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}
miRNA Name Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
hsa-miR-4636 797-804 -0.538 97.0 -0.538 98.0 noncon
hsa-miR-4790-5p 1541-1548 -0.529 97.0 -0.014 33.0 noncon
hsa-miR-3197 550-557 -0.524 99.0 -0.524 99.0 noncon
hsa-miR-4651 281-288 -0.52 98.0 -0.52 98.0 noncon
hsa-miR-6825-5p 2051-2058 -0.518 98.0 -0.014 29.0 noncon
hsa-miR-608 281-288 -0.509 97.0 -0.509 98.0 noncon
hsa-miR-5704 2066-2073 -0.509 98.0 -0.014 24.0 noncon
hsa-miR-6820-5p 459-466 -0.471 95.0 -0.471 96.0 noncon
hsa-miR-6781-5p 849-856 -0.456 94.0 -0.012 19.0 noncon
hsa-miR-6805-5p 57-64 -0.417 97.0 -0.417 97.0 noncon
hsa-miR-3692-5p 702-709 -0.412 99.0 -0.412 99.0 noncon
hsa-miR-4290 1289-1296 -0.407 96.0 -0.011 37.0 noncon
hsa-miR-657 1514-1521 -0.373 98.0 -0.01 50.0 noncon
hsa-miR-6787-5p 717-723 -0.368 92.0 -0.368 93.0 noncon
hsa-miR-492 2077-2084 -0.368 96.0 -0.01 31.0 noncon
hsa-miR-1233-3p 418-425 -0.364 98.0 -0.364 98.0 noncon
hsa-miR-1225-3p 1473-1480 -0.361 96.0 -0.01 44.0 noncon
hsa-miR-486-3p 640-647 -0.361 93.0 -0.361 95.0 noncon
hsa-miR-7846-3p 595-601 -0.36 92.0 -0.36 94.0 noncon
hsa-miR-6769a-5p 953-960 -0.359 98.0 -0.01 34.0 noncon
hsa-miR-6724-5p 656-662 -0.358 97.0 -0.358 97.0 noncon
hsa-miR-663a 717-723 -0.358 91.0 -0.358 93.0 noncon
hsa-miR-6871-3p 347-354 -0.353 98.0 -0.353 98.0 noncon
hsa-miR-3940-3p 319-325 -0.352 93.0 -0.352 95.0 noncon
hsa-miR-6773-5p 656-662 -0.35 96.0 -0.35 97.0 noncon
hsa-miR-6769b-5p 953-960 -0.341 97.0 -0.01 35.0 noncon
hsa-miR-4706 716-722 -0.327 90.0 -0.327 92.0 noncon
hsa-miR-4751 1879-1885 -0.325 95.0 -0.009 37.0 noncon
hsa-miR-4664-5p 1371-1378 -0.324 95.0 -0.009 39.0 noncon
hsa-miR-3692-5p 2168-2174 -0.324 98.0 0.0 0.0 noncon
hsa-miR-4731-5p 284-291 -0.322 97.0 -0.322 98.0 noncon
hsa-miR-6721-5p 692-699 -0.322 95.0 -0.322 96.0 noncon
hsa-miR-4505 399-406 -0.32 96.0 -0.32 97.0 noncon
hsa-miR-1184 1561-1568 -0.318 98.0 -0.009 58.0 noncon
hsa-miR-342-5p 1371-1378 -0.318 95.0 -0.009 36.0 noncon
hsa-miR-132-5p 89-95 -0.313 90.0 -0.313 93.0 noncon
hsa-miR-185-3p 248-255 -0.31 90.0 -0.31 92.0 noncon
hsa-miR-661 908-915 -0.308 97.0 -0.009 41.0 noncon
hsa-miR-3692-5p 986-993 -0.307 97.0 -0.009 48.0 noncon
hsa-miR-551a 628-634 -0.305 90.0 -0.305 93.0 noncon
hsa-miR-4505 942-948 -0.305 95.0 -0.009 37.0 noncon
hsa-miR-551b-3p 628-634 -0.305 90.0 -0.305 93.0 noncon
hsa-miR-4515 541-548 -0.298 94.0 -0.298 95.0 noncon
hsa-miR-4713-5p 190-197 -0.297 96.0 -0.297 97.0 noncon
hsa-miR-4529-5p 214-221 -0.296 92.0 -0.296 95.0 noncon
hsa-miR-4646-3p 1788-1795 -0.293 94.0 -0.008 39.0 noncon
hsa-miR-4751 1405-1412 -0.292 94.0 -0.008 36.0 noncon
hsa-miR-3150a-3p 2052-2058 -0.291 95.0 -0.008 40.0 noncon
hsa-miR-1295a 2067-2073 -0.289 94.0 -0.008 25.0 noncon
hsa-miR-644a 1995-2001 -0.288 94.0 -0.008 45.0 noncon
hsa-miR-6838-3p 615-622 -0.287 96.0 -0.287 97.0 noncon
hsa-miR-6827-5p 76-82 -0.286 91.0 -0.286 93.0 noncon
hsa-miR-671-5p 276-283 -0.286 94.0 -0.286 96.0 noncon
hsa-miR-4726-5p 395-402 -0.282 91.0 -0.282 93.0 noncon
hsa-miR-4755-3p 426-433 -0.28 94.0 -0.28 96.0 noncon
hsa-miR-566 548-554 -0.28 93.0 -0.28 95.0 noncon
hsa-miR-6763-5p 2052-2058 -0.28 94.0 -0.008 39.0 noncon
hsa-miR-6852-5p 891-898 -0.28 96.0 -0.008 50.0 noncon
hsa-miR-3135b 984-991 -0.277 97.0 -0.008 45.0 noncon
hsa-miR-138-5p 2167-2173 -0.273 90.0 -0.002 27.0 noncon
hsa-miR-1267 1524-1531 -0.267 96.0 -0.008 38.0 noncon
hsa-miR-4474-3p 1994-2000 -0.266 93.0 -0.008 34.0 noncon
hsa-miR-4779 1699-1706 -0.265 95.0 -0.008 49.0 noncon
hsa-miR-4438 1947-1953 -0.265 97.0 -0.008 45.0 noncon
hsa-miR-499a-5p 1932-1939 -0.263 95.0 -0.008 39.0 noncon
hsa-miR-4456 955-962 -0.262 94.0 -0.007 42.0 noncon
hsa-miR-1911-3p 2018-2024 -0.26 93.0 -0.007 39.0 noncon
hsa-miR-299-3p 1308-1315 -0.256 94.0 -0.007 40.0 noncon
hsa-miR-4527 705-711 -0.254 92.0 -0.254 94.0 noncon
hsa-miR-1827 771-777 -0.253 93.0 -0.253 95.0 noncon
hsa-miR-3612 772-778 -0.252 94.0 -0.252 95.0 noncon
hsa-miR-4266 1700-1707 -0.251 90.0 -0.007 33.0 noncon