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Aliases for RRP9 Gene

Aliases for RRP9 Gene

  • Ribosomal RNA Processing 9, Small Subunit (SSU) Processome Component, Homolog (Yeast) 2 3 5
  • U3 Small Nucleolar Ribonucleoprotein-Associated 55 KDa Protein 3 4
  • RNA, U3 Small Nucleolar Interacting Protein 2 2 3
  • RRP9 Homolog 3 4
  • RNU3IP2 3 4
  • U3-55K 3 4
  • RRP9, Small Subunit (SSU) Processome Component, Homolog 3
  • U3 Small Nucleolar RNA-Interacting Protein 2 3
  • U3 SnoRNP-Associated 55-KDa Protein 3
  • U3 SnoRNP-Associated 55 KDa Protein 4
  • U355K 4

External Ids for RRP9 Gene

Previous HGNC Symbols for RRP9 Gene

  • RNU3IP2

Summaries for RRP9 Gene

Entrez Gene Summary for RRP9 Gene

  • This gene encodes a member of the WD-repeat protein family. The encoded protein is a component of the nucleolar small nuclear ribonucleoprotein particle (snoRNP) and is essential for 18s rRNA processing during ribosome synthesis. It contains seven WD domains required for nucleolar localization and specific interaction with the U3 small nucleolar RNA (U3 snoRNA). [provided by RefSeq, Oct 2012]

GeneCards Summary for RRP9 Gene

RRP9 (Ribosomal RNA Processing 9, Small Subunit (SSU) Processome Component, Homolog (Yeast)) is a Protein Coding gene. Among its related pathways are rRNA processing in the nucleus and cytosol and Gene Expression. GO annotations related to this gene include poly(A) RNA binding and U3 snoRNA binding.

UniProtKB/Swiss-Prot for RRP9 Gene

  • Component of a nucleolar small nuclear ribonucleoprotein particle (snoRNP) thought to participate in the processing and modification of pre-ribosomal RNA.

Gene Wiki entry for RRP9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RRP9 Gene

Genomics for RRP9 Gene

Regulatory Elements for RRP9 Gene

Enhancers for RRP9 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
GH03G052497 1.6 FANTOM5 Ensembl ENCODE 18.5 -556.6 -556637 1.7 ATF1 CREB3L1 AGO1 ARID4B SIN3A ZNF48 TCF12 SLC30A9 GATA2 FOS RRP9 ITIH4 RAD54L2 RFT1 NISCH NEK4 STAB1 WDR82 TWF2 PBRM1
GH03G052274 1.7 Ensembl ENCODE dbSUPER 16.2 -340.9 -340914 17.3 MLX CREB3L1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 TBX21 SSRP1 LOC101929054 PPM1M TWF2 ITIH4 PBRM1 GLYCTK RRP9 RFT1 RAD54L2 ENSG00000173366
GH03G051383 1.4 ENCODE dbSUPER 17.5 +553.7 553740 9.5 HDGF PKNOX1 ARNT AGO1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 RRP9 RAD54L2 TEX264 GRM2 CACNA2D2 GPR62 PCBP4 PIR60056 MANF
GH03G052236 1.7 FANTOM5 ENCODE dbSUPER 9.9 -296.8 -296848 5.2 HDGF PKNOX1 FOXA2 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 GLYCTK LOC101929054 RAD54L2 WDR82 MIR135A1 GLYCTK-AS1 RRP9 TWF2 PPM1M PBRM1
GH03G052703 1.4 ENCODE dbSUPER 12 -763.8 -763796 4.6 HDGF PKNOX1 FOXA2 MLX CREB3L1 AGO1 ZFP64 WRNIP1 ARID4B SIN3A PBRM1 RFT1 RRP9 SPCS1 GLT8D1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RRP9 on UCSC Golden Path with GeneCards custom track

Promoters for RRP9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000152454 41 1401 HNRNPUL1 HDGF PKNOX1 MLX CREB3L1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1

