Table 2.
Truncated PDB chain/SCOP domain matches with a human Swissprot alternative splice variant and acceptable truncation points based on CHASA-diff analysis
| Swissprot splice variant | PDB chain | PDB |
Sw |
Percentage ID | len PDB | len Sw | Potential breakpoints | Chasa | TrDom/ Swlen | SCOP domain | SCOP domain |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Beg | End | beg | end | beg | end | len | |||||||||
| O15392-3|BIRC5_HUMAN | 1xoxA | 1 | 76 | 1 | 76 | 96 | 117 | 137 | 107,117,87,7 | + | 0.51 | d1xoxa1 | 1 | 70 | 111 |
| O60869-2|EDF1_HUMAN | 1x57A | 8 | 66 | 71 | 129 | 100 | 91 | 139 | 75,80,85,10,1 | + | 0.42 | d1x57a1 | 1 | 59 | 78 |
| P06733-2|ENOA_HUMAN | 1pdyA | 94 | 433 | 1 | 338 | 75 | 434 | 341 | 433,233,133,33,13 | – | 0.12 | d1pdya2 | 93 | 137 | 139 |
| P37231-2|PPARG_HUMAN | 1hraA | 8 | 79 | 109 | 179 | 63 | 80 | 475 | 80,30,5 | + | 0.15 | d1hraa_ | 8 | 79 | 80 |
| P51991-2|ROA3_HUMAN | 1x4bA | 22 | 109 | 7 | 94 | 76 | 116 | 356 | 110,100,10 | + | 0.25 | d1x4ba1 | 15 | 102 | 103 |
| P55957-4|BID_HUMAN | 2bidA | 99 | 197 | 1 | 99 | 100 | 197 | 99 | 197,87,47,17,7 | + | 1.00 | d2bida_ | 99 | 197 | 197 |
| P62993-2|GRB2_HUMAN | 1gbrA | 10 | 68 | 1 | 59 | 100 | 74 | 176 | 69,74,19 | + | 0.34 | d1gbra_ | 10 | 68 | 74 |
| P62993-2|GRB2_HUMAN | 1fhsA | 50 | 112 | 60 | 122 | 100 | 112 | 176 | 102,112,62,12 | + | 0.36 | d1fhsa_ | 50 | 112 | 112 |
| Q01167-2|FOXK2_HUMAN | 1d5vA | 4 | 84 | 258 | 338 | 61 | 94 | 614 | 94,89,84,59,4 | + | 0.13 | d1d5va_ | 4 | 84 | 94 |
| Q07820-2|MCL1_HUMAN | 1wsxA | 6 | 65 | 171 | 230 | 85 | 162 | 271 | 152,162,52,12 | + | 0.22 | d1wsxa_ | 6 | 65 | 162 |
| Q9NR12-2|PDLI7_HUMAN | 1wf7A | 14 | 100 | 11 | 91 | 62 | 103 | 423 | 93,98,103,18 | + | 0.21 | d1wf7a_ | 14 | 100 | 103 |
| Q9NR12-3|PDLI7_HUMAN | 1wf7A | 14 | 100 | 11 | 91 | 62 | 103 | 153 | 93,98,103,18 | + | 0.57 | d1wf7a_ | 14 | 100 | 103 |
The table contains the following columns: Swissprot splice variant, accession number and identifier of splice variant; PDB chain, name and chain of matched PDB entry; PDB beg, PDB end, Sw beg, Sw end: beginning and end of a Blastp match between the sequences of the PDB chain and splice variant, respectively; Percentage ID, proportion of matching residues; len PDB, length of PDB chain in residues; len Sw, length of Swissprot splice variant; potential breakpoints, positions in the PDB chain where a truncation would be permitted by CHASA-diff, based on the exposed hydrophobicity value differences from an ideal value for an intact globular domain of that size (see text for more details), bold residue number is the closest to the actual truncation in the splice variant in question; Chasa, + if there is an acceptable minimum in the vicinity of the breakpoint (within 13 residues in the sequence) as determined by Chasa-diff, – otherwise; TrDom/Swlen, truncated domain length divided by the total length of Swissprot; SCOP domain, matching SCOP domain identifier; SCOP domain beg, end and len, beginning, end of match and length of SCOP domain, respectively.