Index of BLAST dotplots vs. whole genome
BLAST dotplots for chr 10 only
| family number | General Location | Copies (direct / inverted) | Gene type | Other Chromos | Comments | Further | aligned bp | ungapped bp | ungapped min/max matches | ungapped bootstrap matches | synonymous bp | synonyous bootstrap matches | synonymous min/max matches |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | General (420,000) | 6 (4/2) |
hsr201 hypersensitivity-related protein | none | not all full length. 2 in one orientation, 4 in opposite. | first copy has no BLAST homology with rest. | 1800 | 450 | 0/1000 | 182/437 | 57 | 31/1000 | 42/57 |
| 2 | General (510,000) | 4 (4/0) |
O-deacetylbaccatin III-10-O-acetyltransferase | weak homology on 4 and 6 | widely separated copies, all tandem. 2 further copies at 1,416,000 and 1,429,000. | protein-coding sequences align well, but the annotated start sites of 2 of them are downstream of start sites indicated by homology region. | 1404 | 1065 | 14/1000 | 794/895 | 567 | 869/1000 | 529/544 |
| 3 | General (746,000) | 6 (5/1) |
LeOPT1-oligopeptide transporter | weak copies on several chromos; strong copy at 11,085,000 | 2 separate exons; 5 tandem, last one inverted | peptide transporter at 766,000 has a regions similar to family 3 copy just to its left, but this region isn't found in the other copies--another dup? | 1863 | 657 | 152/1000 | 282/550 | 90 | 345/1000 | 73/85 |
| 4 XXXXX |
778,609 | 4 | wall-associated protein kinase | chr 7, plus copies from family 9 and additional single copies at 226,000 and 8,489,000 | 2 separate exons, and only 2 copies here, in reverse orientation | ||||||||
| 5 XXXXX |
1,123,130 | 4 | O-methyltransferase ZRP4 | chr 9 | only 2 copies here: junk at 1,139,000 is unrelated | ||||||||
| 6 | General (1,607,000) | 17 (17/0) |
unknown | weak on chr 2 | all tandem! Another copy at 1,548,000 | plus some partial copies; some annotated as part of single large genes | 2232 | 256 | 0/1000 | 65/251 | 6 | -- | 3/6 |
| 7 | General (2,106,612) | 9 (8/1) |
hypothetical | none | several sub-groups; and tandem except last one (far away from others) is inverted | some duplications here seem recent--more sequence than just genes match with blast | 1584 | 609 | 535/1000 | 348/558 | 156 | 0/1000 | 129/152 |
| 8 | General (2,925,860) | 13 (9/4) |
proline-rich protein | none | first copy is at 2,882,000, last at 3,016,000 | 3 groups plus some others. 2 groups have inverted duplications. Total of 4 inverted relative to others | 1008 | 441 | 4/1000 | 291/436 | 147 | 0/1000 | 128/147 |
| 9 XXXXX |
3,044,670 | 4 | wall-associated protein kinase | see family 4 | part of large multiple inversion-duplication, not really a tandem array | ||||||||
| 10 XXXXX |
9,630,154 | 5 (3/2) |
integral membrane protein | weak copies on several chromos | 5 copies between 9,624,000 and 9,698,000 | 2 of the 5 are inverted. Looks like a tandem dup, an inverted dup, and a very old inverted dup | |||||||
| 11 | 9,960,184 | 6 (6/0) |
lipid transfer protein | chr 3, 4 (all weak). | family 23 is related to this family. Very nice closely spaced tandem array. | one copy is not well annotated as a gene | 429 | 213 | 56/1000 | 69/192 | 30 | 3/1000 | 25/30 |
| 12 XXXXX |
14,076,773 | 5 (3/2) |
CCR4-associated factor | none | first copy at 14,034,000. Part of large multiple inversion/duplication region | a tandem-duplicated inversion-duplication. Not too useful. | |||||||
| 13 ( 13a ) |
14,403,160 | 26 (22/4) |
speckle-type protein | one or two copies on almost every chromosome | first copy at 14,334,000; last at 14,526,000 | mostly tandem, with a couple of 1 gene inverted duplications. fam 13a has 2 trucated copies removed. | 1770 | 177 | 0/1000 | 45/174 | 6 | -- | 4/6 |
| 14 XXXXX |
15,026,061 | 6 | cytochrome P450 | copies on 2, 4, 7 | two exons; only 3 copies of the duplication | ||||||||
| 15 ( 15a ) |
15,712,713 | 9 (9/0) |
