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Aliases for RFNG Gene

Aliases for RFNG Gene

  • RFNG O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase 2 3 5
  • EC 2.4.1.222 4 61
  • O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase 4
  • Radical Fringe (Drosophila) Homolog 2
  • Radical Fringe Homolog (Drosophila) 2

External Ids for RFNG Gene

Previous GeneCards Identifiers for RFNG Gene

  • GC17M079429
  • GC17M9J0047
  • GC17M080541
  • GC17M077599
  • GC17U900606
  • GC17M080005
  • GC17M075405

Summaries for RFNG Gene

GeneCards Summary for RFNG Gene

RFNG (RFNG O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase) is a Protein Coding gene. Diseases associated with RFNG include Renal Cell Carcinoma, Papillary. Among its related pathways are Pre-NOTCH Expression and Processing and Notch signaling pathway (KEGG). GO annotations related to this gene include transferase activity, transferring glycosyl groups and O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity. An important paralog of this gene is LFNG.

UniProtKB/Swiss-Prot for RFNG Gene

  • Glycosyltransferase that initiates the elongation of O-linked fucose residues attached to EGF-like repeats in the extracellular domain of Notch molecules. May be involved in limb formation and in neurogenesis (By similarity).

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RFNG Gene

Genomics for RFNG Gene

Regulatory Elements for RFNG Gene


Enhancers around RFNG on UCSC Golden Path with GeneCards custom track

Promoters for RFNG Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000099527 -69 1801 ARID4B SIN3A DMAP1 ZNF48 ETS1 GLIS2 ELK1 KDM4B ZNF263 SP5

Genomic Location for RFNG Gene

Chromosome:
17
Start:
82,047,902 bp from pter
End:
82,051,831 bp from pter
Size:
3,930 bases
Orientation:
Minus strand

Genomic View for RFNG Gene

Genes around RFNG on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RFNG Gene

Proteins for RFNG Gene

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

    Protein Symbol:
    Q9Y644-RFNG_HUMAN
    Recommended name:
    Beta-1,3-N-acetylglucosaminyltransferase radical fringe
    Protein Accession:
    Q9Y644
    Secondary Accessions:
    • O00588

    Protein attributes for RFNG Gene

    Size:
    331 amino acids
    Molecular mass:
    36424 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    No Data Available

neXtProt entry for RFNG Gene

Selected DME Specific Peptides for RFNG Gene

Q9Y644:
  • CHVDDDNY
  • LQQVTLS
  • FIAVKTT
  • GRPSLDHP
  • SRGLALKMSPWAS
  • FWFATGGAGFC
  • DDDNYVN
  • LFHSHLENLQ
  • HCLLYPDT
  • RLPDDCT
  • IVEGLLGA

Post-translational modifications for RFNG Gene

  • Glycosylation at Asn113
  • Modification sites at PhosphoSitePlus

Other Protein References for RFNG Gene

Domains & Families for RFNG Gene

Gene Families for RFNG Gene

Protein Domains for RFNG Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q9Y644

UniProtKB/Swiss-Prot:

RFNG_HUMAN :
  • Belongs to the glycosyltransferase 31 family.
Family:
  • Belongs to the glycosyltransferase 31 family.
genes like me logo Genes that share domains with RFNG: view

Function for RFNG Gene

Molecular function for RFNG Gene

GENATLAS Biochemistry:
radical fringe,putative regulator of developmental processes through regulation of the sensitivity of NOTCH receptor genes for their specific ligands,essential mediator of somite segmentation and patterning
UniProtKB/Swiss-Prot CatalyticActivity:
Transfers a beta-D-GlcNAc residue from UDP-D-GlcNAc to the fucose residue of a fucosylated protein acceptor.
UniProtKB/Swiss-Prot Function:
Glycosyltransferase that initiates the elongation of O-linked fucose residues attached to EGF-like repeats in the extracellular domain of Notch molecules. May be involved in limb formation and in neurogenesis (By similarity).

Enzyme Numbers (IUBMB) for RFNG Gene

Gene Ontology (GO) - Molecular Function for RFNG Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0016740 transferase activity IEA --
GO:0016757 transferase activity, transferring glycosyl groups IEA --
GO:0033829 O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RFNG: view
genes like me logo Genes that share phenotypes with RFNG: view

Animal Models for RFNG Gene

MGI Knock Outs for RFNG:

Animal Model Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RFNG

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for RFNG Gene

Localization for RFNG Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFNG Gene

Golgi apparatus membrane; Single-pass type II 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 RFNG gene
Compartment Confidence
extracellular 5
golgi apparatus 4
cytoskeleton 2
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for RFNG Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region NAS 10341080
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030173 integral component of Golgi membrane IEA --
genes like me logo Genes that share ontologies with RFNG: view

Pathways & Interactions for RFNG Gene

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

Pathways by source for RFNG Gene

1 GeneGo (Thomson Reuters) pathway for RFNG Gene
1 R&D Systems pathway for RFNG Gene
1 Qiagen pathway for RFNG Gene

SIGNOR curated interactions for RFNG Gene

Activates:

Gene Ontology (GO) - Biological Process for RFNG Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007389 pattern specification process IEA --
GO:0007399 nervous system development IEA --
GO:0009887 animal organ morphogenesis NAS 10341080
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with RFNG: view

Drugs & Compounds for RFNG Gene

No Compound Related Data Available

Transcripts for RFNG Gene

mRNA/cDNA for RFNG Gene

(2) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(12) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RFNG Gene

RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RFNG

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

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c · 2d · 2e · 2f ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c · 9d
SP1: - - - - - - -
SP2: -
SP3: - - - -
SP4: - - -
SP5: - - - -
SP6: -
SP7: - - - - - -
SP8:
SP9: - - - - - -
SP10: - - - - -
SP11: - - -
SP12: - - -

Relevant External Links for RFNG Gene

GeneLoc Exon Structure for
RFNG
ECgene alternative splicing isoforms for
RFNG

Expression for RFNG Gene

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

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



NURSA nuclear receptor signaling pathways regulating expression of RFNG Gene:

RFNG

SOURCE GeneReport for Unigene cluster for RFNG Gene:

Hs.569700

Evidence on tissue expression from TISSUES for RFNG Gene

  • Nervous system(3)
genes like me logo Genes that share expression patterns with RFNG: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RFNG Gene

Orthologs for RFNG Gene

This gene was present in the common ancestor of animals.

Orthologs for RFNG Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RFNG 35
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RFNG 34 35
  • 87.76 (n)
mouse
(Mus musculus)
Mammalia Rfng 34 16 35
  • 83.15 (n)
dog
(Canis familiaris)
Mammalia RFNG 34 35
  • 83.04 (n)
rat
(Rattus norvegicus)
Mammalia Rfng 34
  • 82.23 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 66 (a)
OneToMany
-- 35
  • 63 (a)
OneToMany
chicken
(Gallus gallus)
Aves RFNG 34 35
  • 72.2 (n)
lizard
(Anolis carolinensis)
Reptilia RFNG 35
  • 44 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rfng 34
  • 67.04 (n)
zebrafish
(Danio rerio)
Actinopterygii rfng 34 35
  • 70.71 (n)
fruit fly
(Drosophila melanogaster)
Insecta fng 34 35
  • 56.15 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006439 34
  • 52.21 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 46 (a)
ManyToMany
-- 35
  • 45 (a)
ManyToMany
-- 35
  • 45 (a)
ManyToMany
-- 35
  • 43 (a)
ManyToMany
-- 35
  • 43 (a)
ManyToMany
-- 35
  • 42 (a)
ManyToMany
-- 35
  • 42 (a)
ManyToMany
-- 35
  • 42 (a)
ManyToMany
-- 35
  • 42 (a)
ManyToMany
-- 35
  • 41 (a)
ManyToMany
-- 35
  • 41 (a)
ManyToMany
-- 35
  • 38 (a)
ManyToMany
-- 35
  • 38 (a)
ManyToMany
-- 35
  • 36 (a)
ManyToMany
-- 35
  • 35 (a)
ManyToMany
-- 35
  • 34 (a)
ManyToMany
-- 35
  • 33 (a)
ManyToMany
Species where no ortholog for RFNG was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 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 RFNG Gene

ENSEMBL:
Gene Tree for RFNG (if available)
TreeFam:
Gene Tree for RFNG (if available)

Paralogs for RFNG Gene

Paralogs for RFNG Gene

(2) SIMAP similar genes for RFNG Gene using alignment to 5 proteins:

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

Variants for RFNG Gene

Sequence variations from dbSNP and Humsavar for RFNG Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1000349452 -- 82,052,652(+) AGGAG(C/T)GCGGG intron-variant, upstream-variant-2KB
rs1000364181 -- 82,052,246(+) TCTTT(C/T)TCCCT intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs1001509222 -- 82,047,882(+) GTGGG(G/T)GACTA downstream-variant-500B
rs1001889356 -- 82,051,306(+) GAGCT(C/G)GAGCT upstream-variant-2KB, reference, missense
rs1001912810 -- 82,048,055(+) GCTCC(C/T)GTTGT utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
esv21913 CNV gain+loss 19812545
nsv1112723 CNV deletion 24896259
nsv428351 CNV gain 18775914
nsv457975 CNV loss 19166990
nsv457976 CNV gain 19166990
nsv470620 CNV loss 18288195
nsv470621 CNV gain 18288195
nsv576183 CNV loss 21841781
nsv576187 CNV gain 21841781
nsv576188 CNV loss 21841781
nsv576189 CNV loss 21841781
nsv952392 CNV deletion 24416366

Variation tolerance for RFNG Gene

Residual Variation Intolerance Score: 22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.23; 40.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RFNG Gene

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

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

Disorders for RFNG Gene

MalaCards: The human disease database

(1) MalaCards diseases for RFNG Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
renal cell carcinoma, papillary
  • renal cell carcinoma
- elite association - COSMIC cancer census association via MalaCards
Search RFNG in MalaCards View complete list of genes associated with diseases

Relevant External Links for RFNG

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RFNG
genes like me logo Genes that share disorders with RFNG: view

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

Publications for RFNG Gene

  1. A family of mammalian Fringe genes implicated in boundary determination and the Notch pathway. (PMID: 9187150) Johnston S.H. … Vogt T.F. (Development 1997) 2 3 4 64
  2. Genomic structure, mapping, and expression analysis of the mammalian Lunatic, Manic, and Radical fringe genes. (PMID: 10341080) Moran J.L. … Vogt T.F. (Mamm. Genome 1999) 3 4 64
  3. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. (PMID: 23376485) Prunotto M. … Moll S. (J Proteomics 2013) 3 64
  4. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PMID: 16625196) Zody M.C. … Nusbaum C. (Nature 2006) 4 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 64

Products for RFNG Gene

Sources for RFNG Gene

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