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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.

Additional gene information for RPF1 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 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
GH01H085273 1.8 FANTOM5 ENCODE dbSUPER 10.5 +797.8 797807 6 FEZF1 DMAP1 YY1 SLC30A9 SP3 NFYC MEF2D ZNF610 ZNF585B GLIS1 ENSG00000232622 BCL10 LOC646626 RPF1 DDAH1
GH01H084618 1.6 Ensembl ENCODE dbSUPER 10.9 +141.0 140950 2 PKNOX1 ZFP64 SIN3A ZNF2 ZNF143 FOS SP3 ZC3H11A REST ZNF592 ENSG00000271576 SPATA1 CTBS GNG5 ENSG00000232622 RPF1 MCOLN3 LINC01461 GC01M084581
GH01H084718 1.5 Ensembl ENCODE dbSUPER 10 +241.6 241646 4 PKNOX1 FOXA2 ARID4B DMAP1 YY1 TCF12 GATA2 SP5 REST KAT8 RPF1 SSX2IP GC01P084746
GH01H084630 1.4 Ensembl ENCODE dbSUPER 10.3 +154.3 154260 5 PKNOX1 SIN3A RFX5 FOS RCOR1 ELF1 ZEB2 ZNF217 SMARCA4 MTA1 SPATA1 GNG5 RPF1 CTBS LINC01555 LINC01461
GH01H084697 1.4 Ensembl ENCODE dbSUPER 9.9 +219.6 219556 3 PKNOX1 ZSCAN4 INSM2 SCRT2 FOS CEBPB ZEB2 ZNF398 SMARCB1 NFIC LPAR3 RPF1 SSX2IP LINC01555 CTBS GC01P084746
- 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
ENSR00000009116 463 1801 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 CBX5 ZNF416

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 Lys182 and Lys237
  • 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

Gene Families for RPF1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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

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

No data available for UniProtKB/Swiss-Prot 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 --
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

CRISPR Products

miRNA for RPF1 Gene

miRTarBase miRNAs that target RPF1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RPF1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Subcellular locations from the

Human Protein Atlas (HPA)

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

Drugs & Compounds for RPF1 Gene

No Compound Related Data Available

Transcripts for RPF1 Gene

mRNA/cDNA for RPF1 Gene

Unigene Clusters for RPF1 Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RPF1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 CGAP 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

Evidence on tissue expression from TISSUES for RPF1 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with RPF1: view

Primer Products

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 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 33 34
  • 99.62 (n)
cow
(Bos Taurus)
Mammalia BXDC5 34
  • 95 (a)
OneToOne
RPF1 33
  • 93.51 (n)
dog
(Canis familiaris)
Mammalia RPF1 33 34
  • 93.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RPF1 34
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rpf1 33
  • 89.3 (n)
mouse
(Mus musculus)
Mammalia Rpf1 33 16 34
  • 89.11 (n)
oppossum
(Monodelphis domestica)
Mammalia RPF1 34
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves RPF1 33 34
  • 78.62 (n)
lizard
(Anolis carolinensis)
Reptilia RPF1 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rpf1 33
  • 76.31 (n)
Str.10818 33
zebrafish
(Danio rerio)
Actinopterygii rpf1 33 34
  • 71.55 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009968 33
  • 51.75 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6712 35 33 34
  • 51.56 (n)
worm
(Caenorhabditis elegans)
Secernentea F44G4.1 35 33 34
  • 61.74 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPF1 33 34 36
  • 56.54 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F21670g 33
  • 53.26 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL093C 33
  • 49.82 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons MEE49 33
  • 58.82 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3048 33
rice
(Oryza sativa)
Liliopsida Os06g0137500 33
  • 55 (n)
Os.15940 33
barley
(Hordeum vulgare)
Liliopsida Hv.6401 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 66 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC4F8.04 33
  • 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
rs1000046271 -- 84,485,183(+) CACTG(A/C)AACCT intron-variant
rs1000510086 -- 84,486,625(+) ATGAT(A/G)TGATC intron-variant
rs1000831980 -- 84,484,874(+) TCACC(A/T)TGTTG intron-variant
rs1000873203 -- 84,491,871(+) GTTTA(C/T)ATTTT intron-variant
rs1001191318 -- 84,480,782(+) AGCTC(A/C)TTTGG 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 KA … Baserga SJ (Molecular cell 2002) 2 3 4 60
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  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 60
  5. Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A … Diaz JJ (Molecular biology of the cell 2002) 3 4 60

Products for RPF1 Gene

Sources for RPF1 Gene

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