RUFY1 Gene (Protein Coding)

RUN And FYVE Domain Containing 1

GC05P179550
GIFtS:
39
This gene encodes a protein that contains a RUN domain and a FYVE-type zinc finger domain. The encoded protein binds to phosphatidylinositol-3-phosphate (PI3P) and plays a role in early endosomal trafficking, tethering and fusion through interactions with small GTPases including Rab4, Rab5 and Rab14. Alternatively spliced transcript variants encoding multiple isoforms have been... See more...

Aliases for RUFY1 Gene

Aliases for RUFY1 Gene

  • RUN And FYVE Domain Containing 1 2 3 5
  • ZFYVE12 2 3 4
  • RABIP4 2 3 4
  • Zinc Finger FYVE Domain-Containing Protein 12 3 4
  • RUN And FYVE Domain-Containing Protein 1 3 4
  • FYVE-Finger Protein EIP1 3 4
  • Rab4-Interacting Protein 3 4
  • La-Binding Protein 1 3 4
  • FLJ22251 2
  • RUFY1 5

External Ids for RUFY1 Gene

Previous GeneCards Identifiers for RUFY1 Gene

  • GC00U990921
  • GC05P179802
  • GC05P179045
  • GC05P179090
  • GC05P178910
  • GC05P178977
  • GC05P173702

Summaries for RUFY1 Gene

Entrez Gene Summary for RUFY1 Gene

  • This gene encodes a protein that contains a RUN domain and a FYVE-type zinc finger domain. The encoded protein binds to phosphatidylinositol-3-phosphate (PI3P) and plays a role in early endosomal trafficking, tethering and fusion through interactions with small GTPases including Rab4, Rab5 and Rab14. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

GeneCards Summary for RUFY1 Gene

RUFY1 (RUN And FYVE Domain Containing 1) is a Protein Coding gene. Diseases associated with RUFY1 include Gerstmann Syndrome. Among its related pathways are PI Metabolism and Endocytosis. Gene Ontology (GO) annotations related to this gene include lipid binding and protein transporter activity. An important paralog of this gene is RUFY2.

UniProtKB/Swiss-Prot Summary for RUFY1 Gene

  • Binds phospholipid vesicles containing phosphatidylinositol 3-phosphate and participates in early endosomal trafficking.

Gene Wiki entry for RUFY1 Gene

Additional gene information for RUFY1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RUFY1 Gene

Genomics for RUFY1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RUFY1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RUFY1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RUFY1

Top Transcription factor binding sites by QIAGEN in the RUFY1 gene promoter:
  • AP-4
  • Cdc5
  • ISGF-3
  • Lhx3a
  • LHX3b
  • MyoD
  • Pax-4a

Genomic Locations for RUFY1 Gene

Latest Assembly
chr5:179,550,551-179,610,012
(GRCh38/hg38)
Size:
59,462 bases
Orientation:
Plus strand

Previous Assembly
chr5:178,977,555-179,037,013
(GRCh37/hg19 by Entrez Gene)
Size:
59,459 bases
Orientation:
Plus strand

chr5:178,977,559-179,037,027
(GRCh37/hg19 by Ensembl)
Size:
59,469 bases
Orientation:
Plus strand

Genomic View for RUFY1 Gene

Genes around RUFY1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RUFY1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RUFY1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RUFY1 Gene

Proteins for RUFY1 Gene

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  • Protein details for RUFY1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96T51-RUFY1_HUMAN
    Recommended name:
    RUN and FYVE domain-containing protein 1
    Protein Accession:
    Q96T51
    Secondary Accessions:
    • Q59FF3
    • Q71S93
    • Q9H6I3

    Protein attributes for RUFY1 Gene

    Size:
    708 amino acids
    Molecular mass:
    79818 Da
    Quaternary structure:
    • Interacts with BMX. May interact with SSB. Interacts with RAB4 and RAB5 that have been activated by GTP-binding.
    SequenceCaution:
    • Sequence=AAK50771.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAB15276.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RUFY1 Gene

    Alternative splice isoforms for RUFY1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RUFY1 Gene

Protein Expression for RUFY1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RUFY1 Gene

