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Aliases for RUFY3 Gene

Aliases for RUFY3 Gene

  • RUN And FYVE Domain Containing 3 2 3 5
  • Single Axon-Regulated Protein 3 4
  • Single Axon-Related 1 2 3
  • RIPX 3 4
  • RUN And FYVE Domain-Containing Protein 3 4
  • Rap2 Interacting Protein X 3
  • Rap2-Interacting Protein X 4
  • Protein RUFY3 3
  • KIAA0871 4
  • SINGAR1 3
  • ZFYVE30 3
  • Singar 4

External Ids for RUFY3 Gene

Previous GeneCards Identifiers for RUFY3 Gene

  • GC04P071953
  • GC04P071806
  • GC04P071570
  • GC04P067374
  • GC04P071571
  • GC04P071573

Summaries for RUFY3 Gene

Entrez Gene Summary for RUFY3 Gene

  • This gene encodes a RPIP8, UNC-14, and NESCA domain-containing protein that is required for maintenance of neuronal polarity. In addition, it has been implicated in mediation of gastric cancer cell migration and invasion via interaction with P21-activated kinase-1, which promotes its expression. The encoded protein localizes to F-actin-enriched invadopodia to induce formation of protrusions, thereby facilitating cell migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

GeneCards Summary for RUFY3 Gene

RUFY3 (RUN And FYVE Domain Containing 3) is a Protein Coding gene. Diseases associated with RUFY3 include Gastric Cancer. An important paralog of this gene is RUFY2.

UniProtKB/Swiss-Prot for RUFY3 Gene

  • Plays a role in the generation of neuronal polarity formation and axon growth (By similarity). Implicated in the formation of a single axon by developing neurons (By similarity). May inhibit the formation of additional axons by inhibition of PI3K in minor neuronal processes (By similarity). Plays a role in the formation of F-actin-enriched protrusive structures at the cell periphery (PubMed:25766321). Plays a role in cytoskeletal organization by regulating the subcellular localization of FSCN1 and DBN1 at axonal growth cones (By similarity). Promotes gastric cancer cell migration and invasion in a PAK1-dependent manner (PubMed:25766321).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RUFY3 Gene

Genomics for RUFY3 Gene

Regulatory Elements for RUFY3 Gene

Enhancers for RUFY3 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
GH04F070733 0.9 ENCODE 26.9 +31.5 31478 4.8 PKNOX1 WRNIP1 RAD21 RARA SCRT2 ETV6 CREM SMARCA5 ZNF362 CBFB RUFY3 RNU6-520P RNU6-784P UTP3 JCHAIN PIR34937 ENSG00000272986
GH04F070721 0.9 ENCODE 13.9 +18.1 18070 1.9 ATF1 PKNOX1 ZNF76 SIN3A ZEB1 YY1 GATA2 ZNF366 FOS ZMIZ1 RUFY3 UTP3 JCHAIN ENSG00000272986 PIR34937
GH04F070969 0.9 Ensembl ENCODE 12.2 +266.7 266716 2.2 GATAD2A SOX5 SOX13 TFE3 FOXA3 CEBPB HMG20A THRB TRIM24 SMAD4 DCK RUFY3 GRSF1 UTP3 JCHAIN MOB1B
GH04F070742 0.8 Ensembl 12 +38.3 38297 0.6 ELF3 SOX13 PKNOX1 ESRRA JUN TEAD3 RARA CTBP1 GATA3 FOS RNU6-784P RUFY3 RNU6-520P UTP3 JCHAIN PIR34937 ENSG00000272986
GH04F070836 1 ENCODE 8.3 +134.5 134530 3.8 HDGF CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF48 ZNF2 ETS1 UTP3 JCHAIN RUFY3 DCK GC04P070840 PIR34937
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RUFY3 on UCSC Golden Path with GeneCards custom track

Promoters for RUFY3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001431851 896 3001 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 FOS KLF13 SP3 SP5

Genomic Location for RUFY3 Gene

Chromosome:
4
Start:
70,704,204 bp from pter
End:
70,808,622 bp from pter
Size:
104,419 bases
Orientation:
Plus strand

Genomic View for RUFY3 Gene

Genes around RUFY3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RUFY3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RUFY3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RUFY3 Gene

Proteins for RUFY3 Gene

  • Protein details for RUFY3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7L099-RUFY3_HUMAN
    Recommended name:
    Protein RUFY3
    Protein Accession:
    Q7L099
    Secondary Accessions:
    • B3KM25
    • B4DYW7
    • D9N163
    • O94948
    • Q9UI00

