PMC:7443692 / 17329-19130
Annnotations
LitCovid-sample-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T120 | 35-42 | Chemical | denotes | glycans | http://purl.obolibrary.org/obo/CHEBI_18154 |
| T121 | 170-173 | Chemical | denotes | H2O | http://purl.obolibrary.org/obo/CHEBI_15377 |
| T122 | 771-781 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T123 | 931-938 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T124 | 1046-1057 | Chemical | denotes | polypeptide | http://purl.obolibrary.org/obo/CHEBI_15841 |
| T125 | 1219-1222 | Chemical | denotes | N-G | http://purl.obolibrary.org/obo/CHEBI_73422 |
| T126 | 1360-1363 | Chemical | denotes | Asp | http://purl.obolibrary.org/obo/CHEBI_17053|http://purl.obolibrary.org/obo/CHEBI_22660|http://purl.obolibrary.org/obo/CHEBI_29958 |
| T129 | 1420-1427 | Chemical | denotes | glycine | http://purl.obolibrary.org/obo/CHEBI_15428|http://purl.obolibrary.org/obo/CHEBI_29947|http://purl.obolibrary.org/obo/CHEBI_57305 |
| T132 | 1536-1548 | Chemical | denotes | glycopeptide | http://purl.obolibrary.org/obo/CHEBI_24396 |
LitCovid-sample-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T100 | 0-240 | Sentence | denotes | To determine occupancy of N-linked glycans at each site, we employed a sequential deglycoslyation approach by using Endoglycosidase H and PNGase F in the presence of 18O-H2O after tryptic digestion of S (Wang et al., 2020; Yu et al., 2018). |
| T101 | 241-372 | Sentence | denotes | After LC-MS/MS analyses, the resulting data confirmed that 19 of the canonical sequons had occupancies greater than 95% (Table S5). |
| T102 | 373-537 | Sentence | denotes | One canonical sequence, N0149, had insufficient spectral counts for quantification by this method, but subsequent analyses described below suggested high occupancy. |
| T103 | 538-643 | Sentence | denotes | The two most C-terminal N-linked sites, N1173 and N1194, had reduced occupancy, 52% and 82% respectively. |
| T104 | 644-823 | Sentence | denotes | Reduced occupancy at these sites could reflect hindered en bloc transfer by the oligosaccharyltransferase (OST) due to primary amino acid sequences at or near the N-linked sequon. |
| T105 | 824-1156 | Sentence | denotes | Alternatively, this could reflect these two sites being post-translationally modified after release of the protein by the ribosome by a less efficient STT3B-containing OST, either due to activity or initial folding of the polypeptide, as opposed to co-translationally modified by the STT3A-containing OST (Ruiz-Canada et al., 2009). |
| T106 | 1157-1483 | Sentence | denotes | None of the non-canonical sequons (three N-X-C sites and four N-G-L/I/V sites; Zielinska et al., 2010) showed significant occupancy (>5%), except for N0501, which showed moderate (19%) conversion to 18O-Asp that could be due to deamidation that is facilitated by glycine at the +1 position (Table S5) (Palmisano et al., 2012). |
| T107 | 1484-1639 | Sentence | denotes | Further analysis of this site (see below) by direct glycopeptide analyses allowed us to determine that N0501 undergoes deamidation but is not glycosylated. |
| T108 | 1640-1801 | Sentence | denotes | Thus, all, and only the, 22 canonical sequences for N-linked glycosylation (N-X-S/T) are utilized, with only N1173 and N1194 demonstrating occupancies below 95%. |
LitCovid-sample-UniProt
| Id | Subject | Object | Predicate | Lexical cue | uniprot_id |
|---|---|---|---|---|---|
