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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RUFY3 Gene

protein-coding   GIFtS: 48
GCID: GC04P071570

RUN and FYVE domain containing 3
 Explore 5 diseases affiliated with
RUFY3 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for RUFY3    

Aliases
for RUFY3 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
RUN And FYVE Domain Containing 31 2     SINGAR12
KIAA08711 3     Protein RUFY32
RIPx1 3     Rap2 Interacting Protein X2
Rap2-Interacting Protein X2 3     Singar3
Single Axon-Regulated Protein2 3     Single Axon-Related 12
Singar11     Singar3
RIPX2     

External Ids:    HGNC: 302851   Entrez Gene: 229022   Ensembl: ENSG000000181897   OMIM: 6111945   UniProtKB: Q7L0993   

Export aliases for RUFY3 gene to outside databases

Previous GC identifers: GC04P071953 GC04P071806 GC04P067374


Summaries
for RUFY3 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: RUFY3_HUMAN, Q7L099
Function: Implicated in the formation of a single axon by developing neurons. May inhibit the formation of additional
axons by inhibition of PI3K in minor neuronal processes (By similarity)




Genomic Views
for RUFY3 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_022778.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RUFY3 gene promoter:
         FOXI1   HFH-3   HEN1   POU2F1   POU2F1a   STAT3   HNF-3beta   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: RUFY3 promoter sequence
   Search SABiosciences Chromatin IP Primers for RUFY3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RUFY3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4q13.3   Ensembl cytogenetic band:  4q13.3   HGNC cytogenetic band: 4q13.3

RUFY3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RUFY3 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P071570:  view genomic region     (about GC identifiers)

Start:
 71,569,921 bp from pter      End:
 71,674,336 bp from pter
Size:
 104,416 bases      Orientation:
 plus strand

Proteins
for RUFY3 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: RUFY3_HUMAN, Q7L099 (See protein sequence)
Recommended Name: Protein RUFY3  
Size: 469 amino acids; 52965 Da
Subunit: Interacts with PIK3CA and PIK3R1 (By similarity)
Subcellular location: Cell projection (By similarity). Note=Enriched in F-actin enriched filopodia and lamellipodia of
growth cones of axons and minor processes of hippocampal neurons in culture (By similarity)
Sequence caution: Sequence=BAA74894.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: B3KM25 B4DYW7 D9N163 O94948 Q9UI00
Alternative splicing: 4 isoforms:  Q7L099-1   Q7L099-2   Q7L099-3   Q7L099-4   (Ref.2 (BAG63879) sequence is in conflict in positions: 304:L->S, 431:R->G)

Explore the universe of human proteins at neXtProt for RUFY3: NX_Q7L099

Post-translational modifications:

  • Isoform 1 is partially phosphorylated (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q7L099

    • RUFY3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001032519.1  NP_001124181.1  NP_055776.1  

    ENSEMBL proteins: 
     ENSP00000426165   ENSP00000426734   ENSP00000399771   ENSP00000370394   ENSP00000226328  
     ENSP00000425574   ENSP00000425400   ENSP00000421120   ENSP00000420980   ENSP00000443652  

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    Novus Biologicals RUFY3 Protein
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    Uscn Proteins for RUFY3

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030175filopodium ISS--
    GO:0030426growth cone ISS--


    RUFY3 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for RUFY3

    Protein Domains /
    Families
    for RUFY3 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    RUFY3 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR004012 Run

    Graphical View of Domain Structure for InterPro Entry Q7L099

    ProtoNet protein and cluster: Q7L099

    UniProtKB/Swiss-Prot: RUFY3_HUMAN, Q7L099
    Similarity: Contains 1 RUN domain


    Function
    for RUFY3 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: RUFY3_HUMAN, Q7L099
    Function: Implicated in the formation of a single axon by developing neurons. May inhibit the formation of additional
    axons by inhibition of PI3K in minor neuronal processes (By similarity)

    miRNA
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    hsa-let-7d hsa-miR-513a-5p hsa-miR-139-5p hsa-miR-128 hsa-miR-29b-1* hsa-miR-502-3p hsa-let-7g hsa-let-7a
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    Inhib. RNA
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    Gene Editing
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    Clone
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    Search LifeMap BioReagents cell lines for RUFY3

    In Situ Assay
    Products:       
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----


    RUFY3 for ontologies           About GeneDecksing



    Pathways & Interactions
    for RUFY3 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RUFY3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 11)

    5/12 Interacting proteins for RUFY3 (Q7L0992, 3 ENSP000003703944) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UNC119Q134322, 3MINT-64753 I2D: score=5 
    FOXK1ENSP000003287204STRING: ENSP00000328720
    MAP4ENSP000003533754STRING: ENSP00000353375
    KIF5BENSP000003070784STRING: ENSP00000307078
    LMNAENSP000003572834STRING: ENSP00000357283
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0050771negative regulation of axonogenesis ISS--


    RUFY3 for ontologies           About GeneDecksing



    Drugs & Compounds
    for RUFY3 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RUFY3
    Search CenterWatch for drugs/clinical trials and news about RUFY3 

    Transcripts
    for RUFY3 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for RUFY3 gene (3 alternative transcripts): 
    NM_001037442.2  NM_001130709.1  NM_014961.3  

    Unigene Cluster for RUFY3:

