RPF1 Gene (Protein Coding)

Ribosome Production Factor 1 Homolog

GC01P084479
GIFtS:
33
See more...

Aliases for RPF1 Gene

Aliases for RPF1 Gene

  • Ribosome Production Factor 1 Homolog 2 3 5
  • Ribosome Production Factor 1 2 3 4
  • Brix Domain-Containing Protein 5 3 4
  • Ribosome Biogenesis Protein RPF1 3 4
  • 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
  • RPF1 5

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. Diseases associated with RPF1 include Shwachman-Diamond Syndrome 1. Gene Ontology (GO) annotations related to this gene include rRNA binding. An important paralog of this gene is IMP4.

UniProtKB/Swiss-Prot Summary for RPF1 Gene

Additional gene information for RPF1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RPF1 Gene

Genomics for RPF1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RPF1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RPF1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RPF1

Genomic Locations for RPF1 Gene

Genomic Locations for RPF1 Gene
chr1:84,479,259-84,498,352
(GRCh38/hg38)
Size:
19,094 bases
Orientation:
Plus strand
chr1:84,944,920-84,964,033
(GRCh37/hg19)
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 Structure • Gene Density

RefSeq DNA sequence for RPF1 Gene

Proteins for RPF1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

neXtProt entry for RPF1 Gene

Protein Expression for RPF1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

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:
  • Brix domain
ProtoNet:

Suggested Antigen Peptide Sequences for RPF1 Gene

GenScript: Design optimal peptide antigens:
  • Ribosome biogenesis protein RPF1 (RPF1_HUMAN)
genes like me logo Genes that share domains with RPF1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RPF1 Gene

Function for RPF1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for RPF1 Gene

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

Phenotypes From GWAS Catalog for RPF1 Gene

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 --
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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPF1

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 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for RPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IBA,IDA 12429849
GO:0030687 preribosome, large subunit precursor IBA 21873635
genes like me logo Genes that share ontologies with RPF1: view

Pathways & Interactions for RPF1 Gene

PathCards logo

SuperPathways for RPF1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000460 maturation of 5.8S rRNA IBA 21873635
GO:0000470 maturation of LSU-rRNA IBA 21873635
GO:0006364 rRNA processing IBA 21873635
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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for RPF1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RPF1 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPF1

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

No ASD Table

Relevant External Links for RPF1 Gene

GeneLoc Exon Structure for
RPF1

Expression for RPF1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for RPF1 Gene
mRNA expression by BioGPS for RPF1 GenemRNA expression by GTEx 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, MaxQB, and MOPED for RPF1 Gene



Protein tissue co-expression partners for RPF1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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

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 30 31
  • 99.62 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia BXDC5 31
  • 95 (a)
 OneToOne
RPF1 30
  • 93.51 (n)
Dog
(Canis familiaris)
 Mammalia RPF1 30 31
  • 93.8 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia RPF1 31
  • 91 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Rpf1 30
  • 89.3 (n)
Mouse
(Mus musculus)
 Mammalia Rpf1 30 17 31
  • 89.11 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia RPF1 31
  • 85 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves RPF1 30 31
  • 78.62 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia RPF1 31
  • 81 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia rpf1 30
  • 76.31 (n)
Str.10818 30
Zebrafish
(Danio rerio)
 Actinopterygii rpf1 30 31
  • 71.55 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP009968 30
  • 51.75 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta CG6712 30 31 32
  • 51.56 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea F44G4.1 30 31 32
  • 61.74 (n)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes RPF1 30 31 33
  • 56.54 (n)
 OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0F21670g 30
  • 53.26 (n)
A. gosspyii yeast
(Eremothecium gossypii)
 Saccharomycetes AGOS_AEL093C 30
  • 49.82 (n)
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons MEE49 30
  • 58.82 (n)
Alicante grape
(Vitis vinifera)
 eudicotyledons Vvi.3048 30
Rice
(Oryza sativa)
 Liliopsida Os06g0137500 30
  • 55 (n)
Os.15940 30
Barley
(Hordeum vulgare)
 Liliopsida Hv.6401 30
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 66 (a)
 OneToOne
Fission Yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPAC4F8.04 30
  • 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RPF1: view image

Paralogs for RPF1 Gene

Paralogs for RPF1 Gene

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

  • RPF1_HUMAN
genes like me logo Genes that share paralogs with RPF1: view

Variants for RPF1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RPF1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs2292191 - p.Ser9Gly
rs7528067 - p.Met223Ile

Additional dbSNP identifiers (rs#s) for RPF1 Gene

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)

Additional Variant Information for RPF1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for RPF1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RPF1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
shwachman-diamond syndrome 1
  • sds1
- elite association - COSMIC cancer census association via MalaCards
Search RPF1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RPF1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RPF1: view

No data available for 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
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  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
  5. Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A … Diaz JJ (Molecular biology of the cell 2002) 3 4

ExternalLinks

View latest publications for RPF1 gene in Mastermind

Products for RPF1 Gene

Sources for RPF1 Gene