Hierarchical alignments

  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 two 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.
Valid last name is required.
    
Valid last name is required.
Select Download 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
Vvi1g1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0515 Cone9ag0528 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1000 . . . . . . . . Cmo04g01645 . . . Car04g01622 . Sed07g2016 . Cpe01g01394 Bhi07g01446 Tan04g0955 Cmetu04g0673 . . . . Cla05g02374 Cam05g2544 Cec05g2576 Cco05g2615 Clacu05g2543 Cmu05g2402 Cre05g2519 . . . . Lsi04g00341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi8g1077 Blo01g01217 . Bda01g00375 . . . . . . . . Cma07g00881 . Car07g00871 Sed10g1088 . . Bhi03g01495 Tan03g1149 Cmetu08g1342 . . . . Cla04g00946 Cam04g0986 Cec04g1111 Cco04g1168 Clacu04g1014 Cmu04g1001 Cre04g1056 Cone3ag0216 Cone10ag0196 . . . Csa06g02639 Chy08g00897 . . . . . . Bpe02g00740 Bma01g01972 . . . Cmo07g00914 . . . . . Cpe19g00443 . . . . . . . . . . . . . . . . . Cme08g01245
Vvi8g1078 . . Bda01g00374 . . Bpe03g01260 . Bma10g00066 . . . Cma07g00883 Car03g01073 Car07g00872 Sed14g0355 Cpe10g00253 . Bhi03g01496 Tan03g1148 Cmetu08g1792 . Hepe04g0990 . . Cla04g00945 Cam04g0985 Cec04g1108 Cco04g1167 Clacu04g1013 Cmu04g1000 Cre04g1055 Cone3ag0217 . Cone13ag1227 Cone19ag1213 Lsi01g01273 Csa06g02638 Chy08g00896 . Blo07g01369 . . Bda05g01197 . Bpe02g00739 . . . Cmo03g01186 Cmo07g00915 . . . . . Cpe19g00442 . . . . . . . . . . . . . . . . . Cme08g01247
Vvi8g1079 . . . . . . . . . . . . . . Sed01g3893 . . Bhi03g01497 Tan03g1147 Cmetu09g0005 . Hepe04g0989 . . . . . . . . . . . . . . . . . . . . . . . Bma01g01973 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi8g1080 . . . . . . . . Cmo06g00424 Cmo14g00245 . . . . . . Cpe08g01060 . . . . . . . . . . . . . . . . Cone13ag1228 . . . . Cme04g02453 . . . . . . . . Sed02g0586 . . . . . Car14g00232 . . Bhi11g02010 Tan08g1801 Cmetu04g2072 . Hepe05g0320 . . . . . . . . . Lsi03g01956 Csa03g03356 Chy04g01987 .
Vvi8g1081 . . . . . Bpe03g01261 . Bma10g00065 Cmo06g00423 . . . . . . . Cpe08g01061 . . . . . . . . . . . . . . . . Cone13ag1229 . . . . Cme04g02454 Blo07g01370 . . Bda05g01198 . . . . . . . . . . . . . Bhi11g02011 . . . . . . Cla10g01861 . . . . . . . Csa03g03355 . .
Vvi8g1082 . . Bda01g00373 . . . . . Cmo06g00422 . . . . . . . . . . . . . . . . . . . . . . Cone3ag0218 Cone10ag0197 . . . . . Cme04g02455 . . . . . Bpe02g00738 Bma01g01974 . . . . Cma06g00427 . Car06g00367 . . . Bhi11g02012 . . . . . . . . . . . . . . Csa03g03354 . .
   