| T1724 | 138-144 | Protein | denotes | PNGase | https://www.uniprot.org/uniprot/Q9TW67|https://www.uniprot.org/uniprot/Q9NR70|https://www.uniprot.org/uniprot/Q9NBD6|https://www.uniprot.org/uniprot/Q9JI78|https://www.uniprot.org/uniprot/Q9CTK3|https://www.uniprot.org/uniprot/Q9BVR8|https://www.uniprot.org/uniprot/Q96IV0|https://www.uniprot.org/uniprot/Q8K113|https://www.uniprot.org/uniprot/Q6PJD8|https://www.uniprot.org/uniprot/Q5ZJM3|https://www.uniprot.org/uniprot/Q5XI55|https://www.uniprot.org/uniprot/Q5WNE3|https://www.uniprot.org/uniprot/Q59FB1|https://www.uniprot.org/uniprot/Q503I8|https://www.uniprot.org/uniprot/Q4R6F3|https://www.uniprot.org/uniprot/B4DJE9|https://www.uniprot.org/uniprot/A8X5N2 |
| T1741 | 975-980 | Protein | denotes | STT3B | https://www.uniprot.org/uniprot/Q9D2V2|https://www.uniprot.org/uniprot/Q99LL0|https://www.uniprot.org/uniprot/Q96KY7|https://www.uniprot.org/uniprot/Q96JZ4|https://www.uniprot.org/uniprot/Q921E3|https://www.uniprot.org/uniprot/Q8TCJ2|https://www.uniprot.org/uniprot/Q7TT24|https://www.uniprot.org/uniprot/Q3TDQ1|https://www.uniprot.org/uniprot/E2RG47 |
| T1750 | 1108-1113 | Protein | denotes | STT3A | https://www.uniprot.org/uniprot/Q8WUB4|https://www.uniprot.org/uniprot/Q8TE35|https://www.uniprot.org/uniprot/Q86XU9|https://www.uniprot.org/uniprot/Q5RCE2|https://www.uniprot.org/uniprot/Q2KJI2|https://www.uniprot.org/uniprot/P46978|https://www.uniprot.org/uniprot/P46977|https://www.uniprot.org/uniprot/F1PJP5|https://www.uniprot.org/uniprot/E9PNQ1|https://www.uniprot.org/uniprot/B4DJ24 |
LitCovid-sample-PD-IDO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T53 | 51-55 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | site |
| T54 | 571-576 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | sites |
| T55 | 671-676 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | sites |
| T56 | 868-873 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | sites |
| T57 | 1204-1209 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | sites |
| T58 | 1229-1234 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | sites |
| T59 | 1509-1513 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | site |
LitCovid-sample-PD-FMA
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T71 | 771-781 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T72 | 931-938 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T73 | 946-954 | Body_part | denotes | ribosome | http://purl.org/sig/ont/fma/fma66867 |
| T74 | 1420-1427 | Body_part | denotes | glycine | http://purl.org/sig/ont/fma/fma82753 |
| T75 | 1536-1548 | Body_part | denotes | glycopeptide | http://purl.org/sig/ont/fma/fma82784 |
LitCovid-sample-PD-GO-BP-0
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T52 | 138-146 | http://purl.obolibrary.org/obo/GO_0000224 | denotes | PNGase F |
| T53 | 188-197 | http://purl.obolibrary.org/obo/GO_0007586 | denotes | digestion |
| T54 | 885-900 | http://purl.obolibrary.org/obo/GO_0006412 | denotes | translationally |
| T55 | 1076-1091 | http://purl.obolibrary.org/obo/GO_0006412 | denotes | translationally |
| T56 | 1701-1714 | http://purl.obolibrary.org/obo/GO_0070085 | denotes | glycosylation |
LitCovid-sample-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T49 | 188-197 | http://purl.obolibrary.org/obo/GO_0007586 | denotes | digestion |
| T50 | 885-900 | http://purl.obolibrary.org/obo/GO_0006412 | denotes | translationally |
| T51 | 1076-1091 | http://purl.obolibrary.org/obo/GO_0006412 | denotes | translationally |
| T52 | 1701-1714 | http://purl.obolibrary.org/obo/GO_0070085 | denotes | glycosylation |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32841605-29677181-19659506 | 234-238 | 29677181 | denotes | 2018 |
| 32841605-19167329-19659507 | 1150-1154 | 19167329 | denotes | 2009 |
| 32841605-20510933-19659508 | 1254-1258 | 20510933 | denotes | 2010 |
| 32841605-22256963-19659509 | 1477-1481 | 22256963 | denotes | 2012 |