Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform

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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi19g1154 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00921 . Bma03g00493 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1155 Blo04g00460 . . . . . . . . . . . . . Sed04g3556 . . Bhi05g01991 Tan02g0023 Cmetu01g1284 . Hepe02g0012 . . . . . . . . . . . . . . Csa07g01213 . . . . . . Bpe15g00922 . Bma03g00492 . . . . . . . . Cpe15g00905 . . . . . . . . . . . . . . . . . Chy01g00850 Cme01g01500
Vvi19g1156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1159 Blo04g00459 Blo13g00603 . . . . . . . . . . . . Sed06g1122 Cpe04g00867 . Bhi05g01990 Tan02g0022 Cmetu01g2136 . Hepe02g0011 . . . . . . . . . . . . . . Csa07g01214 . . . . . . Bpe15g00923 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g01499
Vvi19g1160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g00491 . . . . . . . . Cpe15g00906 . . . . . . . . . . . . . . . . . Chy01g00849 .
Vvi19g1163 . . . . Bpe07g00474 . . . . . . . . . . . . Bhi05g01989 . . Lac12g0036 Hepe02g0010 . . . . . . . . . . . . . . Csa07g01215 . . . . . . . . . Bma12g00577 . . . . . . . Cpe15g00907 . . . . . . . . . . . . . . . . . Chy01g00848 Cme01g01498
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 61316837 61321632 - XM_039033143.1 Bhi05g01989 1989
5 61322128 61325989 - XM_039033142.1 Bhi05g01990 1990
5 61331578 61338170 + XM_039031648.1 Bhi05g01991 1991
4 3819238 3823943 - BLOR13371 Blo04g00459 459
4 3826943 3833278 + BLOR13372 Blo04g00460 460
13 28439667 28440788 + BLOR19655 Blo13g00603 603
3 3863205 3864436 - Bma016773.1 Bma03g00491 491
3 3870749 3872892 + Bma016774.1 Bma03g00492 492
3 3874671 3875564 - Bma016775.1 Bma03g00493 493
12 25021996 25022922 - Bma007738.1 Bma12g00577 577
7 8034718 8035629 + Bpe026059 Bpe07g00474 474
15 18998490 18999369 + Bpe024592 Bpe15g00921 921
15 19000299 19007296 - Bpe001843.1 Bpe15g00922 922
15 19009331 19010554 + Bpe001844.1 Bpe15g00923 923
1 7433808 7438751 - Chy1G008480.1 Chy01g00848 848
1 7447984 7450605 - Chy1G008490.1 Chy01g00849 849
1 7454073 7459412 + Chy1G008500.1 Chy01g00850 850
1 19706343 19710464 - MELO3C012594.2.1 Cme01g01498 1498
1 19719544 19722183 - MELO3C012595.2.1 Cme01g01499 1499
1 19726006 19730596 + MELO3C012596.2.1 Cme01g01500 1500
1 7169073 7174364 + PI0011864.1 Cmetu01g1284 1284
1 7162586 7166172 - PI0026638.1 Cmetu01g2136 2136
4 7958308 7959764 + Cp4.1LG04g02260.1 Cpe04g00867 867
15 8690452 8696381 - Cp4.1LG15g09150.1 Cpe15g00905 905
15 8697039 8698698 + Cp4.1LG15g09060.1 Cpe15g00906 906
15 8701164 8702418 + Cp4.1LG15g09070.1 Cpe15g00907 907
7 11916314 11922233 - CsaV3_7G023020.1 Csa07g01213 1213
7 11924273 11928348 + CsaV3_7G023030.1 Csa07g01214 1214
7 11934271 11937448 + CsaV3_7G023040.1 Csa07g01215 1215
2 273748 275470 - Hsped.02g00100.1 Hepe02g0010 10
2 276517 277885 - Hsped.02g00110.1 Hepe02g0011 11
2 280260 286213 + Hsped.02g00120.1 Hepe02g0012 12
12 500216 502357 + Lag0014408.1 Lac12g0036 36
4 44941154 44949006 - Sed0008261.1 Sed04g3556 3556
6 31962100 31964578 + Sed0027194.1 Sed06g1122 1122
2 598251 600081 - Tan0018454.1 Tan02g0022 22
2 602421 608064 + Tan0014015.1 Tan02g0023 23
19 23132271 23133626 + Vvi19g1154 Vvi19g1154 1154
19 23135392 23145621 - Vvi19g1155 Vvi19g1155 1155
19 23172290 23185359 - Vvi19g1156 Vvi19g1156 1156
19 23186036 23190813 + Vvi19g1157 Vvi19g1157 1157
19 23190823 23190979 - Vvi19g1158 Vvi19g1158 1158
19 23194271 23195684 + Vvi19g1159 Vvi19g1159 1159
19 23206319 23207782 + Vvi19g1160 Vvi19g1160 1160
19 23215253 23216894 + Vvi19g1161 Vvi19g1161 1161
19 23237783 23238509 + Vvi19g1162 Vvi19g1162 1162
19 23265198 23266600 + Vvi19g1163 Vvi19g1163 1163
       

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