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

Gene ID: 84154, updated on 7-Apr-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, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 6.1), testis (RPKM 4.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
6q21
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (110982038..111028263)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (112160651..112206881)
105.20220307 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. 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
  2. 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
  3. 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
  4. 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
  5. FBXO22 degrades nuclear PTEN to promote tumorigenesis. Ge MK, et al. Nat Commun, 2020 Apr 6. PMID 32249768, Free PMC Article

See all (91) 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)

Genotypes

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 IBA
Inferred from Biological aspect of Ancestor
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_2023_10

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

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