    Protein attributes for RUFY3 Gene

    Size:
    469 amino acids
    Molecular mass:
    52965 Da
    Quaternary structure:
    • Interacts with PAK1 (PubMed:25766321). Interacts (via C-terminus) with Ras-related Rab-5 proteins (PubMed:20376209). Interacts (via C-terminus) with Ras-related Rap-2 proteins (PubMed:20376209). Interacts with PIK3CA and PIK3R1 (By similarity). Interacts (via N-terminus) with FSCN1; this interaction induces neuron axon development (By similarity). Interacts with DBN1 (By similarity).
    SequenceCaution:
    • Sequence=BAA74894.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for RUFY3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RUFY3 Gene

Post-translational modifications for RUFY3 Gene

  • Phosphorylated by PAK1 (PubMed:25766321). Isoform 1 is partially phosphorylated (By similarity).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RUFY3 Gene

Domains & Families for RUFY3 Gene

Gene Families for RUFY3 Gene

Protein Domains for RUFY3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RUFY3 Gene

Graphical View of Domain Structure for InterPro Entry

Q7L099

UniProtKB/Swiss-Prot:

RUFY3_HUMAN :
  • Contains 1 RUN domain.
Domain:
  • Contains 1 RUN domain.
genes like me logo Genes that share domains with RUFY3: view

Function for RUFY3 Gene

Molecular function for RUFY3 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the generation of neuronal polarity formation and axon growth (By similarity). Implicated in the formation of a single axon by developing neurons (By similarity). May inhibit the formation of additional axons by inhibition of PI3K in minor neuronal processes (By similarity). Plays a role in the formation of F-actin-enriched protrusive structures at the cell periphery (PubMed:25766321). Plays a role in cytoskeletal organization by regulating the subcellular localization of FSCN1 and DBN1 at axonal growth cones (By similarity). Promotes gastric cancer cell migration and invasion in a PAK1-dependent manner (PubMed:25766321).

Gene Ontology (GO) - Molecular Function for RUFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25766321
genes like me logo Genes that share ontologies with RUFY3: view
genes like me logo Genes that share phenotypes with RUFY3: view

Animal Models for RUFY3 Gene

MGI Knock Outs for RUFY3:

Animal Model Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RUFY3 Gene

Localization for RUFY3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RUFY3 Gene

Cytoplasm. Endomembrane system. Cell projection, invadopodium. Perikaryon. Cell projection. Cell projection, growth cone. Cell projection, filopodium. Cell projection, lamellipodium. Note=Colocalizes with PAK1, F-actin, myosins and integrins in invadopodia at the cell periphery (PubMed:25766321). Colocalized with Ras-related Rab-5 proteins in cytoplasmic vesicles (PubMed:20376209). Accumulates in axon growth cones in a F-actin-dependent manner (By similarity). Colocalized with FSCN1 and F-actin at filipodia and lamellipodia of axonal growth cones (By similarity). Colocalized with DBN1 and F-actin at transitional domain of the axonal growth cone (By similarity). {ECO:0000250 UniProtKB:Q5FVJ0, ECO:0000250 UniProtKB:Q9D394, ECO:0000269 PubMed:20376209, ECO:0000269 PubMed:25766321}.

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 RUFY3 gene
Compartment Confidence
cytosol 5
nucleus 2
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for RUFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 25766321
GO:0012505 endomembrane system IEA --
GO:0016020 membrane IEA --
GO:0030027 lamellipodium ISS --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with RUFY3: view

Pathways & Interactions for RUFY3 Gene

SuperPathways for RUFY3 Gene

No Data Available

Interacting Proteins for RUFY3 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 11)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000370394%0d%0a9606.ENSP00000328720%0d%0a9606.ENSP00000353375%0d%0a9606.ENSP00000265175%0d%0a9606.ENSP00000311505%0d%0a9606.ENSP00000262544%0d%0a
Selected Interacting proteins: ENSP00000370394 Q7L099-RUFY3_HUMAN for RUFY3 Gene via STRING IID

Gene Ontology (GO) - Biological Process for RUFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007015 actin filament organization ISS --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0030154 cell differentiation IEA --
GO:0030335 positive regulation of cell migration IDA 25766321
genes like me logo Genes that share ontologies with RUFY3: view

No data available for Pathways by source and SIGNOR curated interactions for RUFY3 Gene

Transcripts for RUFY3 Gene

Unigene Clusters for RUFY3 Gene

RUN and FYVE domain containing 3:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RUFY3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b
SP1: - - - - - - -
SP2: - - - - -
SP3:
SP4: - - -
SP5: - -
SP6: - -
SP7: -
SP8: - - -