Genomic Location for RRP9 Gene

Chromosome:
3
Start:
51,933,426 bp from pter
End:
51,941,941 bp from pter
Size:
8,516 bases
Orientation:
Minus strand

Genomic View for RRP9 Gene

Genes around RRP9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RRP9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RRP9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RRP9 Gene

Proteins for RRP9 Gene

  • Protein details for RRP9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43818-U3IP2_HUMAN
    Recommended name:
    U3 small nucleolar RNA-interacting protein 2
    Protein Accession:
    O43818
    Secondary Accessions:
    • B2R996
    • Q8IZ30

    Protein attributes for RRP9 Gene

    Size:
    475 amino acids
    Molecular mass:
    51841 Da
    Quaternary structure:
    • Interacts specifically with the U3 small nucleolar RNA (U3 snoRNA). Binds a sub-fragment of the U3 snoRNA surrounding the B/C motif (3UBC). This association with the U3BC RNA is dependent on the binding of a protein called 15.5K to the box B/C motif. The association of the protein with the U3BC RNA was found to be also dependent on a conserved RNA structure that flanks the box B/C motif.

    Three dimensional structures from OCA and Proteopedia for RRP9 Gene

neXtProt entry for RRP9 Gene

Post-translational modifications for RRP9 Gene

  • Ubiquitination at isoforms=129
  • Modification sites at PhosphoSitePlus

Other Protein References for RRP9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RRP9 Gene

Domains & Families for RRP9 Gene

Gene Families for RRP9 Gene

Suggested Antigen Peptide Sequences for RRP9 Gene

Graphical View of Domain Structure for InterPro Entry

O43818

UniProtKB/Swiss-Prot:

U3IP2_HUMAN :
  • The WD domains are required for nucleolar localization and U3 small nucleolar RNAs binding.
  • Belongs to the WD repeat RRP9 family.
Domain:
  • The WD domains are required for nucleolar localization and U3 small nucleolar RNAs binding.
Family:
  • Belongs to the WD repeat RRP9 family.
genes like me logo Genes that share domains with RRP9: view

Function for RRP9 Gene

Molecular function for RRP9 Gene

UniProtKB/Swiss-Prot Function:
Component of a nucleolar small nuclear ribonucleoprotein particle (snoRNP) thought to participate in the processing and modification of pre-ribosomal RNA.

Gene Ontology (GO) - Molecular Function for RRP9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0034511 contributes_to U3 snoRNA binding IDA 9418896
genes like me logo Genes that share ontologies with RRP9: view
genes like me logo Genes that share phenotypes with RRP9: view

Animal Model Products

CRISPR Products

miRNA for RRP9 Gene

miRTarBase miRNAs that target RRP9

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RRP9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RRP9 Gene

Localization for RRP9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RRP9 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 RRP9 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for RRP9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA 9418896
GO:0030529 intracellular ribonucleoprotein complex IEA --
GO:0031428 box C/D snoRNP complex IDA 9418896
genes like me logo Genes that share ontologies with RRP9: view

Pathways & Interactions for RRP9 Gene

genes like me logo Genes that share pathways with RRP9: view

Gene Ontology (GO) - Biological Process for RRP9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing TAS --
genes like me logo Genes that share ontologies with RRP9: view

No data available for SIGNOR curated interactions for RRP9 Gene

Drugs & Compounds for RRP9 Gene

No Compound Related Data Available

Transcripts for RRP9 Gene

mRNA/cDNA for RRP9 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(143) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RRP9 Gene

Ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RRP9

Alternative Splicing Database (ASD) splice patterns (SP) for RRP9 Gene

No ASD Table

Relevant External Links for RRP9 Gene

GeneLoc Exon Structure for
RRP9
ECgene alternative splicing isoforms for
RRP9

Expression for RRP9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RRP9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RRP9 Gene

This gene is overexpressed in Urine (13.3), Peripheral blood mononuclear cells (9.8), and Lung (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RRP9 Gene



Protein tissue co-expression partners for RRP9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RRP9 Gene:

