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

RUFY4 Gene

protein-coding   GIFtS: 37
GCID: GC02P218899

RUN And FYVE Domain Containing 4

  Search for RUFY4
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
RUN And FYVE Domain Containing 41 2
RUN And FYVE Domain-Containing Protein 42

External Ids:    HGNC: 248041   Entrez Gene: 2851802   Ensembl: ENSG000001882827   UniProtKB: Q6ZNE93   
ORGUL members:         
NONCODE14:n409773      

Export aliases for RUFY4 gene to outside databases

Previous GC identifers: GC02P218607 GC02P210753


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for RUFY4 Gene: 
RUFY4 (RUN and FYVE domain containing 4) is a protein-coding gene, and is affiliated with the lncRNA class. GO annotations related to this gene include metal ion binding. An important paralog of this gene is FYCO1.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.2  NT_005403.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RUFY4 gene promoter:
         SRF   SRF (504 AA)   p300   CUTL1   Tal-1beta   GATA-1   E47   c-Ets-1   CP2   SEF-1 (1)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRUFY4 promoter sequence
   Search SABiosciences Chromatin IP Primers for RUFY4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RUFY4


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

Entrez Gene cytogenetic band: 2q35   Ensembl cytogenetic band:  2q35   HGNC cytogenetic band: 2q35

RUFY4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RUFY4 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P218899:  view genomic region     (about GC identifiers)

Start:
218,899,657 bp from pter      End:
218,955,304 bp from pter
Size:
55,648 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RUFY4_HUMAN, Q6ZNE9 (See protein sequence)
Recommended Name: RUN and FYVE domain-containing protein 4  
Size: 571 amino acids; 64350 Da
Sequence caution: Sequence=AAI13713.1; Type=Erroneous initiation; Sequence=BAC87417.1; Type=Erroneous translation;
Note=Wrong choice of CDS;
Secondary accessions: Q6ZR96
Alternative splicing: 2 isoforms:  Q6ZNE9-2   Q6ZNE9-3   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for RUFY4: NX_Q6ZNE9

Explore proteomics data for RUFY4 at MOPED 

RUFY4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

RUFY4 Protein Expression

REFSEQ proteins: NP_940885.2  
ENSEMBL proteins: 
 ENSP00000410091   ENSP00000363270   ENSP00000345900   ENSP00000388839  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
ZFYVE: Zinc fingers, FYVE domain containing

3 InterPro protein domains:
 IPR017455 Znf_FYVE-rel
 IPR004012 Run
 IPR011011 Znf_FYVE_PHD

Graphical View of Domain Structure for InterPro Entry Q6ZNE9

ProtoNet protein and cluster: Q6ZNE9

UniProtKB/Swiss-Prot: RUFY4_HUMAN, Q6ZNE9
Similarity: Contains 1 FYVE-type zinc finger
Similarity: Contains 1 RUN domain


RUFY4 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

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

GO IDQualified GO termEvidencePubMed IDs
GO:0046872metal ion binding IEA--
     
RUFY4 for ontologies           About GeneDecksing


Phenotypes:
     3 GenomeRNAi human phenotypes for RUFY4:
 Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e 

Animal Models:
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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RUFY4

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 RUFY4

Search CenterWatch for drugs/clinical trials and news about RUFY4

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for RUFY4 gene: 
NM_198483.3  

Unigene Cluster for RUFY4:

RUN and FYVE domain containing 4
Hs.570069  [show with all ESTs]
Unigene Representative Sequence: NR_034176
11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000497857 ENST00000457754(uc002vgw.3) ENST00000463618 ENST00000465568
ENST00000480164 ENST00000472496 ENST00000374155 ENST00000495721 ENST00000463872
ENST00000344321(uc010fvl.2) ENST00000441828
miRNA
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Inhib. RNA
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Additional mRNA sequence: 

