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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Valid last name is required.
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
Vvi5g409 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0807 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g410 . . . Bda08g00387 . . . Bma05g00940 Cmo08g01151 . . . . . . . . . . . . . . . Cla06g00534 Cam06g0576 Cec06g0573 Cco06g0581 Clacu06g0563 Cmu06g0557 Cre06g1325 Cone14ag0808 . . . . . Chy11g01441 . . . . . Bpe05g00751 . . . . . . Cma08g01180 . Car08g01056 . . Cpe17g00116 Bhi12g01783 . . . . . . . . . . . . . Lsi09g01370 . . Cme11g01946
Vvi5g411 Blo01g00144 . . . . . . . . . Cma06g01443 . Car06g01246 . Sed02g1282 Cpe08g00231 . Bhi01g00874 Tan10g0908 Cmetu06g1351 . . . Lcy11g1485 . . . . . . . Cone14ag0809 . Cone7ag0204 . Lsi05g01469 . . Cme06g00660 . Blo07g00201 Bda11g00554 . . Bpe13g00629 . Bma06g01533 . Cmo06g01446 . . . . . . . . . . . . . . Cla05g00589 Cam05g0648 Cec05g0656 Cco05g0652 Clacu05g0641 Cmu05g0610 Cre05g0678 . Csa03g01385 Chy06g00628 .
Vvi5g412 . . Bda03g01264 . . . Bma04g01174 . . . . Cma14g01668 Car06g01245 Car14g01502 Sed02g1281 Cpe08g00232 Cpe03g01408 Bhi01g00873 Tan10g0907 Cmetu06g1518 . . . . . . . . . . . . . Cone7ag0205 Cone4ag0196 Lsi05g01467 . . Cme06g00659 . . . Bda13g00143 . . . . . Cmo06g01445 Cmo14g01714 . . . . . . . . . . . . . . . . . . . . . Csa03g01384 Chy06g00627 .
Vvi5g413 . . . . . . . . Cmo08g01150 Cmo17g00267 . . . . . . . . . . . . . . Cla06g00535 Cam06g0577 Cec06g0574 Cco06g0582 Clacu06g0564 Cmu06g0558 Cre06g1326 Cone14ag0810 . Cone7ag0206 . . . Chy11g01440 . . . . . . . . . . . . Cma08g01179 Cma17g00280 Car08g01055 Car17g00255 Cpe12g00233 Cpe17g00117 Bhi12g01785 . . Lac12g2354 . . Lcy13g0224 . . . . . . . Lsi09g01367 . . Cme11g01945
Vvi5g414 . . . . . . . . . . . Cma14g01669 . Car14g01504 Sed02g1279 . Cpe03g01409 Bhi01g00871 Tan10g0905 Cmetu06g2408 . Hepe05g1511 . Lcy11g1487 . . . . . . . . . Cone7ag0208 Cone4ag0197 Lsi05g01466 . . Cme06g00658 . Blo07g00202 Bda11g00555 . . Bpe13g00628 Bma02g00703 Bma06g01534 . . Cmo14g01716 . . . . . . . . . . . . . Cla05g00588 Cam05g0646 Cec05g0655 Cco05g0650 Clacu05g0640 Cmu05g0609 Cre05g0677 . Csa03g01383 Chy06g00626 .
