Aliases for RUFY4 Gene

Aliases for RUFY4 Gene

  • RUN And FYVE Domain Containing 4 2 3 5
  • RUN And FYVE Domain-Containing Protein 4 3 4
  • ZFYVE31 2 3
  • FLJ46536 2
  • RUFY4 5

External Ids for RUFY4 Gene

Previous GeneCards Identifiers for RUFY4 Gene

  • GC02P218607
  • GC02P218899
  • GC02P210753

Summaries for RUFY4 Gene

GeneCards Summary for RUFY4 Gene

RUFY4 (RUN And FYVE Domain Containing 4) is a Protein Coding gene. Diseases associated with RUFY4 include Zellweger Syndrome. An important paralog of this gene is FYCO1.

UniProtKB/Swiss-Prot Summary for RUFY4 Gene

  • Positively regulates macroautophagy in primary dendritic cells. Increases autophagic flux, probably by stimulating both autophagosome formation and facilitating tethering with lysosomes. Binds to phosphatidylinositol 3-phosphate (PtdIns3P) through its FYVE-type zinc finger.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RUFY4 Gene

Genomics for RUFY4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RUFY4 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
GH02J218034 Promoter/Enhancer 1.3 Ensembl ENCODE dbSUPER 258.2 +0.1 146 0.6 SP1 ZNF654 CTCF TRIM22 ZNF341 THAP11 ELF1 RAD21 SMC3 GABPB1 RUFY4 TNS1 lnc-RUFY4-2 piR-43325-058 CXCR2
GH02J218033 Promoter/Enhancer 1.3 EPDnew Ensembl dbSUPER 255.5 -0.7 -733 0.8 ZNF341 CTCF SPI1 IKZF1 ZNF48 IKZF2 ZBTB17 DPF2 NBN GATAD2B RUFY4 TNS1 lnc-RUFY4-2
GH02J218035 Promoter/Enhancer 0.5 Ensembl dbSUPER 250.7 -1.4 -1433 0.2 RUFY4 TNS1 lnc-RUFY4-2 HSALNG0022221
GH02J217897 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.1 -128.4 -128355 18 ZNF600 SSRP1 JUND ZMYM3 KLF9 CEBPA ATF3 ZIC2 CHD4 YY1 TNS1 CNOT9 AAMP ZNF142 SLC11A1 STK36 TNS1-AS1 USP37 RUFY4 RNF25
GH02J217992 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 12 -39.6 -39610 5.5 JUND ATF2 CEBPB CTCF RFX5 SMC3 STAT3 RAD21 ZNF189 ZNF48 CNOT9 USP37 RUFY4 lnc-CXCR1-1 HSALNG0022220 TNS1 TNS1-AS1 HSALNG0022218
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RUFY4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RUFY4

Top Transcription factor binding sites by QIAGEN in the RUFY4 gene promoter:
  • c-Ets-1
  • CP2
  • CUTL1
  • E47
  • GATA-1
  • p300
  • SEF-1 (1)
  • SRF
  • SRF (504 AA)
  • Tal-1beta

Genomic Locations for RUFY4 Gene

Latest Assembly
chr2:218,034,934-218,090,584
(GRCh38/hg38)
Size:
55,651 bases
Orientation:
Plus strand

Previous Assembly
chr2:218,899,657-218,955,307
(GRCh37/hg19 by Entrez Gene)
Size:
55,651 bases
Orientation:
Plus strand

chr2:218,899,683-218,955,304
(GRCh37/hg19 by Ensembl)
Size:
55,622 bases
Orientation:
Plus strand

Genomic View for RUFY4 Gene

Genes around RUFY4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RUFY4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RUFY4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RUFY4 Gene

Proteins for RUFY4 Gene

  • Protein details for RUFY4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZNE9-RUFY4_HUMAN
    Recommended name:
    RUN and FYVE domain-containing protein 4
    Protein Accession:
    Q6ZNE9
    Secondary Accessions:
    • Q6ZR96

    Protein attributes for RUFY4 Gene

    Size:
    571 amino acids
    Molecular mass:
    64350 Da
    Quaternary structure:
    • Interacts (via RUN domain) with RAB7A.
    SequenceCaution:
    • Sequence=AAI13713.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC87417.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for RUFY4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RUFY4 Gene

Post-translational modifications for RUFY4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RUFY4 Gene

No data available for DME Specific Peptides for RUFY4 Gene

Domains & Families for RUFY4 Gene

Gene Families for RUFY4 Gene

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

Protein Domains for RUFY4 Gene

Suggested Antigen Peptide Sequences for RUFY4 Gene

GenScript: Design optimal peptide antigens:
  • RUN and FYVE domain-containing protein 4 (RUFY4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6ZNE9

UniProtKB/Swiss-Prot:

RUFY4_HUMAN :
  • The RUN domain and the FYVE-type zinc finger are essential for its function in the positive regulation of macroautophagy.
Domain:
  • The RUN domain and the FYVE-type zinc finger are essential for its function in the positive regulation of macroautophagy.
genes like me logo Genes that share domains with RUFY4: view

Function for RUFY4 Gene

Molecular function for RUFY4 Gene

UniProtKB/Swiss-Prot Function:
Positively regulates macroautophagy in primary dendritic cells. Increases autophagic flux, probably by stimulating both autophagosome formation and facilitating tethering with lysosomes. Binds to phosphatidylinositol 3-phosphate (PtdIns3P) through its FYVE-type zinc finger.
UniProtKB/Swiss-Prot Induction:
By IL4/interleukin-4 in dendritic cells.

