GlyClass

GlycoEnzDB
Comprehensive glycoEnzyme database and dynamic pathway generation

Description: The GlycoEnzDB is a manually curated glycoEnzyme database, primarily focused on humans. It covers 390 enzymes across 28 pathway maps. Facilities are also available to create custom glycosylation reaction pathways using experimental data in SBML format and for pathway simulation
Contacts: Sriram Neelamegham (neel@buffalo.edu), Yusen Zhou (yusenzho@buffalo.edu) or Ted Groth (tgroth@buffalo.edu).

GlycoEnzDB
Create glycosylation pathway
Custom database generation
Instructions/Reference
 
Pathway Map
RFNG



General Information
Gene Symbol:   
RFNG
Protein name:   
Beta-1,3-N-acetylglucosaminyltransferase radical fringe
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
GT31
E.C. No:   
2.4.1.222
Organs:   
Reaction (SNFG):   
+
→
+ UDP
Reaction (IUBMB):   
No specified reaction.
About

• Fringe catalyzes the addition of a β1,3GlcNAc linkage to O-fucose in certain Epidermal Growth Factor-like (EGF) repeats, for example in the extracellular domain of Notch. This then controls Notch dependent signaling.
• This structure may be further elongated to a tetrasaccharide with the structure NeuAcα2-3/6Galβ1-4GlcNAcβ1-3Fuc in mammals.
• Three vertebrate fringe homologues have been identified: Lunatic fringe (Lfng), Manic fringe (Mfng), and Radical fringe (Rfng).
• Since over 100 proteins contain O-fucose consensus sites in EGF repeats, fringe may modify O-fucose on a wide variety of proteins.

Related Pathway
KEGG ORTHOLOGY:   
K05948
KEGG Pathway:   
ko00514  ko04330  ko05165 
Reactome:   
R-HSA-1912420
Related Database
Organism:   
Homo sapiens
Uniprot:   
Q9Y644 
NCBI GeneID:   
5986
GlyMap GeneID:   
5986
DNA aRefSeq:   
NM_002917.1 
Protein RefSeq:   
NP_002908.1 
BRENDA:   
Kinetic info.
OMIM number:   
602578
GeneCards database:   
RFNG
Enzyme Specificity
Glycan Type:  
     O-linked (other)
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     Fuc(a1-?)Ser|Thr
Product:  
     GlcNAc(b1-3)Fuc(a1-?)Ser|Thr
Simulation Parameters
Mechaelis-Menten parameters (suggested)
VM:       (pmol/cell • hr)       KM:       (pM)
Relative conc of enzymes in compartment.(sum will be normalized to 1)
ER Cis- Medial- Trans- TGN










Expression Data in Tissue {ref. 5} Source from NCBI gene database
adrenal appendix bone marrow brain colon duodenum endometrium esophagus fat gall bladder heart kidney liver lung lymph node ovary pancreas placenta prostate salivary gland skin small intestine spleen stomach testis thyroid urinary bladder 20 10 0 RPKM
Expression Data in Cells {ref. 13} Source from Cancer Cell Line Encyclopedia database
Kidney Lung Breast Prostate Large intestine Ovary HL60 haematopoietic and lymphoid tissue Skin Central nervous system 786O A498 ACHN CAKI1 UO31 A549 EKVX HOP62 HOP92 NCIH226 NCIH23 NCIH322 NCIH460 NCIH522 SHP77 BT549 HS578T MCF7 MDAMB231 MDAMB468 T47D DU145 PC3 HCT116 HCT15 HT29 KM12 SW620 OVCAR4 OVCAR8 IGROV1 SKOV3 HL60 K562 RPMI8226 LOXIMVI MALME3M RPMI7951 SKMEL28 SKMEL5 UACC257 UACC62 SF268 SF295 SF539 SNB75 60 50 40 30 20 10 0 Transcripts per million (TPM)
Transcription factor {ref. 10}
No high degree of confidence data
miRNA-GlycoEnzyme Interactome {ref. 9}
RFNG/hsa-miR-1911-3p
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'...AGGUUGCAUAGU GCCUGGU C...
3'   CCUCUGGUGUUA CGGACCA C
 7mer-m8 2018-2024 -0.26 93.0 -0.007 39.0 noncon
5'...ACCCACCUCCCC GCCUGGU G...
3'   CCUCUGGUGUUA CGGACCA C
 7mer-m8 721-727 -0.193 86.0 -0.193 91.0 noncon