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Aliases for RPF1 Gene

Aliases for RPF1 Gene

  • Ribosome Production Factor 1 Homolog 2 3 5
  • Brix Domain-Containing Protein 5 3 4
  • Ribosome Biogenesis Protein RPF1 3 4
  • Ribosome Production Factor 1 2 3
  • Brix Domain Containing 5 2 3
  • BXDC5 3 4
  • Ribosome Production Factor 1 Homolog (S. Cerevisiae) 2
  • RNA Processing Factor 1 (RPF1) 3
  • RNA Processing Factor 1 2
  • 2310066N05Rik 3

External Ids for RPF1 Gene

Previous HGNC Symbols for RPF1 Gene

  • BXDC5

Previous GeneCards Identifiers for RPF1 Gene

  • GC01M085593
  • GC01P084082
  • GC01P084233
  • GC01P084367
  • GC01P084656
  • GC01P084717
  • GC01P084945
  • GC01P083055

Summaries for RPF1 Gene

GeneCards Summary for RPF1 Gene

RPF1 (Ribosome Production Factor 1 Homolog) is a Protein Coding gene. GO annotations related to this gene include poly(A) RNA binding and rRNA binding.

UniProtKB/Swiss-Prot for RPF1 Gene

  • May be required for ribosome biogenesis.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPF1 Gene

Genomics for RPF1 Gene

Regulatory Elements for RPF1 Gene

Enhancers for RPF1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F084618 1.3 Ensembl ENCODE 22.2 +141.0 140950 2.9 PKNOX1 ZFP64 SIN3A ZNF2 CBX5 ZNF143 FOS ZNF263 SP3 REST RPF1 SPATA1 CTBS ENSG00000232622 LOC105378818 GNG5 MCOLN3 LINC01461 GC01M084581
GH01F084298 1.1 ENCODE 18.6 -178.2 -178162 6.8 HDGF ATF1 ARNT CREB3L1 SIN3A FEZF1 ZNF48 ZNF2 YY1 GLIS2 RPF1 SYDE2 LOC105378818 BCL10 MCOLN3 DNASE2B UOX SAMD13 ENSG00000199959 ENSG00000249237
GH01F084582 1.7 FANTOM5 Ensembl ENCODE 10.7 +104.3 104294 1.3 PKNOX1 GLI4 FEZF1 ZNF2 ZNF121 GLIS2 KLF7 ZNF263 SP3 TSHZ1 LOC105378818 RPF1 CTBS SPATA1 GC01M084581 LINC01461
GH01F084478 1.1 ENCODE 16.3 +0.6 571 2.3 PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF416 ZNF143 SYDE2 C1orf52 RPF1 LOC105378818 MCOLN3 GNG5 CTBS SPATA1
GH01F085273 1.6 FANTOM5 ENCODE 10.5 +797.8 797807 6.9 HDGF PKNOX1 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 ENSG00000232622 BCL10 LOC646626 RPF1 DDAH1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RPF1 on UCSC Golden Path with GeneCards custom track

Promoters for RPF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001746913 464 2200 PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF416 ZNF143

Genomic Location for RPF1 Gene

Chromosome:
1
Start:
84,479,237 bp from pter
End:
84,498,350 bp from pter
Size:
19,114 bases
Orientation:
Plus strand

Genomic View for RPF1 Gene

Genes around RPF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPF1 Gene

Proteins for RPF1 Gene

  • Protein details for RPF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H9Y2-RPF1_HUMAN
    Recommended name:
    Ribosome production factor 1
    Protein Accession:
    Q9H9Y2
    Secondary Accessions:
    • Q5VSK7
    • Q6AHX1
    • Q8WXZ8

    Protein attributes for RPF1 Gene

    Size:
    349 amino acids
    Molecular mass:
    40111 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAH71915.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for RPF1 Gene

Post-translational modifications for RPF1 Gene

  • Ubiquitination at Lys 182 and Lys 237
  • Modification sites at PhosphoSitePlus

Other Protein References for RPF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RPF1 Gene

Domains & Families for RPF1 Gene

Protein Domains for RPF1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for RPF1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H9Y2

UniProtKB/Swiss-Prot:

RPF1_HUMAN :
  • Contains 1 Brix domain.
Domain:
  • Contains 1 Brix domain.
genes like me logo Genes that share domains with RPF1: view

No data available for Gene Families for RPF1 Gene

Function for RPF1 Gene

Molecular function for RPF1 Gene

UniProtKB/Swiss-Prot Function:
May be required for ribosome biogenesis.

Gene Ontology (GO) - Molecular Function for RPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,IDA 11864606
GO:0005515 protein binding IPI 25416956
GO:0019843 rRNA binding IEA --
GO:0042134 rRNA primary transcript binding IBA --
GO:0044822 poly(A) RNA binding IDA 22681889
genes like me logo Genes that share ontologies with RPF1: view
genes like me logo Genes that share phenotypes with RPF1: view

Animal Model Products

miRNA for RPF1 Gene

miRTarBase miRNAs that target RPF1

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPF1 Gene

Localization for RPF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPF1 Gene

Nucleus, nucleolus.