AK128393.1 AK131246.1 BC113712.1 NR_034176.1 

4 DOTS entries:

DT.101979181  DT.95152191  DT.121031673  DT.121031681 

11 AceView cDNA sequences:

AK131246 NM_198483 AK128393 BX641664 AW273215 AW452848 BX491177 BI044869 
BI046631 BI044889 BF934300 

GeneLoc Exon Structure

5/8 Alternative Splicing Database (ASD) splice patterns (SP) for RUFY4 (see all 8)    About this scheme

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


ECgene alternative splicing isoforms for RUFY4

(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

RUFY4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ACTGGCCTCC
RUFY4 Expression
About this image


See RUFY4 Protein Expression from SPIRE MOPED and PaxDB
SOURCE GeneReport for Unigene cluster: Hs.570069
    SABiosciences Custom PCR Arrays for RUFY4
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RUFY4

(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 chordates.

Orthologs for RUFY4 gene from 3/8 species (see all 8)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Rufy41 , 5 RUN and FYVE domain containing 41, 5 74.32(n)1
62.99(a)1
  1 (38.38 cM)5
4356261  NM_001170641.11  NP_001164112.11 
 741255415 
chicken
(Gallus gallus)
Aves RUFY41 RUN and FYVE domain-containing protein 4-like 52.68(n)
39.93(a)
  429304  XM_426861.3  XP_426861.3 
lizard
(Anolis carolinensis)
Reptilia RUFY46
RUN and FYVE domain containing 4
12(a)
1 ↔ 1
1(88995981-89018960)


ENSEMBL Gene Tree for RUFY4 (if available)
TreeFam Gene Tree for RUFY4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for RUFY4 gene
FYCO12  EEA12  

RUFY4 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

10/1200 SNPs in RUFY4 are shown (see all 1200)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1147851261,2
C,F--218897923(+) AGAAAC/TCAGCA 1 -- us2k11Minor allele frequency- T:0.04WA 118
rs1409742431,2
--218897929(+) CAGCAC/GCACAC 1 -- us2k10--------
rs608451781,2
C,F--218898007(+) TGTCCC/TCACTG 1 -- us2k12Minor allele frequency- T:0.04WA 120
rs1501441381,2
--218898064(+) GAGAAA/GGCAGG 1 -- us2k10--------
rs1143009461,2
F--218898105(+) GGGGAA/TGTCCT 1 -- us2k11Minor allele frequency- T:0.01WA 118
rs1915431751,2
--218898247(+) CCCCTC/TCTGGG 1 -- us2k10--------
rs1831985541,2
--218898363(+) ACTGGA/TGGCCC 1 -- us2k10--------
rs101967071,2
C,F,H--218898507(+) GACTCG/AGGGCG 1 -- us2k112Minor allele frequency- A:0.36NS EA WA NA CSA 655
rs739906781,2
C,F--218898511(+) CGGGGC/TGTCGT 1 -- us2k13Minor allele frequency- T:0.37WA 122
rs595390481,2
C,F--218898536(+) CGCAGC/TCCCTA 1 -- us2k11Minor allele frequency- T:0.50WA 2

HapMap Linkage Disequilibrium report for RUFY4 (218899657 - 218955304 bp)

Structural Variations
     Database of Genomic Variants (DGV) 5 variations for RUFY4:    About this table     
Variant IDTypeSubtypePubMed ID
esv2721477CNV Deletion23290073
nsv3163CNV Insertion18451855
nsv512786CNV Insertion21212237
esv2494137CNV Insertion19546169
nsv834541CNV Loss17160897

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

(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 RUFY4 gene integrated from 9 sources:
(articles sorted by number of sources associating them with RUFY4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 285180 HGNC: 24804 AceView: FLJ46536 Ensembl:ENSG00000188282 euGenes: HUgn285180
ECgene: RUFY4 H-InvDB: RUFY4

(According to HUGE)
About This Section
  --

(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 RUFY4 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for RUFY4 gene:
Search GeneIP for patents involving RUFY4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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transforming growth factor, beta 1
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The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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