First Previous Page 1 of 2365 Next

Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 29593819 29595717 - Bda002351.1 Bda01g00373 373
1 29596748 29604332 + Bda002352.1 Bda01g00374 374
1 29605310 29606923 + Bda002353.1 Bda01g00375 375
5 59985079 59988644 - Bda022367.1 Bda05g01197 1197
5 59989282 59990927 + Bda022368.1 Bda05g01198 1198
3 31905341 31910549 - XM_039025690.1 Bhi03g01495 1495
3 31911659 31917615 - XM_039025688.1 Bhi03g01496 1496
3 31912331 31917616 - XM_039025689.1 Bhi03g01497 1497
7 42634344 42638685 - XM_039036464.1 Bhi07g01446 1446
11 57251707 57254884 + XM_039048939.1 Bhi11g02010 2010
11 57255921 57260455 + XM_039047544.1 Bhi11g02011 2011
11 57260631 57262782 + XM_039047543.1 Bhi11g02012 2012
1 45923823 45934153 - BLOR01217 Blo01g01217 1217
7 33832648 33836231 - BLOR19301 Blo07g01369 1369
7 33837198 33839092 + BLOR19302 Blo07g01370 1370
1 73559772 73562170 - Bma002754.1 Bma01g01972 1972
1 73563184 73569163 - Bma002755.1 Bma01g01973 1973
1 73570263 73572188 + Bma002756.1 Bma01g01974 1974
10 611968 613754 - Bma003684.1 Bma10g00065 65
10 614420 617913 + Bma003685.1 Bma10g00066 66
2 5126981 5128879 - Bpe008575.1 Bpe02g00738 738
2 5129645 5135336 + Bpe008576.1 Bpe02g00739 739
2 5136314 5137924 + Bpe008577.1 Bpe02g00740 740
3 31198575 31202062 - Bpe013156.3 Bpe03g01260 1260
3 31202745 31204333 + Bpe013157.1 Bpe03g01261 1261
4 24002603 24007487 + CaPI482276_04g009850.1 Cam04g0985 985
4 24009168 24011459 + CaPI482276_04g009860.1 Cam04g0986 986
5 33256684 33262751 - CaPI482276_05g025440.1 Cam05g2544 2544
3 8704845 8720651 - Carg10450-RA Car03g01073 1073
4 9369166 9375464 - Carg01777-RA Car04g01622 1622
6 2013054 2020748 - Carg00941-RA Car06g00367 367
7 4676398 4678479 - Carg25574-RA Car07g00871 871
7 4679275 4684369 - Carg25572-RA Car07g00872 872
14 1092360 1093373 - Carg03723-RA Car14g00232 232
4 27118833 27123707 + CcPI632755_04g011670.1 Cco04g1167 1167
4 27125351 27129103 + CcPI632755_04g011680.1 Cco04g1168 1168
5 34363090 34364498 - CcPI632755_05g026150.1 Cco05g2615 2615
4 30641294 30644819 + CePI673135_04g011080.1 Cec04g1108 1108
4 30676983 30679104 + CePI673135_04g011110.1 Cec04g1111 1111
5 36697461 36702472 - CePI673135_05g025760.1 Cec05g2576 2576
4 25704524 25713615 + Chy4G087050.1 Chy04g01987 1987
8 16386530 16391796 + Chy8G155010.1 Chy08g00896 896
8 16393322 16395463 + Chy8G155020.1 Chy08g00897 897
4 24370683 24375551 + ClG42_04g0101300.10 Clacu04g1013 1013
4 24377220 24379344 + ClG42_04g0101400.10 Clacu04g1014 1014
5 33467520 33472398 - ClG42_05g0254300.10 Clacu05g2543 2543
4 24536194 24541855 + ClCG04G009610.2 Cla04g00945 945
4 24542727 24545038 + ClCG04G009620.1 Cla04g00946 946
5 35304103 35311649 - ClCG05G023480.1 Cla05g02374 2374
10 34516333 34525596 + ClCG10G019580.2 Cla10g01861 1861
6 1967253 1969193 - CmaCh06G004270.1 Cma06g00427 427
7 4160049 4162511 - CmaCh07G008810.1 Cma07g00881 881
7 4163757 4168908 - CmaCh07G008830.1 Cma07g00883 883
4 31112445 31114302 + MELO3C009416.2.1 Cme04g02453 2453
4 31115212 31119676 + MELO3C009415.2.1 Cme04g02454 2454
4 31119687 31123662 + MELO3C009414.2.1 Cme04g02455 2455
8 8874028 8876591 - MELO3C024501.2.1 Cme08g01245 1245
8 8893684 8897886 - MELO3C024499.2.1 Cme08g01247 1247
4 16180739 16183488 + PI0019770.1 Cmetu04g0673 673
4 4689824 4692875 - PI0016490.1 Cmetu04g2072 2072
8 17226731 17228750 + PI0006323.1 Cmetu08g1342 1342
8 17219755 17225230 + PI0004697.1 Cmetu08g1792 1792
