Note! The database itself has recently been updated to v6.00. Some of the information on this
page may not yet have been changed accordingly.
Format of O-GLYCBASE
Fields: Description > Entry accession number and entry date GLYCPROT: Glycoprotein name, and alternative names SPECIES: Species DB_REF: Crossreferences to PIR, SWISS-PROT, PDB and PROSITE. OGLYCAN: Type of carbohydrate linked to serine or threonine SER: Residue numbers of the O-linked serines THR: Residue numbers of the O-linked threonines ASN: Residue numbers of the N-linked asparagines TRP: Residue numbers of the C-linked tryptophans REFERENCES: References of O-glycan assignment. SEQ: Sequence length, including signal peptide. SEQUENCE in one letter code. ex: STPSTPNASKLPGHSTNGT Assignment ...ST.N.......stn..
Where where uppercase T,S,N denote experimentally verified glycosylation sites of threonine, serine and asparagine, respectively and lower case t,s,n denote predicted sites. Dots (.) denote no glycosylation.
COMMENTS: contain any comments END End of entry
Format of O-Unique.
This non-redundant database contains 53 entries only including mammalian mucin type
glycoproteins. It contains 265 O-glycosylation sites.
Ex: 50 A29789 (pir) ( 17, 0) mucin - sheep (fragment) SSVPGESATPQQPGALSESTTQLPGVTGTSAVTGSEPGLPSTGVSGLPGT SS....S.T.......S.STT.....T.TS..T.S.....ST..S....T
The leukosialins are cut into peptides marked (p1-4) as this is the only regions
where the assignment can be performed. Including the rest of the sequences would
introduce false negative sites. (See comments in O-GLYCBASE).
This data set can be used for benchmark studies. It is identical to the data set
used to train the neural networks used in the
netOglyc prediction server (Hansen et al. 1995).
Data can no longer be retrieved by anonymous ftp. Only http is supported:
NEW DATA, COMMENTS AND SUGGESTIONS
PAPER TO REFERENCE WHILE REPORTING RESULTS:
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.
Last change: Sep 18, 2001,Ramneek Gupta