Phenotypes From GWAS Catalog for RUFY4 Gene

Gene Ontology (GO) - Molecular Function for RUFY4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0032266 phosphatidylinositol-3-phosphate binding IBA,IDA 26416964
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RUFY4: view
genes like me logo Genes that share phenotypes with RUFY4: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RUFY4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RUFY4 Gene

Localization for RUFY4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RUFY4 Gene

Cytoplasmic vesicle, autophagosome.

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 RUFY4 gene
Compartment Confidence
nucleus 2
plasma membrane 1
cytoskeleton 1
peroxisome 1
endosome 1
cytosol 1
lysosome 1
mitochondrion 0

Gene Ontology (GO) - Cellular Components for RUFY4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005776 autophagosome IBA,IDA 26416964
GO:0031410 cytoplasmic vesicle IEA --
genes like me logo Genes that share ontologies with RUFY4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RUFY4 Gene

Pathways & Interactions for RUFY4 Gene

PathCards logo

SuperPathways for RUFY4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RUFY4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000045 autophagosome assembly IBA,IDA 26416964
GO:0006914 autophagy IEA --
GO:0016239 positive regulation of macroautophagy IMP 26416964
GO:0071353 cellular response to interleukin-4 IDA 26416964
genes like me logo Genes that share ontologies with RUFY4: view

No data available for Pathways by source and SIGNOR curated interactions for RUFY4 Gene

Drugs & Compounds for RUFY4 Gene

No Compound Related Data Available

Transcripts for RUFY4 Gene

mRNA/cDNA for RUFY4 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RUFY4

Alternative Splicing Database (ASD) splice patterns (SP) for RUFY4 Gene

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: - - -
SP6:
SP7: - - -
SP8: - -

Relevant External Links for RUFY4 Gene

GeneLoc Exon Structure for
RUFY4

Expression for RUFY4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RUFY4 Gene

mRNA differential expression in normal tissues according to GTEx for RUFY4 Gene

This gene is overexpressed in Spleen (x5.2).

Protein differential expression in normal tissues from HIPED for RUFY4 Gene

This gene is overexpressed in Plasma (42.1) and Breast (25.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RUFY4 Gene



Protein tissue co-expression partners for RUFY4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RUFY4

SOURCE GeneReport for Unigene cluster for RUFY4 Gene:

Hs.570069
genes like me logo Genes that share expression patterns with RUFY4: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RUFY4 Gene

Orthologs for RUFY4 Gene

This gene was present in the common ancestor of animals.

Orthologs for RUFY4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RUFY4 29 30
  • 97.57 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RUFY4 29
  • 81.52 (n)
MGC157327 30
  • 62 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia RUFY4 29 30
  • 79.58 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rufy4 29
  • 74.85 (n)
Mouse
(Mus musculus)
Mammalia Rufy4 29 16 30
  • 74.32 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RUFY4 30
  • 37 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RUFY4 29 30
  • 65.92 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RUFY4 30
  • 15 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG4030 30
  • 6 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea rabn-5 30
  • 11 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 14 (a)
OneToMany
Species where no ortholog for RUFY4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Zebrafish (Danio rerio)

Evolution for RUFY4 Gene

ENSEMBL:
Gene Tree for RUFY4 (if available)
TreeFam:
Gene Tree for RUFY4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RUFY4: view image
Alliance of Genome Resources:
Additional Orthologs for RUFY4

Paralogs for RUFY4 Gene

Paralogs for RUFY4 Gene

genes like me logo Genes that share paralogs with RUFY4: view

Variants for RUFY4 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RUFY4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RUFY4 Gene

Variant ID Type Subtype PubMed ID
esv2494137 CNV insertion 19546169
esv2721477 CNV deletion 23290073
esv3445788 CNV insertion 20981092
nsv3163 CNV insertion 18451855
nsv512786 CNV insertion 21212237
nsv584488 CNV loss 21841781
nsv834541 CNV loss 17160897
nsv954835 CNV deletion 24416366

Variation tolerance for RUFY4 Gene

Gene Damage Index Score: 4.22; 62.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RUFY4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RUFY4
Leiden Open Variation Database (LOVD)
RUFY4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RUFY4 Gene

Disorders for RUFY4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RUFY4 Gene - From: COP

Disorder Aliases PubMed IDs
zellweger syndrome
  • cerebrohepatorenal syndrome
- elite association - COSMIC cancer census association via MalaCards
Search RUFY4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RUFY4

genes like me logo Genes that share disorders with RUFY4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RUFY4 Gene

Publications for RUFY4 Gene

  1. RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4. (PMID: 26416964) Terawaki S … Pierre P (The Journal of cell biology 2015) 3 4
  2. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. (PMID: 32814053) Haenig C … Wanker EE (Cell reports 2020) 3
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. (PMID: 29892012) Chen S … Yu H (Nature genetics 2018) 3
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3

Products for RUFY4 Gene

Sources for RUFY4 Gene