glycine rich protein | chr 6, probably an array | 6 main copies, but 3 others weakly related just past them (15,739,000 -15,751,000). Nice tandem array. fam15a_cds just has the 6 main copies. | Maybe related to family 16--weak homology at farthest copies | 879 | 408 | 156/1000 | 215/352 | 147 | 32/1000 | 110/134 |
| 16 | 15,844,166 | 9 (8/1) |
unknown? | none | Good array. | One inverted copy, weak homology | 768 | 555 | 168/1000 | 361/526 | 261 | 148/1000 | 213/252 |
| 17 ( 17a ) |
16,548,753 | 5 (4/1) |
disease resistance protein | another single copy at 19,769,000 | 2 exons, a bit confusing. Another partial copy just to left. | fam 17a does not have the isolated single copy | 4263 | 1551 | 0/1000 | 915/1338 | 606 | 40/1000 | 520/572 |
| 18 | 18,227,548 | 4 (4/0) |
epoxide hydrolase | small piece on chr 5 | 4 copies, nice tandem array | some homology in introns too | 987 | 896 | 999/1000 | 446/774 | 375 | 707/1000 | 300/350 |
| 19 | 19,036,776 | 10 (8/2) |
cytochrome P450 | chr 2, 6, 7, 8, plus family 14 | good array; 2 inverted copies | 2031 | 1128 | 0/1000 | 832/1128 | 459 | 0/1000 | 409/459 | |
| 20 ( 20a ) |
19,720,959 | 23 (21/3) |
glutathione s-transferase | chr 1, 3, 7, 9, 10 (10,930,000: 1 copy) | first copy at 19,711,000 is a pseudogene deleted at 3' half: use fam20a_cds, which lacks this sequence | 2 adjacent ones (plus one other) are inverted; all the rest in tandem. Also has interspersed TE duplication. | 825 | 642 | 0/1000 | 422/609 | 123 | 0/1000 | 110/122 |
| 21 | 20,189,115 | 11 (11/0) |
nucleoid DNA binding protein | chr 12 (good copy) | left-hand copy part of larger dup; nice array, interspersed with LTR elements | all tandem | 1395 | 990 | 0/1000 | 729/983 | 273 | 0/1000 | 252/271 |
| 22 XXXXX |
20,437,636 | 4 | chitinase | chr 3, 5, 6 | only 2 copies, 2 exons each | ||||||||
| 23 | 20,887,576 | 9 (9/0) |
lipid transfer protein | chr 2,3,4,6,8,11,12, plus 10 (family 11) | first copy at 20,882,000; last copy at 20,924,000 | first copy has only weak homology; possible other weak copies in this area (pseudogenes?) | 522 | 345 | 275/1000 | 208/335 | 135 | 19/1000 | 118/133 |
| 24 XXXXX |
21,062,328 | 4 (3/1) |
beta expansin EXPB6 | chr 2, 3, 4, 5, 8, 10 (1 copy at 20,692,000) | last copy is reverse orientation | ||||||||
| 25 | 21,220,736 | 6 (6/0) |
ethylene-forming enzyme | chr 11 | 4 main copies, plus small part of a fifth, with 2 other genes (ethylene-forming enzyme) sharing a bit at 21,242,000 and 21,248,000. I include the 2 other genes even though homology is weak. | all tandem | 1098 | 825 | 729/1000 | 465/754 | 288 | 455/1000 | 241/278 |
| 26 | 11,093,000 | 4 (4/0) |
Putative Glucan 1,3-beta-glucosidase precursor | chr 5, 8 | plus a bit of a 5th copy at very end of the main annotated gene | several large introns; copies 2-4 annotated as part of 1 gene | 1548 | 1410 | 771/1000 | 1005/1053 | 804 | 719/1000 | 683/700 |
| 27 | 12,390,000 | 4 (4/0) |
putative lipase | none | weak homology with significant intron variation | all tandem | 1293 | 870 | 995/1000 | 597/666 | 330 | 686/1000 | 306/310 |
| 28 | 14,236,000 | 8 (5/3) |
hypothetical protein | chr 4, 5, 6, 8, 9, 11 | 5 in one orientation, 3 in opposite | 1572 | 927 | 0/1000 | 364/872 | 225 | 0/1000 | 110/223 | |
| 29 XXXXX |
14,772,000 | 8 | hypothetical protein | chr 2, 10 (around 15,000,000) | Part of a large inverted duplication. first copy at 14,718,000; last copy at 14,778,000 | big mess; forget it for now | |||||||
| 30 | 20,757,000 | 5 (5/0) |
hypothetical protein | chr 5 | 5 good copies plus a bit of a 6th; one has very strong homology to chr 5 copy. Good array | Most of it part of one annotated protein. All tandem. | 852 | 438 | 969/1000 | 115/241 | 21 | -- | 15/18 |
| 31 | 21,181,000 | 4 (4/0) |
putative metalloproteinase | chr 2, 4, 6 | nice tandem array | weak homology, but close together all in tandem | 1209 | 684 | 1000/1000 | 429/513 | 213 | 461/1000 | 198/206 |