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Aliases for RPF2 Gene

Aliases for RPF2 Gene

  • Ribosome Production Factor 2 Homolog 2 3 5
  • Ribosome Biogenesis Protein RPF2 Homolog 3 4
  • Brix Domain-Containing Protein 1 3 4
  • Brix Domain Containing 1 2 3
  • BXDC1 3 4
  • Ribosomal Processing Factor 2 Homolog (S. Cerevisiae) 2
  • Ribosome Production Factor 2 Homolog (S. Cerevisiae) 2
  • Ribosomal Processing Factor 2 Homolog 3
  • Homolog Of Rpf2 3
  • BA397G5.4 3

External Ids for RPF2 Gene

Previous HGNC Symbols for RPF2 Gene

  • BXDC1

Previous GeneCards Identifiers for RPF2 Gene

  • GC06P111410
  • GC06P111306
  • GC06P108874

Summaries for RPF2 Gene

GeneCards Summary for RPF2 Gene

RPF2 (Ribosome Production Factor 2 Homolog) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include rRNA binding.

UniProtKB/Swiss-Prot for RPF2 Gene

  • Involved in ribosomal large subunit assembly. May regulate the localization of the 5S RNP/5S ribonucleoprotein particle to the nucleolus.

Additional gene information for RPF2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPF2 Gene

Genomics for RPF2 Gene

GeneHancer (GH) Regulatory Elements for RPF2 Gene

Promoters and enhancers for RPF2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I110981 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 559.7 +0.3 314 2.7 PKNOX1 CLOCK SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 RPF2 CDC40 GTF3C6 RNU6-957P GC06M111009
GH06I110873 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.1 -105.5 -105460 6.6 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 SP3 NFYC NBN AMD1 MFSD4B ENSG00000220506 BRD7P4 RPF2 CDK19 CNN2P9 FCF1P5 GTF3C6 RNU6-957P
GH06I110813 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 15.8 -166.7 -166708 4.1 CLOCK ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF263 SP3 CDK19 AMD1 MFSD4B ENSG00000220506 FCF1P5 RPF2 CNN2P9 BRD7P4 CDC40
GH06I110944 Enhancer 1.3 FANTOM5 Ensembl ENCODE 20.2 -37.1 -37096 1.4 PKNOX1 ATF1 SMAD1 BMI1 BATF IRF4 SCRT2 ZNF207 ATF7 ETV6 RPF2 CDK19 AMD1 SLC16A10 GTF3C6 LOC442244
GH06I110957 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.6 -23.2 -23224 2 HDGF SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 GTF3C6 TRAF3IP2-AS1 METTL24 ENSG00000220506 MFSD4B ENSG00000255389 ENSG00000272356 FCF1P5 RPF2 SLC16A10
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RPF2 on UCSC Golden Path with GeneCards custom track

Genomic Locations for RPF2 Gene

Genomic Locations for RPF2 Gene
chr6:110,982,015-111,028,263
(GRCh38/hg38)
Size:
46,249 bases
Orientation:
Plus strand
chr6:111,303,218-111,349,466
(GRCh37/hg19)

Genomic View for RPF2 Gene

Genes around RPF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPF2 Gene

Proteins for RPF2 Gene

  • Protein details for RPF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H7B2-RPF2_HUMAN
    Recommended name:
    Ribosome production factor 2 homolog
    Protein Accession:
    Q9H7B2
    Secondary Accessions:
    • Q5VXN1
    • Q8N4A1

    Protein attributes for RPF2 Gene

    Size:
    306 amino acids
    Molecular mass:
    35583 Da
    Quaternary structure:
    No Data Available

neXtProt entry for RPF2 Gene

Post-translational modifications for RPF2 Gene

No Post-translational modifications

Other Protein References for RPF2 Gene

No data available for DME Specific Peptides for RPF2 Gene

Domains & Families for RPF2 Gene

Gene Families for RPF2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RPF2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for RPF2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H7B2

UniProtKB/Swiss-Prot:

RPF2_HUMAN :
  • Belongs to the RPF2 family.
Family:
  • Belongs to the RPF2 family.
genes like me logo Genes that share domains with RPF2: view

Function for RPF2 Gene

Molecular function for RPF2 Gene

UniProtKB/Swiss-Prot Function:
Involved in ribosomal large subunit assembly. May regulate the localization of the 5S RNP/5S ribonucleoprotein particle to the nucleolus.

