induced by oxidative stress, and facilitates their degradation in cells. Zhang Y, et al. Protein Cell, 2014 Feb. PMID 24515614, Free PMC Article

    See all (111) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical significance of ribosome production factor 2 homolog in hepatocellular carcinoma.
      Title: Clinical significance of ribosome production factor 2 homolog in hepatocellular carcinoma.
    2. BXDC1 and EBNA1BP2 function in a dynamic scaffold for ribosome biogenesis.
      Title: Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus.
    Submit: New GeneRIF Correction

    Phenotypes

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    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21087

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5S rRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables rRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein localization to nucleolus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of signal transduction by p53 class mediator IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ribosomal large subunit assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ribosomal large subunit biogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromosome IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ribosome production factor 2 homolog
    Names
    brix domain containing 1
    brix domain-containing protein 1
    homolog of Rpf2
    ribosomal processing factor 2 homolog
    ribosome biogenesis protein RPF2 homolog

    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_001289111.2 → NP_001276040.1  ribosome production factor 2 homolog isoform 2

      See identical proteins and their annotated locations for NP_001276040.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate 5' exon and initiates translation at an alternate start codon, compared to variant 1. This results in a protein (isoform 2) that has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AL357515, AL833613, BG529605
      Conserved Domains (1) summary
      cl00935
      Location:3 → 234
      Brix; Brix domain

    2. NM_032194.3 → NP_115570.1  ribosome production factor 2 homolog isoform 1

      See identical proteins and their annotated locations for NP_115570.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL357515, AL833613, BC035314, BG529605
      Consensus CDS
      CCDS5088.1
      UniProtKB/Swiss-Prot
      Q5VXN1, Q8N4A1, Q9H7B2
      UniProtKB/TrEMBL
      A8K800
      Related
      ENSP00000402338.2, ENST00000441448.7
      Conserved Domains (1) summary
      cl00935
      Location:6 → 297
      Brix; Brix domain

    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
      110982038..111028263
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      112160651..112206881
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H7B2.2 GenPept UniProtKB/Swiss-Prot:Q9H7B2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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