Vvi5g415 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g416 . . Bda03g01295 . . . . . Cmo08g01149 Cmo17g00266 Cma06g01441 Cma14g01672 Car06g01243 Car14g01506 . Cpe08g00234 Cpe03g01411 Bhi01g00869 Tan10g0903 . Lac12g2339 . . Lcy11g1490 Cla06g00536 Cam06g0578 Cec06g0575 Cco06g0583 Clacu06g0565 Cmu06g0559 Cre06g1327 Cone14ag0811 Cone15ag0810 . . Lsi05g01464 . Chy11g01439 Cme06g00654 . . . . . . . . . Cmo06g01443 Cmo14g01718 Cma08g01178 Cma17g00279 Car08g01054 Car17g00254 Cpe12g00232 Cpe17g00118 Bhi12g01786 . . . . . . Cla05g00586 Cam05g0644 Cec05g0653 Cco05g0648 Clacu05g0638 Cmu05g0606 Cre05g0675 Lsi09g01366 Csa03g01380 Chy06g00622 Cme11g01944
Vvi5g417 . . . . Bpe04g01188 . Bma04g01178 . Cmo08g01148 Cmo17g00265 . . . . . . . . . . . . . . Cla06g00537 Cam06g0579 Cec06g0576 Cco06g0584 Clacu06g0566 Cmu06g0560 Cre06g1328 Cone14ag0812 Cone15ag0811 . . . . Chy11g01438 . . . . . . . . . . . . Cma08g01177 Cma17g00278 Car08g01053 Car17g00253 Cpe12g00231 Cpe17g00119 Bhi12g01733 . . . . . . . . . . . . . Lsi09g01365 . . Cme11g01943
Vvi5g418 . . Bda03g01296 . . . . . . . . . . . Sed12g0894 . . Bhi01g00867 Tan10g0901 Cmetu06g0369 . . . Lcy11g1493 . . . . . . . Cone14ag0813 . . . Lsi05g01463 . . Cme06g00653 . . . . . . Bma02g00701 . . . . . . . . . . . . . . . . . Cla05g00585 Cam05g0643 Cec05g0652 Cco05g0647 Clacu05g0637 Cmu05g0605 Cre05g0674 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 18975793 18978868 + Bda017396.1 Bda03g01264 1264
3 27907997 27910539 + Bda017513.2 Bda03g01295 1295
3 27951382 27953477 - Bda017516.1 Bda03g01296 1296
8 4027802 4030245 - Bda024833.1 Bda08g00387 387
11 5769810 5770742 - Bda005291.1 Bda11g00554 554
11 5771333 5773915 - Bda005292.1 Bda11g00555 555
13 1910417 1913203 + Bda001003.1 Bda13g00143 143
1 16410599 16425665 + XM_039023861.1 Bhi01g00867 867
1 16427603 16434198 - XM_039040503.1 Bhi01g00869 869
1 16458956 16462588 + XM_039038519.1 Bhi01g00871 871
1 16478406 16483347 + XM_039049222.1 Bhi01g00873 873
1 16483750 16485833 + XM_039049239.1 Bhi01g00874 874
12 55946913 55953407 - XM_039018654.1 Bhi12g01733 1733
12 57215836 57220687 - XM_039020411.1 Bhi12g01783 1783
12 57252284 57262252 + XM_039018845.1 Bhi12g01785 1785
12 57306667 57313395 + XM_039018779.1 Bhi12g01786 1786
1 1969714 1989499 - BLOR00144 Blo01g00144 144
7 2489042 2490043 - BLOR18133 Blo07g00201 201
7 2515636 2517040 - BLOR18134 Blo07g00202 202
2 28083453 28085552 + Bma015355.1 Bma02g00701 701
2 28099978 28102272 + Bma015356.1 Bma02g00703 703
4 30570719 30573850 - Bma031133 Bma04g01174 1174
4 31304470 31307328 - Bma019920.3 Bma04g01178 1178
5 47431479 47433935 - Bma022076.1 Bma05g00940 940
6 51693104 51693962 - Bma024647.1 Bma06g01533 1533
6 51694134 51696715 - Bma024648.1 Bma06g01534 1534
4 13954342 13958012 - Bpe015886.2 Bpe04g01188 1188
5 20916167 20918624 - Bpe018165.1 Bpe05g00751 751
13 13230385 13232967 + Bpe010327.1 Bpe13g00628 628
13 13233418 13234320 + Bpe010328.1 Bpe13g00629 629
5 5584022 5587732 + CaPI482276_05g006430.1 Cam05g0643 643
5 5593187 5599906 - CaPI482276_05g006440.1 Cam05g0644 644
5 5610943 5614002 + CaPI482276_05g006460.1 Cam05g0646 646
5 5618082 5624406 + CaPI482276_05g006480.1 Cam05g0648 648
6 7799021 7803624 - CaPI482276_06g005760.1 Cam06g0576 576