    RUN and FYVE domain containing 3
    Hs.743966  [show with all ESTs]
    Unigene Representative Sequence: NM_001037442
    16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000514898 ENST00000503876 ENST00000417478(uc003hfp.4) ENST00000381006(uc003hfr.3 uc011cay.2)
    ENST00000226328(uc003hfq.3 uc011cax.2) ENST00000513597 ENST00000502653
    ENST00000504805 ENST00000512103 ENST00000507333 ENST00000503025 ENST00000512331
    ENST00000515479 ENST00000515442 ENST00000513593 ENST00000536664

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat RUFY3
    8/38 QIAGEN miScript miRNA Assays for microRNAs that regulate RUFY3 (see all 38):
    hsa-let-7d hsa-miR-513a-5p hsa-miR-139-5p hsa-miR-128 hsa-miR-29b-1* hsa-miR-502-3p hsa-let-7g hsa-let-7a
    SwitchGear 3'UTR luciferase reporter plasmid: RUFY3 3' UTR sequence
    Inhib. RNA
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    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat RUFY3
    Clone
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    Additional cDNA sequence: 

    AB020678.1 AF112221.1 AK000911.1 AK021769.1 AK022074.1 AK294421.1 AK296501.1 AK302637.1 
    BC051716.1 BC053837.1 BC071988.1 BC098433.1 

    24/27 DOTS entries (see all 27):

    DT.100650958  DT.450798  DT.100793738  DT.40233954  DT.121231561  DT.95093666  DT.121231637  DT.40190998 
    DT.40283898  DT.91878373  DT.99971240  DT.121231581  DT.40284258  DT.92425876  DT.100699793  DT.100793739 
    DT.121231569  DT.121231588  DT.121231639  DT.92425872  DT.95093614  DT.95201665  DT.97845413  DT.100018239 

    24/353 AceView cDNA sequences (see all 353):

    BM920380 AA514623 AA989122 AI814929 CD107089 BU622102 AA290805 BQ061064 
    N80059 BQ777148 BM678618 T33158 BQ716425 AI131059 AI917398 BQ268881 
    BM715178 AI302329 BU608384 AA278829 AA127226 AA257056 BX478308 BE669927 

    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for RUFY3 (see all 8)    About this scheme

    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:                          -           -                                                                                                                     


    ECgene alternative splicing isoforms for RUFY3

    Expression
    for RUFY3 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RUFY3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    RUFY3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    4 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BrainHypothalamusBrain
    BrainThalamusBrain
    Neural TubeDiencephalonNeural Tube
    Neural TubeTelencephalonNeural Tube
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See RUFY3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RUFY3

    SOURCE GeneReport for Unigene cluster: Hs.743966
        SABiosciences Custom PCR Arrays for RUFY3
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    In Situ
    Assay Products:     
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    Orthologs
    for RUFY3 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for RUFY3 gene from 5/22 species (see all 22)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves RUFY31 RUN and FYVE domain containing 3 81.5(n)
    86.89(a)    		   422645  XM_420599.3  XP_420599.2 
    lizard
    (Anolis carolinensis)    		 Reptilia RUFY36
    		 --
    		 90(a)
    		 1 ↔ 1
    		 5(147115611-147149869)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.85162 Xenopus laevis transcribed sequence with moderate similarity more 78.69(n)    BQ736314.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii rufy31 RUN and FYVE domain containing 3 76.58(n)
    83.78(a)    		   541522  NM_001014335.1  NP_001014357.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG310646
    		 --
    		 26(a)
    		 1 → many
    		 3R(23055227-23064803)


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

    Paralogs
    for RUFY3 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RUFY3 gene
    RUFY22  RUNDC3A2  RUNDC3B2  RUFY12  
    2 SIMAP similar genes for RUFY3 using alignment to 7 protein entries:     RUFY3_HUMAN (see all proteins):
    RUFY2    RUFY1

    RUFY3 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for RUFY3
    PGOHUM00000235345


    Genomic Variants
    for RUFY3 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for RUFY3
         1 Indel: 59210
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RUFY3
    DNA2.0 Custom Variant and Variant Library Synthesis for RUFY3

    Disorders / Diseases
    for RUFY3 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    RUFY3 for disorders           About GeneDecksing

    OMIM gene information: 611194    OMIM disorders: --

    5 diseases for RUFY3:    About MalaCards
    prader-willi syndrome    malignant fibroxanthoma    gastric cancer    malaria
    neuronitis


    Export disorders for RUFY3 gene to outside databases

    Publications
    for RUFY3 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for RUFY3 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with RUFY3)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Singar1, a novel RUN domain-containing protein, suppresses formation of surplus axons for neuronal polarity. (PubMed id 17439943)1, 3 Mori T....Inagaki N. (2007)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10048485)1, 2 Nagase T....Ohara O. (1998)
    5. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    6. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    7. Rab5(Q79L) interacts with the carboxyl terminus of RU FY3. (PubMed id 20376209)1 Yoshida H....Matsuda S. (2010)
    8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    9. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (2005)
    10. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)

    External Searches for RUFY3 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing RUFY3 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 22902 HGNC: 30285 AceView: RIPX Ensembl:ENSG00000018189 euGenes: HUgn22902
    ECgene: RUFY3 H-InvDB: RUFY3

    Other Databases showing RUFY3 gene

    (According to HUGE)
    About This Section
    HUGE: KIAA0871

    Specialized Databases showing RUFY3 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RUFY3 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
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    IP news from LifeMap Sciences, Inc.)
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    		Patent Information for RUFY3 gene:
    Search GeneIP for patents involving RUFY3

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