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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
  • 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
  • RIPX 3
  • RIPx 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. 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).

Additional gene information for RUFY3 Gene

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

Genomics for RUFY3 Gene

GeneHancer (GH) Regulatory Elements for RUFY3 Gene

Promoters and enhancers for RUFY3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J070703 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 655 +1.2 1166 4.4 HDGF FOXA2 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 RUFY3 ENSG00000272986 JCHAIN UTP3 PIR34937
GH04J070721 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 663.9 +18.1 18070 1.9 PKNOX1 ATF1 YY1 FOS ATF7 RUNX3 REST SMARCA4 MYNN NBN RUFY3 UTP3 JCHAIN ENSG00000272986 PIR34937
GH04J070733 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 27 +31.5 31478 4.8 PKNOX1 BATF RAD21 RARA YY1 EGR1 SCRT2 ATF7 ETV6 BCLAF1 RUFY3 RNU6-520P RNU6-784P UTP3 JCHAIN PIR34937 ENSG00000272986
GH04J070992 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.2 +291.0 291035 6.2 PKNOX1 SMAD1 FOXA2 MLX ARNT ARID4B SIN3A YY1 SLC30A9 POLR2B DCK RUFY3 MOB1B JCHAIN GC04M071034
GH04J070836 Promoter/Enhancer 1.5 Ensembl ENCODE 8.4 +134.5 134530 3.8 HDGF ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B ZNF207 GC04P070840 UTP3 JCHAIN RUFY3 DCK GRSF1 PIR34937
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RUFY3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RUFY3 gene promoter:
  • HEN1
  • HFH-3
  • FOXI1
  • HNF-3beta
  • POU2F1a
  • STAT3
  • POU2F1

Genomic Locations for RUFY3 Gene

Genomic Locations for RUFY3 Gene
chr4:70,704,204-70,808,622
(GRCh38/hg38)
Size:
104,419 bases
Orientation:
Plus strand
chr4:71,569,921-71,674,336
(GRCh37/hg19)
Size:
104,416 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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RUFY3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RUFY3 Gene

Graphical View of Domain Structure for InterPro Entry

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

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

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).

Phenotypes From GWAS Catalog for RUFY3 Gene

Gene Ontology (GO) - Molecular Function for RUFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25766321
GO:0035091 phosphatidylinositol binding IBA --
GO:0046872 metal ion binding IEA --
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:
  • Rufy3 Rufy3<tm1b(EUCOMM)Hmgu>
  • Rufy3 Rufy3<tm1.1Migar>

Animal Model Products

Clone 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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RUFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 25766321
GO:0005829 cytosol IDA --
GO:0012505 endomembrane system IEA --
GO:0016020 membrane IEA --
GO:0030027 lamellipodium ISS --
genes like me logo Genes that share ontologies with RUFY3: view

Pathways & Interactions for RUFY3 Gene

SuperPathways for RUFY3 Gene

No Data Available

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

Drugs & Compounds for RUFY3 Gene

No Compound Related Data Available

Transcripts for RUFY3 Gene

mRNA/cDNA for RUFY3 Gene

(18) REFSEQ mRNAs :
(12) Additional mRNA sequences :
(12) Selected AceView cDNA sequences:
(15) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RUFY3 Gene

RUN and FYVE domain containing 3:
Representative Sequences:

Clone 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 CGAP 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, 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).

Evidence on tissue expression from TISSUES for RUFY3 Gene

  • Nervous system(5)
  • Adrenal gland(4.3)
  • Lung(2.4)
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 , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33
  • 99.78 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RUFY3 34 33
  • 93.76 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rufy3 33
  • 91.31 (n)
oppossum
(Monodelphis domestica)
Mammalia RUFY3 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rufy3 16 34 33
  • 90.64 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RUFY3 34
  • 90 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RUFY3 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves RUFY3 34 33
  • 81.45 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RUFY3 34
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rufy3 33
  • 79.93 (n)
Str.9922 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8516 33
zebrafish
(Danio rerio)
Actinopterygii rufy3 34 33
  • 76.58 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG31064 34
  • 27 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RUFY3: view image

Paralogs for RUFY3 Gene

Paralogs for RUFY3 Gene

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

  • RUFY3_HUMAN
  • B4DKC2_HUMAN
  • D6RCQ1_HUMAN
  • D6REM9_HUMAN
  • D6RH24_HUMAN
  • H0Y8G6_HUMAN
  • H0Y8I0_HUMAN

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 Variation AA Info Type
rs869312879 uncertain-significance, not specified 70,775,172(+) GG/GGG coding_sequence_variant, frameshift, non_coding_transcript_variant
rs1000013352 -- 70,785,354(+) T/A intron_variant
rs10000135 -- 70,729,423(+) A/T genic_upstream_transcript_variant, intron_variant
rs1000059466 -- 70,764,686(+) C/A intron_variant
rs1000104068 -- 70,721,509(+) A/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_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)

Additional Variant Information for RUFY3 Gene

Human Gene Mutation Database (HGMD)
RUFY3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RUFY3

SNP Genotyping and Copy Number Assay Products

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

Disorders for RUFY3 Gene

Additional Disease Information for RUFY3

No disorders were found for RUFY3 Gene.

No data available for MalaCards , 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 & disease 2015) 3 4 58
  2. Rab5(Q79L) interacts with the carboxyl terminus of RUFY3. (PMID: 20376209) Yoshida H … Matsuda S (International journal of biological sciences 2010) 3 4 58
  3. Singar1, a novel RUN domain-containing protein, suppresses formation of surplus axons for neuronal polarity. (PMID: 17439943) Mori T … Inagaki N (The Journal of biological chemistry 2007) 2 3 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. 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 58

Products for RUFY3 Gene

Sources for RUFY3 Gene

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