6 7812135 7822112 + CaPI482276_06g005770.1 Cam06g0577 577
6 7824861 7831207 + CaPI482276_06g005780.1 Cam06g0578 578
6 7831226 7836163 - CaPI482276_06g005790.1 Cam06g0579 579
6 8974386 8979537 - Carg17392-RA Car06g01243 1243
6 8983312 8987625 + Carg17390-RA Car06g01245 1245
6 8987708 8988365 + Carg17389-RA Car06g01246 1246
8 7204705 7209357 + Carg15932-RA Car08g01053 1053
8 7209942 7213834 - Carg15933-RA Car08g01054 1054
8 7214802 7223461 - Carg15934-RA Car08g01055 1055
8 7224105 7227501 + Carg15935-RA Car08g01056 1056
14 12423618 12429028 - Carg23831-RA Car14g01502 1502
14 12430386 12434102 - Carg23829-RA Car14g01504 1504
14 12439650 12445705 + Carg23827-RA Car14g01506 1506
17 1566217 1571462 + Carg05459-RA Car17g00253 253
17 1572244 1576545 - Carg05460-RA Car17g00254 254
17 1578269 1589964 - Carg05461-RA Car17g00255 255
5 5280667 5284373 + CcPI632755_05g006470.1 Cco05g0647 647
5 5288273 5296185 - CcPI632755_05g006480.1 Cco05g0648 648
5 5307395 5310451 + CcPI632755_05g006500.1 Cco05g0650 650
5 5314586 5320930 + CcPI632755_05g006520.1 Cco05g0652 652
6 6239012 6248189 - CcPI632755_06g005810.1 Cco06g0581 581
6 6248465 6258380 + CcPI632755_06g005820.1 Cco06g0582 582
6 6261116 6265878 + CcPI632755_06g005830.1 Cco06g0583 583
6 6267429 6272655 - CcPI632755_06g005840.1 Cco06g0584 584
5 5291220 5294933 + CePI673135_05g006520.1 Cec05g0652 652
5 5300107 5306837 - CePI673135_05g006530.1 Cec05g0653 653
5 5318166 5321222 + CePI673135_05g006550.1 Cec05g0655 655
5 5325346 5331693 + CePI673135_05g006560.1 Cec05g0656 656
6 6338319 6347934 - CePI673135_06g005730.1 Cec06g0573 573
6 6348219 6358056 + CePI673135_06g005740.1 Cec06g0574 574
6 6360555 6365656 + CePI673135_06g005750.1 Cec06g0575 575
6 6367183 6372260 - CePI673135_06g005760.1 Cec06g0576 576
6 4239634 4244929 - Chy6G111500.1 Chy06g00622 622
6 4257504 4260332 + Chy6G111540.1 Chy06g00626 626
6 4262822 4266616 + Chy6G111550.1 Chy06g00627 627
6 4267545 4269138 + Chy6G111560.1 Chy06g00628 628
11 21183907 21188596 + Chy11G200180.1 Chy11g01438 1438
11 21190270 21194546 - Chy11G200190.1 Chy11g01439 1439
11 21196592 21212976 - Chy11G200200.1 Chy11g01440 1440
11 21222265 21225437 + Chy11G200210.1 Chy11g01441 1441
5 5301880 5305588 + ClG42_05g0063700.10 Clacu05g0637 637
5 5318447 5325129 - ClG42_05g0063800.10 Clacu05g0638 638
5 5336167 5339225 + ClG42_05g0064000.10 Clacu05g0640 640
5 5343288 5349606 + ClG42_05g0064100.10 Clacu05g0641 641
6 6349154 6358183 - ClG42_06g0056300.10 Clacu06g0563 563
6 6358464 6367985 + ClG42_06g0056400.10 Clacu06g0564 564
6 6370658 6377000 + ClG42_06g0056500.10 Clacu06g0565 565
6 6377019 6381855 - ClG42_06g0056600.10 Clacu06g0566 566
5 5362678 5366861 + ClCG05G005480.1 Cla05g00585 585
5 5379441 5386775 - ClCG05G005490.2 Cla05g00586 586
5 5397537 5400927 + ClCG05G005510.1 Cla05g00588 588
5 5404017 5411511 + ClCG05G005520.2 Cla05g00589 589
6 6417489 6424790 - ClCG06G005690.2 Cla06g00534 534
6 6425532 6432550 + ClCG06G005700.2 Cla06g00535 535
6 6437417 6447741 + ClCG06G005705.1 Cla06g00536 536
6 6447769 6456011 - ClCG06G005720.1 Cla06g00537 537
6 9246578 9251223 - CmaCh06G014410.1 Cma06g01441 1441
6 9255273 9261410 + CmaCh06G014430.1 Cma06g01443 1443
8 7244497 7249804 + CmaCh08G011770.1 Cma08g01177 1177