Phenotypes From GWAS Catalog for RPF2 Gene

Gene Ontology (GO) - Molecular Function for RPF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA,IDA 22658674
GO:0008097 5S rRNA binding IDA 24120868
GO:0019843 rRNA binding IBA --
genes like me logo Genes that share ontologies with RPF2: view
genes like me logo Genes that share phenotypes with RPF2: view

miRNA for RPF2 Gene

miRTarBase miRNAs that target RPF2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPF2 Gene

Localization for RPF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPF2 Gene

Nucleus, nucleolus. Note=Associated with the nucleolus in an RNA-dependent manner.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RPF2 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RPF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IDA,IBA --
genes like me logo Genes that share ontologies with RPF2: view

Pathways & Interactions for RPF2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RPF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000027 ribosomal large subunit assembly IBA --
GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA --
GO:0042254 ribosome biogenesis IEA --
GO:0042273 ribosomal large subunit biogenesis IMP 24120868
GO:1901796 regulation of signal transduction by p53 class mediator IMP 24120868
genes like me logo Genes that share ontologies with RPF2: view

No data available for Pathways by source and SIGNOR curated interactions for RPF2 Gene

Drugs & Compounds for RPF2 Gene

No Compound Related Data Available

Transcripts for RPF2 Gene

Unigene Clusters for RPF2 Gene

Ribosome production factor 2 homolog (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RPF2 Gene

No ASD Table

Relevant External Links for RPF2 Gene

GeneLoc Exon Structure for
RPF2
ECgene alternative splicing isoforms for
RPF2

Expression for RPF2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RPF2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RPF2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (21.8) and Pancreas (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RPF2 Gene



Protein tissue co-expression partners for RPF2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RPF2 Gene:

RPF2

SOURCE GeneReport for Unigene cluster for RPF2 Gene:

Hs.372265

Evidence on tissue expression from TISSUES for RPF2 Gene

  • Skin(4.2)
genes like me logo Genes that share expression patterns with RPF2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPF2 Gene

Orthologs for RPF2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RPF2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RPF2 33 34
  • 99.89 (n)
dog
(Canis familiaris)
Mammalia RPF2 33 34
  • 93.57 (n)
cow
(Bos Taurus)
Mammalia RPF2 33 34
  • 92.81 (n)
mouse
(Mus musculus)
Mammalia Rpf2 33 16 34
  • 88.56 (n)
oppossum
(Monodelphis domestica)
Mammalia RPF2 34
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rpf2 33
  • 87.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RPF2 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves RPF2 33 34
  • 78.64 (n)
lizard
(Anolis carolinensis)
Reptilia RPF2 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rpf2 33
  • 74.07 (n)
Str.551 33
African clawed frog
(Xenopus laevis)
Amphibia bxdc1-prov 33
zebrafish
(Danio rerio)
Actinopterygii rpf2 33 34
  • 65.57 (n)
-- 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4223 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003048 33
  • 51.8 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7993 33 34
  • 51.07 (n)
worm
(Caenorhabditis elegans)
Secernentea Y54E10A.10 33 34
  • 49.12 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPF2 33 34 36
  • 52.13 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A07931g 33
  • 49.88 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR215C 33
  • 48.91 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G23620 33
  • 52.66 (n)
rice
(Oryza sativa)
Liliopsida Os01g0513800 33
  • 50.34 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1078 34
  • 59 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC926.08c 33
  • 51.73 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU08595 33
  • 49.58 (n)
Species where no ortholog for RPF2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RPF2 Gene

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

Paralogs for RPF2 Gene

Pseudogenes.org Pseudogenes for RPF2 Gene

genes like me logo Genes that share paralogs with RPF2: view

No data available for Paralogs for RPF2 Gene

Variants for RPF2 Gene

Sequence variations from dbSNP and Humsavar for RPF2 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000058466 -- 111,025,807(+) C/T 3_prime_UTR_variant
rs1000212519 -- 110,990,899(+) G/ genic_upstream_transcript_variant, intron_variant
rs1000235831 -- 111,021,038(+) G/A intron_variant
rs1000236581 -- 110,980,369(+) C/A upstream_transcript_variant
rs1000266863 -- 111,020,867(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RPF2 Gene

Variant ID Type Subtype PubMed ID
esv2627811 CNV deletion 19546169
esv3610372 CNV loss 21293372
esv3610373 CNV loss 21293372
nsv1016001 CNV gain 25217958
nsv1020627 CNV gain 25217958
nsv1032572 CNV gain 25217958
nsv830773 CNV loss 17160897

Variation tolerance for RPF2 Gene

Residual Variation Intolerance Score: 73% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.91; 59.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPF2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPF2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPF2 Gene

Disorders for RPF2 Gene

Additional Disease Information for RPF2

No disorders were found for RPF2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RPF2 Gene

Publications for RPF2 Gene

  1. The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress. (PMID: 24120868) Sloan KE … Watkins NJ (Cell reports 2013) 3 4 58
  2. Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus. (PMID: 19170763) Hirano Y … Horigome T (Genes to cells : devoted to molecular & cellular mechanisms 2009) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. 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. (PMID: 12048200) Morita D … Mizuta K (The Journal of biological chemistry 2002) 2 3 58

Products for RPF2 Gene

Sources for RPF2 Gene

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