  • Phosphorylation on Tyr-389 and/or Tyr-400 is required for interaction with BMX and endosomal targeting.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RUFY1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RUFY1 Gene

Domains & Families for RUFY1 Gene

Gene Families for RUFY1 Gene

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

Protein Domains for RUFY1 Gene

InterPro:
Blocks:
  • Zn-finger, RING
  • Zn-finger, FYVE type
ProtoNet:

Suggested Antigen Peptide Sequences for RUFY1 Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger FYVE domain-containing protein 12 (RUFY1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96T51

UniProtKB/Swiss-Prot:

RUFY1_HUMAN :
  • The FYVE-type zinc finger domain mediates interactions with phosphatidylinositol 3-phosphate in membranes of early endosomes and penetrates bilayers. The FYVE domain insertion into PtdIns(3)P-enriched membranes is substantially increased in acidic conditions.
Domain:
  • The FYVE-type zinc finger domain mediates interactions with phosphatidylinositol 3-phosphate in membranes of early endosomes and penetrates bilayers. The FYVE domain insertion into PtdIns(3)P-enriched membranes is substantially increased in acidic conditions.
genes like me logo Genes that share domains with RUFY1: view

Function for RUFY1 Gene

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  6. Cell Lines for research

Molecular function for RUFY1 Gene

UniProtKB/Swiss-Prot Function:
Binds phospholipid vesicles containing phosphatidylinositol 3-phosphate and participates in early endosomal trafficking.

Phenotypes From GWAS Catalog for RUFY1 Gene

Gene Ontology (GO) - Molecular Function for RUFY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21988832
GO:0008289 lipid binding IEA --
GO:0017124 SH3 domain binding IPI 11877430
GO:0042169 SH2 domain binding IPI 11877430
GO:0042802 identical protein binding IPI --
genes like me logo Genes that share ontologies with RUFY1: view
genes like me logo Genes that share phenotypes with RUFY1: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RUFY1

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RUFY1 Gene

Localization for RUFY1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RUFY1 Gene

Cytoplasm. Early endosome membrane. Peripheral membrane protein.

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 RUFY1 gene
Compartment Confidence
endosome 5
cytosol 5
nucleus 4
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1
lysosome 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Vesicles (3)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RUFY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
GO:0005768 endosome IEA,IDA 11877430
GO:0005829 cytosol IDA,TAS --
GO:0016020 membrane IEA --
GO:0016607 nuclear speck IDA --
genes like me logo Genes that share ontologies with RUFY1: view

Pathways & Interactions for RUFY1 Gene

genes like me logo Genes that share pathways with RUFY1: view

Pathways by source for RUFY1 Gene

1 KEGG pathway for RUFY1 Gene

SIGNOR curated interactions for RUFY1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for RUFY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006661 phosphatidylinositol biosynthetic process TAS --
GO:0006897 endocytosis IEA --
GO:0007264 small GTPase mediated signal transduction IEA --
GO:0015031 protein transport IBA 21873635
GO:0030100 regulation of endocytosis IBA,IPI 11877430
genes like me logo Genes that share ontologies with RUFY1: view

Drugs & Compounds for RUFY1 Gene

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  1. Drug products for research

(1) Drugs for RUFY1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with RUFY1: view

Transcripts for RUFY1 Gene

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mRNA/cDNA for RUFY1 Gene

3 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
14 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 RUFY1

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for RUFY1 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17a · 17b · 17c ^
SP1: - - - - -
SP2: - - - - - - - - -
SP3: - - - - -
SP4: - - - - - - -
SP5: - -
SP6:
SP7:
SP8: - -
SP9: -
SP10:

ExUns: 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b
SP1: - - -
SP2: - - -
SP3: - - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for RUFY1 Gene

GeneLoc Exon Structure for
RUFY1

Expression for RUFY1 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RUFY1 Gene

mRNA expression in normal human tissues for RUFY1 Gene
mRNA expression by BioGPS for RUFY1 GenemRNA expression by GTEx for RUFY1 Gene

Protein differential expression in normal tissues from HIPED for RUFY1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (17.3), Lymph node (11.1), and Lavage (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RUFY1 Gene



Protein tissue co-expression partners for RUFY1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RUFY1

SOURCE GeneReport for Unigene cluster for RUFY1 Gene:

Hs.306769

mRNA Expression by UniProt/SwissProt for RUFY1 Gene:

Q96T51-RUFY1_HUMAN
Tissue specificity: Broadly expressed, with highest levels in lung, testis, kidney and brain.

