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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RPF2 Gene

protein-coding   GIFtS: 48
GCID: GC06P111306

ribosome production factor 2 homolog (S. cerevisiae)

(Previous name: brix domain containing 1 )
(Previous symbol: BXDC1)
  Search for RPF2
in our new
 Human Malady Compendium 
Biological research products
for RPF2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Ribosome Production Factor 2 Homolog (S. Cerevisiae)1 2     Ribosome Biogenesis Protein RPF2 Homolog2 3
BXDC11 2 3     FLJ210871
BA397G5.41     Homolog Of Rpf22
Brix Domain Containing 11 2     Ribosomal Processing Factor 2 Homolog2
Brix Domain-Containing Protein 12 3     Ribosome Production Factor 2 Homolog2

External Ids:    HGNC: 208701   Entrez Gene: 841542   Ensembl: ENSG000001974987   UniProtKB: Q9H7B23   

Export aliases for RPF2 gene to outside databases

Previous GC identifers: GC06P111410 GC06P108874


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

  --

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_025741.15  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for RPF2
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRPF2 promoter sequence
   Search SABiosciences Chromatin IP Primers for RPF2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RPF2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q21   Ensembl cytogenetic band:  6q21   HGNC cytogenetic band: 6q21

RPF2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPF2 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P111306:  view genomic region     (about GC identifiers)

Start:
111,303,218 bp from pter      End:
111,347,303 bp from pter
Size:
44,086 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: RPF2_HUMAN, Q9H7B2 (See protein sequence)
Recommended Name: Ribosome production factor 2 homolog  
Size: 306 amino acids; 35583 Da
Subcellular location: Nucleus, nucleolus. Note=Associated with the nucleolus in an RNA-dependent manner
Secondary accessions: Q5VXN1 Q8N4A1

Explore the universe of human proteins at neXtProt for RPF2: NX_Q9H7B2

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H7B2

  • RPF2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_115570.1  
    ENSEMBL proteins: 
     ENSP00000357857   ENSP00000402338   ENSP00000414026  

    Human Recombinant Protein Products: 
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for RPF2

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730nucleolus IDA--


    RPF2 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for RPF2


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    RPF2 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR007109 Brix

    Graphical View of Domain Structure for InterPro Entry Q9H7B2

    ProtoNet protein and cluster: Q9H7B2

    1 Blocks protein family: IPB007109 Brix domain

    UniProtKB/Swiss-Prot: RPF2_HUMAN, Q9H7B2
    Similarity: Belongs to the RPF2 family
    Similarity: Contains 1 Brix domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    miRNA
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    Inhib. RNA
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RPF2

    4 GenomeRNAi human phenotypes for RPF2:
     G0/1 arrest  Increased S DNA content  Nuclear 60S biogenesis defects  Synthetic lethal with Ras 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RPF2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/312 Interacting proteins for RPF2 (Q9H7B23 ENSP000004023384) via UniProtKB, MINT, STRING, and/or I2D (see all 312)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=4 
    HIST1H4BP628053I2D: score=4 
    HIST1H4CP628053I2D: score=4 
    HIST1H4DP628053I2D: score=4 
    HIST1H4EP628053I2D: score=4 
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RPF2
    Search CenterWatch for drugs/clinical trials and news about RPF2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RPF2 gene: 
    NM_032194.1  

    Unigene Cluster for RPF2:

    Ribosome production factor 2 homolog (S. cerevisiae)
    Hs.372265  [show with all ESTs]
    Unigene Representative Sequence: AL833613
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000368864 ENST00000441448(uc003pun.3 uc003puo.3) ENST00000425871


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    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for RPF2 (see all 4)
    OriGene shRNA RFP: RPF2
    OriGene siRNA: RPF2
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    Clone
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RPF2
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RPF2

    Additional cDNA sequence: 

    AK024740.1 AK056264.1 AK292165.1 AK301662.1 AL833613.1 BC005347.1 BC035314.1 

    8 DOTS entries:

    DT.413903  DT.97793674  DT.120805623  DT.95173586  DT.121368375  DT.91985118  DT.121368368  DT.97792817 

    24/205 AceView cDNA sequences (see all 205):

    BM787019 BQ011419 BC035314 BM982648 BQ010984 AI885480 AA404386 AI638766 
    BG286825 AW819530 AI989527 BQ016301 AW294027 AA809843 BM838484 BM700470 
    BM796820 BU615400 BQ216082 AW089370 BX281051 CB148131 AI082003 C20819 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RPF2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATACTTTTGG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    RPF2 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    OvaryPrimary FolliclePrimary OocyteFemale Gametocytes, Germ Cells
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See RPF2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RPF2

    SOURCE GeneReport for Unigene cluster: Hs.372265
        SABiosciences Custom PCR Arrays for RPF2
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RPF2

