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    Rpf2 ribosome production factor 2 homolog [ Mus musculus (house mouse) ]

    Gene ID: 67239, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Rpf2provided by MGI
    Official Full Name
    ribosome production factor 2 homologprovided by MGI
    Primary source
    MGI:MGI:1914489
    See related
    Ensembl:ENSMUSG00000038510 AllianceGenome:MGI:1914489
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Bxdc1; 2810470K21Rik
    Summary
    Predicted to enable 5S rRNA binding activity and DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); protein localization to nucleolus; and regulation of signal transduction by p53 class mediator. Predicted to be located in chromosome and nucleoplasm. Predicted to be active in nucleolus. Is expressed in cerebral cortex ventricular layer and cortical plate. Orthologous to human RPF2 (ribosome production factor 2 homolog). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in CNS E11.5 (RPKM 9.1), liver E14 (RPKM 6.9) and 18 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rpf2 in Genome Data Viewer
    Location:
    10 B1; 10 21.76 cM
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (40099242..40123035, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (40223246..40247039, complement)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene solute carrier family 16 (monocarboxylic acid transporters), member 10 Neighboring gene predicted gene, 25613 Neighboring gene CapStarr-seq enhancer MGSCv37_chr10:39873206-39873472 Neighboring gene STARR-positive B cell enhancer ABC_E11435 Neighboring gene predicted gene, 31992 Neighboring gene STARR-seq mESC enhancer starr_26412 Neighboring gene CapStarr-seq enhancer MGSCv37_chr10:39952398-39952599 Neighboring gene STARR-positive B cell enhancer ABC_E10600 Neighboring gene STARR-seq mESC enhancer starr_26413 Neighboring gene general transcription factor IIIC, polypeptide 6, alpha Neighboring gene small nucleolar RNA, C/D box 3A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. A molecular profile of a hematopoietic stem cell niche. Hackney JA, et al. Proc Natl Acad Sci U S A, 2002 Oct 1. PMID 12226475, Free PMC Article
    2. Beads-free protein immunoprecipitation for a mass spectrometry-based interactome and posttranslational modifications analysis. Mikula M, et al. Proteome Sci, 2015. PMID 26336360, Free PMC Article
    3. The level of the transcription factor Pax6 is essential for controlling the balance between neural stem cell self-renewal and neurogenesis. Sansom SN, et al. PLoS Genet, 2009 Jun. PMID 19521500, Free PMC Article
    4. New roles for the de-ubiquitylating enzyme OTUD4 in an RNA-protein network and RNA granules. Das R, et al. J Cell Sci, 2019 Jun 17. PMID 31138677, Free PMC Article
    5. ATG5 is required for B cell polarization and presentation of particulate antigens. Arbogast F, et al. Autophagy, 2019 Feb. PMID 30196744, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    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 MGI

    Function Evidence Code Pubs
    enables 5S rRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables 5S rRNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables rRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in maturation of LSU-rRNA IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of signal transduction by p53 class mediator ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of signal transduction by p53 class mediator ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ribosomal large subunit assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ribosomal large subunit biogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ribosomal large subunit biogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    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
    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_001042556.1 → NP_001036021.1  ribosome production factor 2 homolog isoform 2

      See identical proteins and their annotated locations for NP_001036021.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate splice site in the 5' region and initiates translation at a downstream start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AB041810, AK051135
      Consensus CDS
      CCDS35885.1
      UniProtKB/TrEMBL
      G3X926
      Related
      ENSMUSP00000035456.6, ENSMUST00000045114.13
      Conserved Domains (1) summary
      cl00935
      Location:1 → 253
      Brix; Brix domain

    2. NM_023323.3 → NP_075812.3  ribosome production factor 2 homolog isoform 1

      See identical proteins and their annotated locations for NP_075812.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK012641, AK051135, BQ828311
      Consensus CDS
      CCDS59543.1
      UniProtKB/Swiss-Prot
      Q8R3K6, Q9CQ34, Q9CSY9, Q9CYR9, Q9JJ80
      Related
      ENSMUSP00000138581.2, ENSMUST00000183309.8
      Conserved Domains (1) summary
      cl00935
      Location:6 → 286
      Brix; Brix domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      40099242..40123035 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9JJ80.2 GenPept UniProtKB/Swiss-Prot:Q9JJ80

    Gene LinkOut

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

    Other Literature Sources
    Chemical Information
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