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
 

Glycogene class
A4GNT
ABO
B3GALNT2
B3GALT1
B3GALT2
B3GALT5
B3GAT1
B3GAT2
B3GLCT
B3GNT2
B3GNT3
B3GNT4
B3GNT6
B3GNT7
B4GALNT2
B4GALNT3
B4GALNT4
B4GALT1
B4GALT2
B4GALT3
B4GALT4
B4GALT5
C1GALT1
C1GALT1C1
CHST1
CHST10
CHST2
CHST3
CHST4
CHST5
CHST8
CHST9
CMAS
EOGT
FKRP
FKTN
FPGT
FUCA1
FUT1
FUT2
FUT3
FUT4
FUT5
FUT6
FUT7
FUT9
GAL3ST2
GAL3ST3
GAL3ST4
GALNT1
GALNT10
GALNT11
GALNT12
GALNT13
GALNT14
GALNT15
GALNT16
GALNT17
GALNT18
GALNT2
GALNT3
GALNT4
GALNT5
GALNT6
GALNT7
GALNT8
GALNT9
GALNTL6
GCNT1
GCNT2
GCNT3
GCNT4
GXYLT1
GXYLT2
LFNG
MFNG
MGAT5B
NEU1
NEU2
NEU3
NEU4
OGT
POFUT1
POFUT2
POGLUT1
POGLUT2
POGLUT3
POMGNT1
POMGNT2
POMT1
POMT2
RFNG
RXYLT1
ST3GAL1
ST3GAL2
ST3GAL3
ST3GAL4
ST3GAL6
ST6GAL1
ST6GAL2
ST6GALNAC1
ST6GALNAC2
ST6GALNAC3
ST6GALNAC4
ST8SIA2
ST8SIA3
ST8SIA4
ST8SIA6
TMTC1
TMTC2
TMTC3
TMTC4
XXYLT1
Pathway Map

GCNT1



General Information
Gene Symbol:   
GCNT1
Protein name:   
Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
E.C. No:   
Organs:   
Reaction (SNFG):   
+
+ UDP
Reaction (IUBMB):   
No specified reaction.

About

• This is C2GnT-1 or C2GnT-L (leukocyte type) or core-2 GlcNAcT that forms the core-2 branch on O-glycans. It is widely expressed in human leukocytes and also other tissue.
• Its level is low in naive T-cells but increases upon T-cell activation.
• C2GnT-I upregulation also promotes metastasis in colorectral, lung and prostate cancer.
• C2GnT-I is a major contributor to L- and P-selectin binding during inflammation.
• Addition of sulfotransferase activity can result in the formation of 6-sulfo sialyl Lex structures on these core-2 glycans that act as L-selectin ligands in the HEV.
• GCNT1 is over-expressed in some diseases Wiskott-Aldrich syndrome (WAS), leukemia and AIDS. This contributes to immunodeficient conditions due to abherent T-cell function.
• Core2 branch is a scaffold for the subsequent production of lactosamine disaccharide repeat, poly-N-acetyllactosamine (Galβ1-4GlcNAc)n which is a ligand for galectin-3.
• Core-2 branch in general adds bulk to the O-glyans and this may reduce other interactions like TRAIL binding to DR4-- thus it is immunomodulatory.


Related Pathway
KEGG ORTHOLOGY:   
KEGG Pathway:   
Reactome:   

Related Database
Organism:   
Homo sapiens
Uniprot:   
NCBI GeneID:   
GlyMap GeneID:   
DNA aRefSeq:   
Protein RefSeq:   
BRENDA:   
OMIM number:   
GeneCards database:   

Enzyme Specificity
Glycan Type:  
     O-linked (mucin type)
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     Gal(b1-3)GalNAc(a1-?)Ser|Thr
Product:  
     Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-?)Ser|Thr
Constraints:  
     !NeuAc(a2-3)Gal(b1-3)GalNAc(a1-?)&!Gal(b1-3 [3S])GalNAc(a1-?)

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 30 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 100 80 60 40 20 0 Transcripts per million (TPM)
Transcription factor {ref. 10}
Transcriptional start site (TSS) 0 200 -2000 -1800 -1600 -1400 -1200 -1000 -800 -600 -400 -200
ENST00000376730 ENST00000442371 ENST00000444201 ENST00000480311 TCF12 RUNX3 TSC22D4 MYB BATF3 ETV6 MTA2 SP1 CREM CREM IRF4 BATF RBPJ JUNB JUND FOS ELF3 MYC FOSL2 ARID3A