RRP9

SOURCE GeneReport for Unigene cluster for RRP9 Gene:

Hs.153768

Evidence on tissue expression from TISSUES for RRP9 Gene

  • Skin(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with RRP9: 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 RRP9 Gene

Orthologs for RRP9 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RRP9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RRP9 34 35
  • 99.51 (n)
dog
(Canis familiaris)
Mammalia RRP9 34 35
  • 89.19 (n)
cow
(Bos Taurus)
Mammalia RRP9 34 35
  • 89.12 (n)
mouse
(Mus musculus)
Mammalia Rrp9 34 16 35
  • 87.65 (n)
rat
(Rattus norvegicus)
Mammalia Rrp9 34
  • 86.88 (n)
oppossum
(Monodelphis domestica)
Mammalia RRP9 35
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RRP9 35
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves RRP9 34 35
  • 71.99 (n)
lizard
(Anolis carolinensis)
Reptilia RRP9 35
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rrp9 34
  • 64.23 (n)
Str.7914 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.8086 34
zebrafish
(Danio rerio)
Actinopterygii rrp9 34 35
  • 66.43 (n)
Dr.6359 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2843 34
fruit fly
(Drosophila melanogaster)
Insecta U3-55K 35 34
  • 54.58 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005320 34
  • 51.69 (n)
worm
(Caenorhabditis elegans)
Secernentea T02H6.1 34 35
  • 48.77 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR102C 34
  • 48.86 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B11077g 34
  • 45.41 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RRP9 34 35 37
  • 44.47 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons YAO 34
  • 47.39 (n)
rice
(Oryza sativa)
Liliopsida Os03g0625900 34
  • 47.91 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01367 34
  • 54.05 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 52 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC2E1P5.05 34
  • 47.86 (n)
Species where no ortholog for RRP9 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 RRP9 Gene

ENSEMBL:
Gene Tree for RRP9 (if available)
TreeFam:
Gene Tree for RRP9 (if available)

Paralogs for RRP9 Gene

No data available for Paralogs for RRP9 Gene

Variants for RRP9 Gene

Sequence variations from dbSNP and Humsavar for RRP9 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
VAR_035887 A breast cancer sample
VAR_035888 A breast cancer sample
rs1000066535 -- 51,933,300(+) GGAAA(A/G)GGATA downstream-variant-500B
rs1000141923 -- 51,933,253(+) AGGGA(C/T)AGGAG downstream-variant-500B
rs1001031386 -- 51,940,491(+) ATCTA(C/T)ATGCA intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for RRP9 Gene

Variant ID Type Subtype PubMed ID
nsv1003453 CNV gain 25217958
nsv508922 CNV insertion 20534489
nsv520211 CNV gain 19592680
nsv590280 CNV loss 21841781
nsv954857 CNV deletion 24416366

Variation tolerance for RRP9 Gene

Residual Variation Intolerance Score: 55.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.28; 40.78% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RRP9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RRP9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RRP9 Gene

Disorders for RRP9 Gene

Relevant External Links for RRP9

Genetic Association Database (GAD)
RRP9
Human Genome Epidemiology (HuGE) Navigator
RRP9
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RRP9

No disorders were found for RRP9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RRP9 Gene

Publications for RRP9 Gene

  1. cDNA cloning and characterization of the human U3 small nucleolar ribonucleoprotein complex-associated 55-kilodalton protein. (PMID: 9418896) Pluk H. … van Venrooij W.J. (Mol. Cell. Biol. 1998) 2 3 4 64
  2. 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
  3. Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments. (PMID: 12032086) Verheggen C. … Bertrand E. (EMBO J. 2002) 2 3 64
  4. The hU3-55K protein requires 15.5K binding to the box B/C motif as well as flanking RNA elements for its association with the U3 small nucleolar RNA in Vitro. (PMID: 12381732) Granneman S. … Watkins N.J. (J. Biol. Chem. 2002) 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 RRP9 Gene

Sources for RRP9 Gene

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