9 2126883 2133071 + PI0024042.1 Cmetu09g0005 5
3 9263027 9265412 - CmoCh03G011860.1 Cmo03g01186 1186
4 8395312 8398989 - CmoCh04G016450.1 Cmo04g01645 1645
6 2031132 2033075 - CmoCh06G004220.1 Cmo06g00422 422
6 2033664 2037129 - CmoCh06G004230.1 Cmo06g00423 423
6 2037485 2038971 - CmoCh06G004240.1 Cmo06g00424 424
7 4378619 4381011 - CmoCh07G009140.1 Cmo07g00914 914
7 4381972 4387102 - CmoCh07G009150.1 Cmo07g00915 915
14 1129547 1130689 - CmoCh14G002450.1 Cmo14g00245 245
4 24547548 24552415 + CmPI595203_04g010000.1 Cmu04g1000 1000
4 24554085 24556209 + CmPI595203_04g010010.1 Cmu04g1001 1001
5 33205454 33210331 - CmPI595203_05g024020.1 Cmu05g2402 2402
3 1151084 1152907 - Conep03aG0022200.1 Cone3ag0216 216
3 1153272 1156039 - Conep03aG0022300.1 Cone3ag0217 217
3 1158158 1158961 + Conep03aG0022400.1 Cone3ag0218 218
6 2575701 2576858 + Conep06aG0052700.1 Cone6ag0515 515
9 2532276 2533357 + Conep09aG0053800.1 Cone9ag0528 528
10 976828 978245 - Conep10aG0020200.1 Cone10ag0196 196
10 981687 985123 + Conep10aG0020300.1 Cone10ag0197 197
13 9425744 9428200 - Conep13aG0126000.1 Cone13ag1227 1227
13 9428770 9429798 + Conep13aG0126100.1 Cone13ag1228 1228
13 9429987 9431979 + Conep13aG0126200.1 Cone13ag1229 1229
19 8451451 8454742 - Conep19aG0124800.1 Cone19ag1213 1213
1 8393917 8400612 - Cp4.1LG01g13140.1 Cpe01g01394 1394
8 8084489 8086095 + Cp4.1LG08g10560.1 Cpe08g01060 1060
8 8086383 8092920 + Cp4.1LG08g10540.1 Cpe08g01061 1061
10 1514548 1529836 + Cp4.1LG10g04350.1 Cpe10g00253 253
19 3934535 3939769 + Cp4.1LG19g03790.1 Cpe19g00442 442
19 3940537 3943265 + Cp4.1LG19g03820.1 Cpe19g00443 443
4 29206940 29211742 + CrPI670011_04g010550.1 Cre04g1055 1055
4 29213403 29215530 + CrPI670011_04g010560.1 Cre04g1056 1056
5 36553565 36558593 - CrPI670011_05g025190.1 Cre05g2519 2519
3 30364616 30366532 - CsaV3_3G036600.1 Csa03g03354 3354
3 30367141 30371205 - CsaV3_3G036610.1 Csa03g03355 3355
3 30371955 30373431 - CsaV3_3G036620.1 Csa03g03356 3356
6 23225946 23232224 + CsaV3_6G040240.1 Csa06g02638 2638
6 23233076 23236157 + CsaV3_6G040250.1 Csa06g02639 2639
4 64385269 64390732 + Hsped.04g09890.1 Hepe04g0989 989
4 64404897 64412483 + Hsped.04g09900.1 Hepe04g0990 990
5 3951619 3953424 - Hsped.05g03200.1 Hepe05g0320 320
1 11000527 11006580 - Lsi01G012730.1 Lsi01g01273 1273
3 30959868 30986757 + Lsi03G019560.1 Lsi03g01956 1956
4 3414952 3420430 - Lsi04G003410.1 Lsi04g00341 341
1 68180643 68185797 + Sed0017409.1 Sed01g3893 3893
2 43527057 43537457 + Sed0015840.1 Sed02g0586 586
7 35096567 35103467 - Sed0026487.4 Sed07g2016 2016
10 11322782 11328895 + Sed0010767.1 Sed10g1088 1088
14 3636574 3644618 - Sed0001057.1 Sed14g0355 355
3 67698785 67703088 + Tan0016853.1 Tan03g1147 1147
3 67755471 67762896 + Tan0006235.1 Tan03g1148 1148
3 67764149 67766338 + Tan0018550.1 Tan03g1149 1149
4 8420975 8425269 - Tan0012015.2 Tan04g0955 955
8 69986681 69988808 + Tan0016810.1 Tan08g1801 1801
1 10730 27033 + Vvi1g1 Vvi1g1 1
1 220861 222178 + Vvi1g10 Vvi1g10 10
1 997177 1000812 - Vvi1g100 Vvi1g100 100
1 15701473 15704472 + Vvi1g1000 Vvi1g1000 1000
8 18265207 18269207 - Vvi8g1077 Vvi8g1077 1077
8 18270756 18280508 - Vvi8g1078 Vvi8g1078 1078
8 18284335 18284878 - Vvi8g1079 Vvi8g1079 1079
8 18292878 18294427 + Vvi8g1080 Vvi8g1080 1080
8 18294778 18298975 + Vvi8g1081 Vvi8g1081 1081
8 18300063 18301983 + Vvi8g1082 Vvi8g1082 1082
       

DecoBrowse