miRNA-GlycoEnzyme Interactome {ref. 9}
miRNA Name Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
hsa-miR-96-5p 359-366 -0.587 99.0 -0.587 99.0 con
hsa-miR-1271-5p 359-366 -0.568 99.0 -0.568 99.0 con
hsa-miR-125a-5p 325-332 -0.506 99.0 -0.506 99.0 con
hsa-miR-125b-5p 325-332 -0.498 99.0 -0.498 99.0 con
hsa-miR-1537-5p 415-422 -0.478 98.0 -0.478 99.0 noncon
hsa-miR-4319 325-332 -0.474 99.0 -0.474 99.0 con
hsa-miR-4301 209-216 -0.472 99.0 -0.472 99.0 noncon
hsa-miR-29b-2-5p 3741-3748 -0.438 99.0 -0.021 71.0 noncon
hsa-miR-483-3p.1 215-222 -0.434 99.0 -0.434 99.0 noncon
hsa-miR-591 3651-3658 -0.431 98.0 -0.118 78.0 noncon
hsa-miR-125a-5p 558-565 -0.418 98.0 -0.288 96.0 con
hsa-miR-125b-5p 558-565 -0.418 98.0 -0.288 96.0 con
hsa-miR-4319 558-565 -0.418 98.0 -0.288 96.0 con
hsa-miR-3194-3p 155-162 -0.413 98.0 -0.413 99.0 noncon
hsa-miR-1911-5p 3512-3519 -0.407 97.0 -0.141 85.0 noncon
hsa-miR-6841-5p 2011-2018 -0.402 97.0 -0.14 87.0 noncon
hsa-miR-1225-3p 2356-2363 -0.384 97.0 -0.134 84.0 noncon
hsa-miR-5587-5p 388-394 -0.358 97.0 -0.358 98.0 noncon
hsa-miR-5091 543-549 -0.357 92.0 -0.248 88.0 noncon
hsa-miR-6841-5p 45-51 -0.354 96.0 -0.354 97.0 noncon
hsa-miR-2278 516-523 -0.347 99.0 -0.241 98.0 noncon
hsa-miR-4506 3298-3305 -0.335 97.0 -0.118 87.0 noncon
hsa-miR-5699-5p 103-110 -0.334 98.0 -0.334 98.0 noncon
hsa-miR-8064 1181-1188 -0.331 97.0 -0.117 86.0 noncon
hsa-miR-7159-5p 460-467 -0.325 98.0 -0.259 98.0 noncon
hsa-miR-6793-3p 3603-3610 -0.32 98.0 -0.113 90.0 noncon
hsa-miR-1193 352-358 -0.318 97.0 -0.318 98.0 noncon
hsa-miR-370-5p 352-358 -0.315 97.0 -0.315 98.0 noncon
hsa-miR-4639-5p 333-340 -0.313 98.0 -0.313 98.0 noncon
hsa-miR-6752-3p 107-114 -0.313 95.0 -0.313 96.0 noncon
hsa-miR-183-5p.2 359-365 -0.311 95.0 -0.311 96.0 con
hsa-miR-4480 2046-2053 -0.309 97.0 -0.109 88.0 noncon
hsa-miR-155-5p 183-190 -0.308 96.0 -0.308 97.0 noncon
hsa-miR-133a-3p.1 3607-3613 -0.305 91.0 -0.108 74.0 noncon
hsa-miR-3158-5p 152-159 -0.305 98.0 -0.305 98.0 noncon
hsa-miR-5010-3p 36-43 -0.301 98.0 -0.301 98.0 noncon
hsa-miR-3176 235-242 -0.297 97.0 -0.297 98.0 noncon
hsa-miR-1229-3p 2501-2508 -0.293 96.0 -0.104 86.0 noncon
hsa-miR-532-3p 211-217 -0.292 98.0 -0.292 98.0 noncon
hsa-miR-6749-3p 213-219 -0.287 93.0 -0.287 95.0 noncon
hsa-miR-936 3530-3537 -0.287 95.0 -0.102 79.0 noncon
hsa-miR-552-3p 1072-1079 -0.286 95.0 -0.102 81.0 noncon
hsa-miR-4421 889-896 -0.285 95.0 -0.102 82.0 noncon
hsa-miR-4645-3p 2561-2568 -0.284 95.0 -0.101 78.0 noncon
hsa-miR-6511a-3p 2500-2507 -0.282 95.0 -0.101 80.0 noncon
hsa-miR-6511b-3p 2500-2507 -0.282 94.0 -0.101 80.0 noncon
hsa-miR-516a-5p 1727-1733 -0.279 90.0 -0.1 78.0 noncon
hsa-miR-5699-3p 889-896 -0.275 95.0 -0.098 83.0 noncon
hsa-miR-3200-3p 694-700 -0.273 95.0 -0.097 87.0 noncon
hsa-miR-222-5p 3531-3538 -0.272 96.0 -0.097 82.0 noncon
hsa-miR-3689e 3316-3323 -0.271 94.0 -0.097 82.0 noncon
hsa-miR-3689a-5p 3316-3323 -0.271 94.0 -0.097 82.0 noncon
hsa-miR-3689b-5p 3316-3323 -0.271 94.0 -0.097 82.0 noncon
hsa-miR-3689f 3316-3323 -0.271 95.0 -0.097 82.0 noncon
hsa-miR-628-5p 71-77 -0.27 96.0 -0.27 97.0 noncon
hsa-miR-6826-3p 267-273 -0.268 92.0 -0.268 94.0 noncon
hsa-miR-4714-5p 1528-1535 -0.268 96.0 -0.096 84.0 noncon
hsa-miR-3659 743-750 -0.266 94.0 -0.095 80.0 noncon
hsa-miR-1257 2603-2610 -0.262 95.0 -0.094 79.0 noncon
hsa-miR-181c-3p 2444-2450 -0.259 97.0 -0.093 86.0 noncon
hsa-miR-301a-5p 132-139 -0.257 98.0 -0.257 98.0 noncon
hsa-miR-3649 3286-3293 -0.257 91.0 -0.092 73.0 noncon
hsa-miR-301b-5p 132-139 -0.257 98.0 -0.257 98.0 noncon
hsa-miR-3065-5p 459-466 -0.256 98.0 -0.205 97.0 noncon
hsa-miR-3156-3p 210-216 -0.255 95.0 -0.255 96.0 noncon
hsa-miR-142-3p.2 2547-2554 -0.253 95.0 -0.091 83.0 con
hsa-miR-6795-3p 267-273 -0.251 96.0 -0.251 97.0 noncon
hsa-miR-6069 2677-2684 -0.251 91.0 -0.09 75.0 noncon