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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

RUFY4 Gene

protein-coding GIFtS: 39
GCID: GC02P218899

RUN and FYVE domain containing 4

Explore 1 disease affiliated with
RUFY4 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
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
FLJ46536¹
RUN And FYVE Domain-Containing Protein 4²

External Ids:	HGNC: 24804¹	Entrez Gene: 285180²	Ensembl: ENSG00000188282⁷	UniProtKB: Q6ZNE9³

ORGUL members:
	NONCODE: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

(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_000002.11 NC_018913.1 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 plasmid: RUFY4 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 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: 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

RUFY4 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_940885.2

ENSEMBL proteins:

ENSP00000410091 ENSP00000363270 ENSP00000345900 ENSP00000388839

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

RUFY4 for domains About GeneDecksing

3 InterPro domains/families:

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

(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

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0046872	metal ion binding	IEA	--

RUFY4 for ontologies About GeneDecksing

3 GenomeRNAi human phenotypes for RUFY4:

Decreased NANOG protein expres

Decreased OCT4 protein express

Decreased POU5F1-GFP protein e

(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 Central^TM Interacting Genes and Proteins Networks for RUFY4

(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 RUFY4
Search CenterWatch for drugs/clinical trials and news about RUFY4

(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,
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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

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Additional cDNA 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 BX641664 AK128393 NM_198483 AW273215 AW452848 BX491177 BI046631

BI044869 BF934300 BI044889

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
CGAP TAG: ACTGGCCTCC

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

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In Situ
Assay Products:

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(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 RUFY4 gene from 3/15 species (see all 15) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
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	--	--	8(a)	possible ortholog	5(147153349-147158976)
honey bee (Apis mellifera)	Insecta	--	--	13(a)	possible ortholog	Group9.20(119366-145875)

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

RUFY4 for paralogs About GeneDecksing

(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

SNP ID	Valid	Clinical significance	Chr 2 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs114785126^1,2	F,	--	218897923(+)	`AGAAAC/TCAGCA`	1	--	us2k¹		1		WA	118
rs140974243^1,2		--	218897929(+)	`CAGCAC/GCACAC`	1	--	us2k¹		0	--	--	--	--
rs60845178^1,2	C,	--	218898007(+)	`TGTCCC/TCACTG`	1	--	us2k¹		2		WA	120
rs150144138^1,2		--	218898064(+)	`GAGAAA/GGCAGG`	1	--	us2k¹		0	--	--	--	--
rs114300946^1,2		--	218898105(+)	`GGGGAA/TGTCCT`	1	--	us2k¹		1		WA	118
rs191543175^1,2		--	218898247(+)	`CCCCTC/TCTGGG`	1	--	us2k¹		0	--	--	--	--
rs183198554^1,2		--	218898363(+)	`ACTGGA/TGGCCC`	1	--	us2k¹		0	--	--	--	--
rs10196707^1,2	C,F,H,	--	218898507(+)	`GACTCG/AGGGCG`	1	--	us2k¹		12		NS EA WA NA CSA	655
rs73990678^1,2	C,	--	218898511(+)	`CGGGGC/TGTCGT`	1	--	us2k¹		3		WA	122
rs59539048^1,2	C,	--	218898536(+)	`CGCAGC/TCCCTA`	1	--	us2k¹		1		WA	2

HapMap Linkage Disequilibrium report for RUFY4 (218899657 - 218955304 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for RUFY4
1 Indel: 98137

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(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

RUFY4 for disorders About GeneDecksing

1 disease for RUFY4: About MalaCards

malaria

Export disorders for RUFY4 gene to outside databases

(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

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)
Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)² Hillier L.W....Wilson R.K. (2005)
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)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)² Ota T.... Sugano S. (2004)
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

		AND	OR
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

Name	Description
PharmGKB entry for RUFY4	Pharmacogenomics, SNPs, Pathways

Intellectual Property for RUFY4 gene
(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

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About This Section


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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RUFY4

	Browse SwitchGear 3'UTR luciferase reporter plasmids for RUFY4
	SwitchGear Promoter luciferase reporter plasmids for RUFY4

Search ThermoFisher Antibodies for RUFY4

Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RUFY4

GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

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

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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RUFY4 Gene

RUN and FYVE domain containing 4

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RUFY4 Gene

RUN and FYVE domain containing 4

Aliasesfor RUFY4 gene

Summariesfor RUFY4 gene

Genomic Viewsfor RUFY4 gene

Proteinsfor RUFY4 gene

Protein Domains /Familiesfor RUFY4 gene

Functionfor RUFY4 gene

Pathways & Interactionsfor RUFY4 gene

Drugs & Compoundsfor RUFY4 gene

Transcriptsfor RUFY4 gene

Expression for RUFY4 gene

Orthologsfor RUFY4 gene

Paralogsfor RUFY4 gene

Genomic Variantsfor RUFY4 gene

Disorders / Diseasesfor RUFY4 gene

Publicationsfor RUFY4 gene

External Searches for RUFY4 gene

Genome Databases showing RUFY4 gene

Other Databases showing RUFY4 gene

Specialized Databases showing RUFY4 gene

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Productsfor RUFY4 gene

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Aliases
for RUFY4 gene

Summaries
for RUFY4 gene

Genomic Views
for RUFY4 gene

Proteins
for RUFY4 gene

Protein Domains /
Families
for RUFY4 gene

Function
for RUFY4 gene

Pathways & Interactions
for RUFY4 gene

Drugs & Compounds
for RUFY4 gene

Transcripts
for RUFY4 gene

Expression
for RUFY4 gene

Orthologs
for RUFY4 gene

Paralogs
for RUFY4 gene

Genomic Variants
for RUFY4 gene

Disorders / Diseases
for RUFY4 gene

Publications
for RUFY4 gene

Intellectual Property
for RUFY4 gene

Products
for RUFY4 gene