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for RPF2 gene from 10/34 species (see all 34)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rpf21 , 5 ribosome production factor 2 homolog (S. cerevisiae)1, 5 88.56(n)1
    92.16(a)1
      10 (21.76 cM)5
    672391  NM_023323.31  NP_075812.31 
     402232465 
    chicken
    (Gallus gallus)
    Aves RPF21 ribosome production factor 2 homolog (S. cerevisiae) 77.63(n)
    86.18(a)
      428624  XM_426181.3  XP_426181.2 
    lizard
    (Anolis carolinensis)
    Reptilia RPF26
    --
    80(a)
    1 ↔ 1
    1(192059310-192082545)
    African clawed frog
    (Xenopus laevis)
    Amphibia bxdc1-prov2 brix domain containing 1 76.83(n)    BC046945.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BI673159.12   -- 77.61(n)   337815  BI673159.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG79931 CG7993 50.94(n)
    47.18(a)
      42183  NM_142437.2  NP_650694.2 
    worm
    (Caenorhabditis elegans)
    Secernentea Y54E10A.101 Protein Y54E10A.10 49.12(n)
    43.46(a)
      171892  NM_058716.4  NP_491117.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes RPF2(YKR081C)4
    RPF21
    Essential protein involved in the processing of pre-rRNA more4
    Rpf2p1
    52.13(n)1
    48.23(a)1
      11(592540-591506)4
    8539561, 4  NP_013007.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G236201 ribosome production factor 2-like protein 52.66(n)
    45.08(a)
      821942  NM_113266.3  NP_566734.1 
    rice
    (Oryza sativa)
    Liliopsida Os01g05138001 hypothetical protein 50.34(n)
    44.14(a)
      4323989  NM_001049720.1  NP_001043185.1 


    ENSEMBL Gene Tree for RPF2 (if available)
    TreeFam Gene Tree for RPF2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RPF2 gene

    RPF2 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for RPF2
    PGOHUM00000247649 PGOHUM00000246042


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/934 NCBI SNPs in RPF2 are shown (see all 934    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs763723871,2
    C,--111301291(+) TTCAG-/CCTTCT 1 -- us2k10--------
    rs353465831,2
    C,F,--111301292(+) TCAGAC/-TTCTG 1 -- us2k13Minor allele frequency- -:0.50NA CSA 6
    rs1125778241,2
    C,--111301302(+) GACTTG/CCTGAA 1 -- us2k11Minor allele frequency- C:0.50WA 2
    rs1393396211,2
    --111301404(+) TGCAGA/GTGCTT 1 -- us2k10--------
    rs801592971,2
    F,--111301455(+) GAGTCA/GGCATA 1 -- us2k11Minor allele frequency- G:0.05NA 120
    rs1835338351,2
    --111301482(+) CTCCTA/GGAGAA 1 -- us2k10--------
    rs1477392381,2
    --111301554(+) GCACGC/TGCTTG 1 -- us2k10--------
    rs45918991,2
    C,F,A,--111301613(+) GGAGAT/CGGAGG 1 -- us2k19Minor allele frequency- C:0.37NA WA CSA EA 369
    rs23418631,2
    C,F,A,--111301628(-) CTCAGG/CTTACT 1 -- us2k19Minor allele frequency- C:0.37NA WA CSA EA 369
    rs610886671,2
    C,--111301669(+) AGAGTG/AAGACT 1 -- us2k11Minor allele frequency- A:0.50WA 2

    HapMap Linkage Disequilibrium report for RPF2 (111303218 - 111347303 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for RPF2
         1 CNV: 99664

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    RPF2 for disorders           About MalaCards

    RPF2 for disorders           About GeneDecksing

    Human Genome Epidemiology (HuGE) Navigator: RPF2 (1 document)

    Export disorders for RPF2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for RPF2 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with RPF2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus. (PubMed id 19170763)1, 2 Hirano Y....Horigome T. (2009)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. 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. (PubMed id 12048200)1, 3 Morita D....Mizuta K. (2002)
    5. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (2002)
    6. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    8. Proliferating cell nuclear antigen (PCNA)-associated KIAA0101/PAF15 protein is a cell cycle-regulated anaphase-promoting complex/cyc losome substrate. (PubMed id 21628590)1 Emanuele M.J....Elledge S.J. (2011)
    9. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    10. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 84154 HGNC: 20870 AceView: BXDC1 Ensembl:ENSG00000197498 euGenes: HUgn84154
    ECgene: RPF2 H-InvDB: RPF2

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RPF2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for RPF2 gene:
    Search GeneIP for patents involving RPF2

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     OriGene Antibodies for RPF2   OriGene shRNA RFP for RPF2  
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     RPF2 Proteins, Antibodies, CLIAs, and ELISAs
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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    VWF
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    von Willebrand factor
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