8 7250339 7254038 - CmaCh08G011780.1 Cma08g01178 1178
8 7255077 7263869 - CmaCh08G011790.1 Cma08g01179 1179
8 7264835 7268794 + CmaCh08G011800.1 Cma08g01180 1180
14 12467455 12471698 - CmaCh14G016680.1 Cma14g01668 1668
14 12472559 12475771 - CmaCh14G016690.1 Cma14g01669 1669
14 12481632 12487909 + CmaCh14G016720.1 Cma14g01672 1672
17 1464912 1470200 + CmaCh17G002780.1 Cma17g00278 278
17 1470388 1474553 - CmaCh17G002790.1 Cma17g00279 279
17 1475613 1487371 - CmaCh17G002800.1 Cma17g00280 280
6 4218587 4222696 + MELO3C006572.2.1 Cme06g00653 653
6 4223264 4234559 - MELO3C006573.2.1 Cme06g00654 654
6 4246467 4249854 + MELO3C006576.2.1 Cme06g00658 658
6 4252129 4257149 + MELO3C006577.2.1 Cme06g00659 659
6 4257540 4259561 + MELO3C006578.2.1 Cme06g00660 660
11 27494941 27501078 + MELO3C021394.2.1 Cme11g01943 1943
11 27501679 27506889 - MELO3C021393.2.1 Cme11g01944 1944
11 27509635 27522340 - MELO3C021392.2.1 Cme11g01945 1945
11 27522685 27527129 + MELO3C021391.2.1 Cme11g01946 1946
6 4456143 4459610 + PI0001852.1 Cmetu06g0369 369
6 4491097 4493144 + PI0010454.1 Cmetu06g1351 1351
6 4485351 4490885 + PI0003288.2 Cmetu06g1518 1518
6 4479824 4483312 + PI0010381.1 Cmetu06g2408 2408
6 10449608 10454295 - CmoCh06G014430.1 Cmo06g01443 1443
6 10458165 10462176 + CmoCh06G014450.1 Cmo06g01445 1445
6 10462404 10463956 + CmoCh06G014460.1 Cmo06g01446 1446
8 7341665 7346912 + CmoCh08G011480.1 Cmo08g01148 1148
8 7347603 7351141 - CmoCh08G011490.1 Cmo08g01149 1149
8 7351850 7360739 - CmoCh08G011500.1 Cmo08g01150 1150
8 7361114 7365214 + CmoCh08G011510.1 Cmo08g01151 1151
14 13423553 13427664 - CmoCh14G017140.1 Cmo14g01714 1714
14 13428927 13431957 - CmoCh14G017160.1 Cmo14g01716 1716
14 13438487 13451818 + CmoCh14G017180.1 Cmo14g01718 1718
17 1582906 1590155 + CmoCh17G002650.1 Cmo17g00265 265
17 1592235 1596364 - CmoCh17G002660.1 Cmo17g00266 266
17 1598551 1610200 - CmoCh17G002670.1 Cmo17g00267 267
5 5145413 5149121 + CmPI595203_05g006050.1 Cmu05g0605 605
5 5161957 5168636 - CmPI595203_05g006060.1 Cmu05g0606 606
5 5179698 5182756 + CmPI595203_05g006090.1 Cmu05g0609 609
5 5186817 5193135 + CmPI595203_05g006100.1 Cmu05g0610 610
6 6156438 6165491 - CmPI595203_06g005570.1 Cmu06g0557 557
6 6165772 6175286 + CmPI595203_06g005580.1 Cmu06g0558 558
6 6177957 6184275 + CmPI595203_06g005590.1 Cmu06g0559 559
6 6184294 6189139 - CmPI595203_06g005600.1 Cmu06g0560 560
4 915468 917904 - Conep04aG0020500.1 Cone4ag0196 196
4 918943 921507 - Conep04aG0020600.1 Cone4ag0197 197
7 863223 864348 - Conep07aG0020900.1 Cone7ag0204 204
7 867336 875857 - Conep07aG0021000.1 Cone7ag0205 205
7 876902 884023 + Conep07aG0021100.1 Cone7ag0206 206
7 889116 890925 - Conep07aG0021300.1 Cone7ag0208 208
14 4800948 4803226 - Conep14aG0082400.1 Cone14ag0807 807
14 4804917 4808232 - Conep14aG0082500.1 Cone14ag0808 808
14 4814471 4816181 + Conep14aG0082600.1 Cone14ag0809 809
14 4820200 4825480 + Conep14aG0082700.1 Cone14ag0810 810
14 4826245 4830691 + Conep14aG0082800.1 Cone14ag0811 811
14 4836392 4842408 - Conep14aG0082900.1 Cone14ag0812 812
14 4849567 4852209 - Conep14aG0083000.1 Cone14ag0813 813
15 5027891 5032529 + Conep15aG0082500.1 Cone15ag0810 810
15 5034487 5040161 - Conep15aG0082600.1 Cone15ag0811 811
