Free for academic non-profit institutions. Other users need a Commercial license

RFNG Gene(Protein Coding)

RFNG O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase

GCID:
GC17M082047
GIFtS:
48
Genes Participants
UDN Logo

Aliases for RFNG Gene

Aliases for RFNG Gene

  • RFNG O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase 2 3 5
  • EC 2.4.1.222 4 56
  • 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, 1. Among its related pathways are Development NOTCH1-mediated pathway for NF-KB activity modulation and PI3K-Akt signaling pathway. Gene Ontology (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. Modulates NOTCH1 activity by modifying O-fucose residues at specific EGF-like domains resulting in enhancement of NOTCH1 activation by DLL1 and JAG1. May be involved in limb formation and in neurogenesis.

Additional gene information for RFNG Gene

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

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for RFNG Gene

Promoters and enhancers for RFNG 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
GH17I082050 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 561 -0.1 -52 3.1 HDGF ARID4B SIN3A DMAP1 ETS1 GLIS2 ELK1 ATF7 SP3 SP5 RFNG GPS1 PIR58356
GH17I081336 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE dbSUPER 30.5 +709.9 709888 10.8 PKNOX1 SMAD1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 GC17P081340 GC17M081340 FAAP100 RFNG TMEM105 DUS1L HGS ENSG00000265678 LINC00482 TEPSIN
GH17I081700 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 27 +349.0 349041 4.2 HDGF CLOCK MLX ARID4B SIN3A DMAP1 ZBTB7B IRF4 YY1 POLR2B ENSG00000262049 ENSG00000262660 MRPL12 ARL16 ENSG00000260563 FAAP100 NARF-IT1 ENSG00000262652 ARL2BPP9 RFNG
GH17I081384 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 18.8 +655.7 655727 22.4 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF263 BAHCC1 ENSG00000279692 ENSG00000262877 CEP131 GPS1 HGS ENSG00000260011 FAAP100 ENSG00000260369 ENSG00000265678
GH17I082492 Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 27.9 -443.7 -443662 6 CLOCK ZFP64 FEZF1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 GC17M082508 TRX-CAT1-8 PIR58219 TBCD NARF ENSG00000260563 GPS1 NARF-IT1 ENSG00000262652 FOXK2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RFNG on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RFNG gene promoter:

Genomic Locations for RFNG Gene

Genomic Locations for RFNG Gene
chr17:82,047,902-82,051,831
(GRCh38/hg38)
Size:
3,930 bases
Orientation:
Minus strand
chr17:80,005,778-80,009,707
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for RFNG Gene

Proteins for RFNG Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for RFNG Gene

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

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 isoforms=113
  • Modification sites at PhosphoSitePlus

Other Protein References for RFNG Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for RFNG Gene

Gene Families for RFNG Gene

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

Protein Domains for RFNG Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for RFNG Gene

GenScript: Design optimal peptide antigens:

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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. Modulates NOTCH1 activity by modifying O-fucose residues at specific EGF-like domains resulting in enhancement of NOTCH1 activation by DLL1 and JAG1. May be involved in limb formation and in neurogenesis.

Enzyme Numbers (IUBMB) for RFNG Gene

Phenotypes From GWAS Catalog 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

Clone Products

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
See all subcellular structures

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 BioSystems pathway 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:0008593 regulation of Notch signaling pathway IEA,ISS --
GO:0009887 animal organ morphogenesis NAS 10341080
genes like me logo Genes that share ontologies with RFNG: view

Drugs & Compounds for RFNG Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for RFNG Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

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:

Clone Products

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

Products:

  1. Primer
  2. Gene Expression Assay

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

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

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 34
  • 96 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia RFNG 33 34
  • 87.76 (n)
mouse
(Mus musculus)
 Mammalia Rfng 33 16 34
  • 83.15 (n)
dog
(Canis familiaris)
 Mammalia RFNG 33 34
  • 83.04 (n)
rat
(Rattus norvegicus)
 Mammalia Rfng 33
  • 82.23 (n)
oppossum
(Monodelphis domestica)
 Mammalia -- 34
  • 66 (a)
 OneToMany
-- 34
  • 63 (a)
 OneToMany
chicken
(Gallus gallus)
 Aves RFNG 33 34
  • 72.2 (n)
lizard
(Anolis carolinensis)
 Reptilia RFNG 34
  • 44 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia rfng 33
  • 67.04 (n)
zebrafish
(Danio rerio)
 Actinopterygii rfng 33 34
  • 70.71 (n)
fruit fly
(Drosophila melanogaster)
 Insecta fng 33 34
  • 56.15 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP006439 33
  • 52.21 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 46 (a)
 ManyToMany
-- 34
  • 45 (a)
 ManyToMany
-- 34
  • 45 (a)
 ManyToMany
-- 34
  • 43 (a)
 ManyToMany
-- 34
  • 43 (a)
 ManyToMany
-- 34
  • 42 (a)
 ManyToMany
-- 34
  • 42 (a)
 ManyToMany
-- 34
  • 42 (a)
 ManyToMany
-- 34
  • 42 (a)
 ManyToMany
-- 34
  • 41 (a)
 ManyToMany
-- 34
  • 41 (a)
 ManyToMany
-- 34
  • 38 (a)
 ManyToMany
-- 34
  • 38 (a)
 ManyToMany
-- 34
  • 36 (a)
 ManyToMany
-- 34
  • 35 (a)
 ManyToMany
-- 34
  • 34 (a)
 ManyToMany
-- 34
  • 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

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for RFNG Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000349452 -- 82,052,652(-) C/T upstream_transcript_variant
rs1000364181 -- 82,052,246(-) C/T upstream_transcript_variant
rs1001509222 -- 82,047,882(-) T/G downstream_transcript_variant
rs1001889356 -- 82,051,306(-) C/G/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, upstream_transcript_variant
rs1001912810 -- 82,048,055(-) T/C 3_prime_UTR_variant

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)

Additional Variant Information for RFNG Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorder Aliases PubMed IDs
renal cell carcinoma, papillary, 1
  • rccp1
- elite association - COSMIC cancer census association via MalaCards
Search RFNG in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RFNG

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 SH … Vogt TF (Development (Cambridge, England) 1997) 2 3 4 58
  2. Genomic structure, mapping, and expression analysis of the mammalian Lunatic, Manic, and Radical fringe genes. (PMID: 10341080) Moran JL … Vogt TF (Mammalian genome : official journal of the International Mammalian Genome Society 1999) 3 4 58
  3. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. (PMID: 23376485) Prunotto M … Moll S (Journal of proteomics 2013) 3 58
  4. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PMID: 16625196) Zody MC … Nusbaum C (Nature 2006) 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 58

Products for RFNG Gene

Sources for RFNG Gene

Content
Loading form....