Evidence on tissue expression from TISSUES for RUFY1 Gene

  • Nervous system(4.7)
  • Liver(4.3)
  • Skin(2)
genes like me logo Genes that share expression patterns with RUFY1: view

Primer products for research

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 RUFY1 Gene

Orthologs for RUFY1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RUFY1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia LOC462328 30
  • 98.58 (n)
RUFY1 31
  • 96 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RUFY1 30 31
  • 90.28 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RUFY1 30 31
  • 89.58 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Rufy1 30
  • 88.66 (n)
Mouse
(Mus musculus)
 Mammalia Rufy1 30 17 31
  • 87.48 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia RUFY1 31
  • 82 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia RUFY1 31
  • 78 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves RUFY1 30 31
  • 76.06 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia RUFY1 31
  • 84 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia rufy1 30
  • 69.92 (n)
Str.16805 30
Zebrafish
(Danio rerio)
 Actinopterygii LOC100330077 30
  • 64.56 (n)
RUFY1 31
  • 62 (a)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta CG31064 31
  • 27 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 44 (a)
 OneToMany
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.10485 30
Species where no ortholog for RUFY1 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)
  • 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 RUFY1 Gene

ENSEMBL:
Gene Tree for RUFY1 (if available)
TreeFam:
Gene Tree for RUFY1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RUFY1: view image

Paralogs for RUFY1 Gene

Paralogs for RUFY1 Gene

(28) SIMAP similar genes for RUFY1 Gene using alignment to 5 proteins:

  • RUFY1_HUMAN
  • H0Y9Y8_HUMAN
  • H0YA47_HUMAN
  • H0YAC8_HUMAN
  • J3KPP6_HUMAN

Pseudogenes.org Pseudogenes for RUFY1 Gene

genes like me logo Genes that share paralogs with RUFY1: view

Variants for RUFY1 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RUFY1 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
VAR_035985 A breast cancer sample p.Cys267Phe
rs6879322 - p.His298Gln

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RUFY1 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 RUFY1 Gene

Variant ID Type Subtype PubMed ID
esv2759397 CNV gain 17122850
esv3429456 CNV duplication 20981092
esv3607747 CNV gain 21293372
esv3607748 CNV gain 21293372
esv3890773 CNV gain 25118596
nsv1022509 CNV gain 25217958
nsv1074895 CNV deletion 25765185
nsv1137049 CNV deletion 24896259
nsv1145083 CNV deletion 24896259
nsv281 OTHER inversion 15895083
nsv477188 CNV novel sequence insertion 20440878
nsv477317 CNV novel sequence insertion 20440878
nsv5159 CNV insertion 18451855
nsv7375 OTHER inversion 18451855

Variation tolerance for RUFY1 Gene

Residual Variation Intolerance Score: 7.78% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.11; 38.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RUFY1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RUFY1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RUFY1 Gene

Disorders for RUFY1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RUFY1 Gene - From: COP

Disorder Aliases PubMed IDs
gerstmann syndrome
  • aphasia-angular gyrus syndrome
- elite association - COSMIC cancer census association via MalaCards
Search RUFY1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RUFY1

Genetic Association Database
(GAD)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with RUFY1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RUFY1 Gene

Publications for RUFY1 Gene

  1. Interaction between tyrosine kinase Etk and a RUN domain- and FYVE domain-containing protein RUFY1. A possible role of ETK in regulation of vesicle trafficking. (PMID: 11877430) Yang J … Qiu Y (The Journal of biological chemistry 2002) 2 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. 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
  4. Rabip4' is an effector of rab5 and rab4 and regulates transport through early endosomes. (PMID: 14617813) Fouraux MA … Pruijn GJ (Molecular biology of the cell 2004) 3 4
  5. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. (PMID: 32694731) Aregger M … Moffat J (Nature metabolism 2020) 3

ExternalLinks

View latest publications for RUFY1 gene in Mastermind

Products for RUFY1 Gene

Sources for RUFY1 Gene