3 11343739 11348044 - Cp4.1LG03g11010.1 Cpe03g01408 1408
3 11349110 11352766 - Cp4.1LG03g10950.1 Cpe03g01409 1409
3 11359046 11364974 + Cp4.1LG03g11080.1 Cpe03g01411 1411
8 1526872 1528017 - Cp4.1LG08g04400.1 Cpe08g00231 231
8 1528902 1533341 - Cp4.1LG08g04420.1 Cpe08g00232 232
8 1537932 1541951 + Cp4.1LG08g04510.1 Cpe08g00234 234
12 1545585 1551112 + Cp4.1LG12g02290.1 Cpe12g00231 231
12 1551822 1555961 - Cp4.1LG12g02330.1 Cpe12g00232 232
12 1558361 1569329 - Cp4.1LG12g02340.1 Cpe12g00233 233
17 718203 721963 - Cp4.1LG17g01250.1 Cpe17g00116 116
17 722901 731380 + Cp4.1LG17g01170.1 Cpe17g00117 117
17 732694 736536 + Cp4.1LG17g01180.1 Cpe17g00118 118
17 737050 743657 - Cp4.1LG17g01270.1 Cpe17g00119 119
5 5939094 5942825 + CrPI670011_05g006740.1 Cre05g0674 674
5 5947645 5954316 - CrPI670011_05g006750.1 Cre05g0675 675
5 5965491 5968552 + CrPI670011_05g006770.1 Cre05g0677 677
5 5972542 5978857 + CrPI670011_05g006780.1 Cre05g0678 678
6 7201762 7206474 - CrPI670011_06g013250.1 Cre06g1325 1325
6 7211652 7221845 + CrPI670011_06g013260.1 Cre06g1326 1326
6 7224499 7229622 + CrPI670011_06g013270.1 Cre06g1327 1327
6 7231211 7236418 - CrPI670011_06g013280.1 Cre06g1328 1328
3 10364032 10370322 - CsaV3_3G013800.1 Csa03g01380 1380
3 10380685 10384418 + CsaV3_3G013830.1 Csa03g01383 1383
3 10385382 10390870 + CsaV3_3G013840.1 Csa03g01384 1384
3 10391021 10393339 + CsaV3_3G013850.1 Csa03g01385 1385
5 64600343 64603869 - Hsped.05g15110.1 Hepe05g1511 1511
12 40559412 40567078 - Lag0016711.1 Lac12g2339 2339
12 40687992 40698090 - Lag0016726.1 Lac12g2354 2354
11 38777714 38779818 - Maker00032151 Lcy11g1485 1485
11 38790507 38794267 - Maker00031390 Lcy11g1487 1487
11 38809364 38809786 + Maker00031815 Lcy11g1490 1490
11 38823277 38830482 - Maker00031345 Lcy11g1493 1493
13 2299752 2309922 + Maker00024010 Lcy13g0224 224
5 22488913 22492927 + Lsi05G014630.1 Lsi05g01463 1463
5 22494107 22507011 - Lsi05G014640.1 Lsi05g01464 1464
5 22518848 22522041 + Lsi05G014660.1 Lsi05g01466 1466
5 22525349 22530493 + Lsi05G014670.1 Lsi05g01467 1467
5 22531273 22533045 + Lsi05G014680.1 Lsi05g01469 1469
9 21696552 21701395 + Lsi09G013650.1 Lsi09g01365 1365
9 21700801 21709729 - Lsi09G013660.1 Lsi09g01366 1366
9 21711815 21716779 - Lsi09G013670.1 Lsi09g01367 1367
9 21724013 21730693 + Lsi09G013700.1 Lsi09g01370 1370
2 49479236 49482779 + Sed0009038.1 Sed02g1279 1279
2 49484132 49490549 + Sed0000546.2 Sed02g1281 1281
2 49491024 49492761 + Sed0023151.1 Sed02g1282 1282
12 5566371 5571499 + Sed0024119.2 Sed12g0894 894
10 7546023 7550525 + Tan0008261.1 Tan10g0901 901
10 7551596 7558340 - Tan0017123.2 Tan10g0903 903
10 7577875 7581508 + Tan0018777.1 Tan10g0905 905
10 7588503 7593545 + Tan0001352.2 Tan10g0907 907
10 7594074 7595297 + Tan0014885.1 Tan10g0908 908
5 4117625 4127404 - Vvi5g409 Vvi5g409 409
5 4127405 4132500 - Vvi5g410 Vvi5g410 410
5 4133107 4134158 - Vvi5g411 Vvi5g411 411
5 4134798 4139324 - Vvi5g412 Vvi5g412 412
5 4144868 4176378 + Vvi5g413 Vvi5g413 413
5 4177157 4180017 - Vvi5g414 Vvi5g414 414
5 4183224 4186559 - Vvi5g415 Vvi5g415 415
5 4194128 4204982 + Vvi5g416 Vvi5g416 416
5 4205508 4215917 - Vvi5g417 Vvi5g417 417
5 4221452 4226424 - Vvi5g418 Vvi5g418 418
       

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