Relevant External Links for RUFY3 Gene

GeneLoc Exon Structure for
RUFY3
ECgene alternative splicing isoforms for
RUFY3

Expression for RUFY3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RUFY3 Gene

Protein differential expression in normal tissues from HIPED for RUFY3 Gene

This gene is overexpressed in Frontal cortex (17.2), Fetal Brain (14.7), Spinal cord (11.6), and Brain (11.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RUFY3 Gene



Protein tissue co-expression partners for RUFY3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RUFY3 Gene:

RUFY3

SOURCE GeneReport for Unigene cluster for RUFY3 Gene:

Hs.740904

mRNA Expression by UniProt/SwissProt for RUFY3 Gene:

Q7L099-RUFY3_HUMAN
Tissue specificity: Overexpressed in gastric cancer cells and tissues (at protein level) (PubMed:25766321).
genes like me logo Genes that share expression patterns with RUFY3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for RUFY3 Gene

Orthologs for RUFY3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RUFY3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RUFY3 34 35
  • 99.78 (n)
dog
(Canis familiaris)
Mammalia RUFY3 34 35
  • 93.76 (n)
rat
(Rattus norvegicus)
Mammalia Rufy3 34
  • 91.31 (n)
oppossum
(Monodelphis domestica)
Mammalia RUFY3 35
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rufy3 34 16 35
  • 90.64 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RUFY3 35
  • 90 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RUFY3 35
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves RUFY3 34 35
  • 81.45 (n)
lizard
(Anolis carolinensis)
Reptilia RUFY3 35
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rufy3 34
  • 79.93 (n)
Str.9922 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.8516 34
zebrafish
(Danio rerio)
Actinopterygii rufy3 34 35
  • 76.58 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG31064 35
  • 27 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 36 (a)
OneToMany
Species where no ortholog for RUFY3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • 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)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RUFY3 Gene

ENSEMBL:
Gene Tree for RUFY3 (if available)
TreeFam:
Gene Tree for RUFY3 (if available)

Paralogs for RUFY3 Gene

Paralogs for RUFY3 Gene

(2) SIMAP similar genes for RUFY3 Gene using alignment to 7 proteins:

Pseudogenes.org Pseudogenes for RUFY3 Gene

genes like me logo Genes that share paralogs with RUFY3: view

Variants for RUFY3 Gene

Sequence variations from dbSNP and Humsavar for RUFY3 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs869312879 Uncertain significance 70,775,172(+) AGACG(-/G)GTCAG nc-transcript-variant, reference, frameshift-variant
rs10000135 -- 70,729,423(+) agcta(A/T)ttttt intron-variant
rs10007671 -- 70,756,792(+) TTCTT(A/C)CTGCA intron-variant
rs10007937 -- 70,738,952(+) ctagg(C/T)gatgc intron-variant
rs10009233 -- 70,731,352(+) catct(G/T)ttaaa intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RUFY3 Gene

Variant ID Type Subtype PubMed ID
esv3332844 CNV duplication 20981092
esv3428522 CNV insertion 20981092
nsv1012495 CNV gain 25217958
nsv4380 CNV insertion 18451855
nsv819488 CNV loss 19587683
nsv829965 CNV gain 17160897
nsv829966 CNV loss 17160897

Variation tolerance for RUFY3 Gene

Residual Variation Intolerance Score: 32.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.68; 32.08% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RUFY3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RUFY3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RUFY3 Gene

Disorders for RUFY3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RUFY3 Gene - From: GeneCards

Disorder Aliases PubMed IDs
gastric cancer
  • stomach cancer
- elite association - COSMIC cancer census association via MalaCards
Search RUFY3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RUFY3

Genetic Association Database (GAD)
RUFY3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RUFY3
genes like me logo Genes that share disorders with RUFY3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RUFY3 Gene

Publications for RUFY3 Gene

  1. PAK1 regulates RUFY3-mediated gastric cancer cell migration and invasion. (PMID: 25766321) Wang G. … Li F. (Cell Death Dis. 2015) 3 4 64
  2. Rab5(Q79L) interacts with the carboxyl terminus of RUFY3. (PMID: 20376209) Yoshida H. … Matsuda S. (Int. J. Biol. Sci. 2010) 3 4 64
  3. Singar1, a novel RUN domain-containing protein, suppresses formation of surplus axons for neuronal polarity. (PMID: 17439943) Mori T. … Inagaki N. (J. Biol. Chem. 2007) 2 3 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. 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

Products for RUFY3 Gene

Sources for RUFY3 Gene

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