Aliases for RFNG Gene

Aliases for RFNG Gene

  • RFNG O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase 2 3 5
  • Beta-1,3-N-Acetylglucosaminyltransferase Radical Fringe 3 4
  • O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase 3 4
  • EC 2.4.1.222 4 51
  • Radical Fringe (Drosophila) Homolog 2
  • Radical Fringe Homolog (Drosophila) 2
  • Radical Fringe Homolog 3
  • RFNG 5

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 Congenital Muscular Dystrophy-Dystroglycanopathy Type A11 and Dowling-Degos Disease. Among its related pathways are Signaling by GPCR and Development NOTCH1-mediated pathway for NF-KB activity modulation. 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 Summary 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.

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

Genomics for RFNG Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RFNG 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 RFNG on the GeneHancer Hub at the UCSC Golden Path

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

Top Transcription factor binding sites by QIAGEN in the RFNG gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • c-Myc
  • Max

Genomic Locations for RFNG Gene

Latest Assembly
chr17:82,047,902-82,051,831
(GRCh38/hg38)
Size:
3,930 bases
Orientation:
Minus strand

Previous Assembly
chr17:80,005,778-80,009,687
(GRCh37/hg19 by Entrez Gene)
Size:
3,910 bases
Orientation:
Minus strand

chr17:80,005,778-80,009,707
(GRCh37/hg19 by Ensembl)
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

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

Protein Domains for RFNG Gene

InterPro:
Blocks:
  • Fringe-like
ProtoNet:

Suggested Antigen Peptide Sequences for RFNG Gene

GenScript: Design optimal peptide antigens:
  • RFNG protein (A6H8Z0_HUMAN)
  • cDNA FLJ50909, highly similar to Beta-1,3-N-acetylglucosaminyltransferase radical fringe (EC 2.4.1.222) (B4DXP6_HUMAN)
  • O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase (RFNG_HUMAN)

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

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Transfers a beta-D-GlcNAc residue from UDP-D-GlcNAc to the fucose residue of a fucosylated protein acceptor.; EC=2.4.1.222;.
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

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:0008375 acetylglucosaminyltransferase activity IBA 21873635
GO:0016740 transferase activity IEA --
GO:0016757 transferase activity, transferring glycosyl groups IEA --
GO:0033829 O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity IBA 21873635
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:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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
plasma membrane 1
mitochondrion 1
nucleus 1
cytosol 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RFNG Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005576 extracellular region NAS 10341080
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of 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
  • Development Notch Signaling Pathway
1 R&D Systems pathway for RFNG Gene
1 Qiagen pathway for RFNG Gene
  • Notch Signaling

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

No Compound Related Data Available

Transcripts for RFNG Gene

mRNA/cDNA for RFNG Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
12 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 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

Expression for RFNG Gene

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

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



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

SOURCE GeneReport for Unigene cluster for RFNG Gene:

Hs.569700

Evidence on tissue expression from TISSUES for RFNG Gene

  • Nervous system(3.4)
genes like me logo Genes that share expression patterns with RFNG: view

Primer products for research

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 31
  • 96 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia RFNG 30 31
  • 87.76 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Rfng 30 17 31
  • 83.15 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RFNG 30 31
  • 83.04 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rfng 30
  • 82.23 (n)
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 66 (a)
OneToMany
-- 31
  • 63 (a)
OneToMany
Chicken
(Gallus gallus)
Aves RFNG 30 31
  • 72.2 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RFNG 31
  • 44 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rfng 30
  • 67.04 (n)
Zebrafish
(Danio rerio)
Actinopterygii rfng 30 31
  • 70.71 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta fng 30 31
  • 56.15 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006439 30
  • 52.21 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 46 (a)
ManyToMany
-- 31
  • 45 (a)
ManyToMany
-- 31
  • 45 (a)
ManyToMany
-- 31
  • 43 (a)
ManyToMany
-- 31
  • 43 (a)
ManyToMany
-- 31
  • 42 (a)
ManyToMany
-- 31
  • 42 (a)
ManyToMany
-- 31
  • 42 (a)
ManyToMany
-- 31
  • 42 (a)
ManyToMany
-- 31
  • 41 (a)
ManyToMany
-- 31
  • 41 (a)
ManyToMany
-- 31
  • 38 (a)
ManyToMany
-- 31
  • 38 (a)
ManyToMany
-- 31
  • 36 (a)
ManyToMany
-- 31
  • 35 (a)
ManyToMany
-- 31
  • 34 (a)
ManyToMany
-- 31
  • 33 (a)
ManyToMany
Species where no ortholog for RFNG was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for RFNG Gene

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

Paralogs for RFNG Gene

Paralogs for RFNG Gene

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

  • RFNG_HUMAN
  • A6H8Z0_HUMAN
  • B4DXP6_HUMAN
  • F5H3H7_HUMAN
  • J3QLN0_HUMAN
genes like me logo Genes that share paralogs with RFNG: view

Variants for RFNG Gene

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

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs189385594 Benign: not provided 82,051,566(-) G/A
NM_002917.2(RFNG):c.201C>T (p.Thr67=)
SYNONYMOUS

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

Human Gene Mutation Database (HGMD)
RFNG
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFNG

SNP Genotyping and Copy Number Assays for research

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

Disorders for RFNG Gene

MalaCards: The human disease database

(4) MalaCards diseases for RFNG Gene - From: COP

Disorder Aliases PubMed IDs
congenital muscular dystrophy-dystroglycanopathy type a11
  • congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies type a11
dowling-degos disease
  • dark dot disease
spondylocostal dysostosis 3, autosomal recessive
  • scdo3
adams-oliver syndrome
  • adams oliver syndrome
- 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

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
  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
  3. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. (PMID: 23376485) Prunotto M … Moll S (Journal of proteomics 2013) 3
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3
  5. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PMID: 16625196) Zody MC … Nusbaum C (Nature 2006) 4

Products for RFNG Gene

Sources for RFNG Gene