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 RPF1 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for RPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IEA,IDA 12429849
GO:0030687 preribosome, large subunit precursor IBA --
genes like me logo Genes that share ontologies with RPF1: view

Pathways & Interactions for RPF1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000027 ribosomal large subunit assembly IBA --
GO:0000460 maturation of 5.8S rRNA IBA --
GO:0000470 maturation of LSU-rRNA IBA --
GO:0006364 rRNA processing IEA --
GO:0042254 ribosome biogenesis IEA --
genes like me logo Genes that share ontologies with RPF1: view

No data available for Pathways by source and SIGNOR curated interactions for RPF1 Gene

Transcripts for RPF1 Gene

mRNA/cDNA for RPF1 Gene

Unigene Clusters for RPF1 Gene

Ribosome production factor 1 homolog (S. cerevisiae):
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RPF1 Gene

No ASD Table

Relevant External Links for RPF1 Gene

GeneLoc Exon Structure for
RPF1
ECgene alternative splicing isoforms for
RPF1

Expression for RPF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RPF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RPF1 Gene

This gene is overexpressed in Lung (53.7) and Blymphocyte (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RPF1 Gene



Protein tissue co-expression partners for RPF1 Gene

NURSA nuclear receptor signaling pathways regulating expression of RPF1 Gene:

RPF1

SOURCE GeneReport for Unigene cluster for RPF1 Gene:

Hs.481202
genes like me logo Genes that share expression patterns with RPF1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for RPF1 Gene

Orthologs for RPF1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RPF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RPF1 34 35
  • 99.62 (n)
cow
(Bos Taurus)
Mammalia BXDC5 35
  • 95 (a)
OneToOne
RPF1 34
  • 93.51 (n)
dog
(Canis familiaris)
Mammalia RPF1 34 35
  • 93.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RPF1 35
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rpf1 34
  • 89.3 (n)
mouse
(Mus musculus)
Mammalia Rpf1 34 16 35
  • 89.11 (n)
oppossum
(Monodelphis domestica)
Mammalia RPF1 35
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves RPF1 34 35
  • 78.62 (n)
lizard
(Anolis carolinensis)
Reptilia RPF1 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rpf1 34
  • 76.31 (n)
Str.10818 34
zebrafish
(Danio rerio)
Actinopterygii rpf1 34 35
  • 71.55 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009968 34
  • 51.75 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6712 36 34 35
  • 51.56 (n)
worm
(Caenorhabditis elegans)
Secernentea F44G4.1 36 34 35
  • 61.74 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPF1 34 35 37
  • 56.54 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F21670g 34
  • 53.26 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL093C 34
  • 49.82 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons MEE49 34
  • 58.82 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3048 34
rice
(Oryza sativa)
Liliopsida Os06g0137500 34
  • 55 (n)
Os.15940 34
barley
(Hordeum vulgare)
Liliopsida Hv.6401 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 66 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC4F8.04 34
  • 51.42 (n)
Species where no ortholog for RPF1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 RPF1 Gene

ENSEMBL:
Gene Tree for RPF1 (if available)
TreeFam:
Gene Tree for RPF1 (if available)

Paralogs for RPF1 Gene

(1) SIMAP similar genes for RPF1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with RPF1: view

No data available for Paralogs for RPF1 Gene

Variants for RPF1 Gene

Sequence variations from dbSNP and Humsavar for RPF1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1056979 -- 84,490,348(+) CTCTC(A/C)ACAGT reference, synonymous-codon
rs1056980 -- 84,490,361(+) TACCA(A/G)ACTCA reference, missense
rs1056981 -- 84,490,363(+) CCAAA(C/T)TCACA reference, synonymous-codon
rs10874447 -- 84,484,972(+) tagcc(A/G)gacca intron-variant
rs10874448 -- 84,496,958(+) CCTCC(A/G)CCTCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RPF1 Gene

Variant ID Type Subtype PubMed ID
nsv830437 CNV gain+loss 17160897
nsv946037 CNV duplication 23825009

Variation tolerance for RPF1 Gene

Residual Variation Intolerance Score: 81.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.65; 89.17% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RPF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPF1 Gene

Disorders for RPF1 Gene

Relevant External Links for RPF1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RPF1

No disorders were found for RPF1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RPF1 Gene

Publications for RPF1 Gene

  1. The sigma(70)-like motif: a eukaryotic RNA binding domain unique to a superfamily of proteins required for ribosome biogenesis. (PMID: 11864606) Wehner K.A. … Baserga S.J. (Mol. Cell 2002) 2 3 4 64
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A. … Diaz J.-J. (Mol. Biol. Cell 2002) 3 4 64

Products for RPF1 Gene

Sources for RPF1 Gene

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