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AGRP

Asteraceae Genomic Research Platform

Gene Search

Example:
Example:

Hierarchical alignments with the Vitis vinifera genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Vitis vinifera as a reference, and by comparing homologous gene locus maps and Ks values between Vitis vinifera and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 219×23,647 macro-matrices.
Select Vivi_1 Arla_1 Armi_1 Sain_1 Ceso_1 Cati_1 Ccar_1 Cien_1 Cich_1 Lssa_1 Laca_1 Tako_1 Tamo_1 Pslu_1 Lomi_1 Lomi_2 Enbr_1 Ecan_1 Soca_1 Glco_1 Artr_1 Aary_1 Aary_2 Aann_1 Chma_1 Chmo_1 Chmo_2 Chmo_3 Chla_1 Chna_1 Cind_1 Pdy_1 Cobi_1 Hean_1 Bial_1 Bial_2 Dapi_1 Dapi_2 Hetu_1 Hetu_2 Hetu_3 Amtr_1 Smso_1 Smso_2 Taer_1 Fro_1 Fso_1 Ftr_1 Fra_1 Fli_1 Stre_1 Mimi_1 Cobi_2 Hean_2 Bial_3 Bial_4 Dapi_3 Dapi_4 Hetu_4 Hetu_5 Hetu_6 Amtr_2 Smso_3 Smso_4 Taer_2 Fro_2 Fso_2 Ftr_2 Fra_2 Fli_2
Vivi19g01154 Arla1g00079 Armi1g00089 Sain12g00090 Ceso2g03209 Cati3g00120 Ccar2g02321 Cien5g03533 . Lssa7g03774 Laca7g03085 Tako4g03032 Tamo4g02121 Pslu1g20740 Lomi1g00451 Lomi2g04191 Enbr6g03166 Ecan3g00211 Soca5g05371 Glco3g01539 Artr3g10780 . . Aann4g00759 Chma7g07481 Chmo13g01114 Chmo14g01033 Chmo15g00982 Chla6g05635 Chna2g00953 Cind3g02049 Pdy4g00849 . . . . . . . . . . . . . . . . . . . . Cobi4g02806 Hean11g01546 Bial4g03025 Bial16g02452 Dapi7g00556 Dapi23g00577 . Hetu31g00957 Hetu33g01081 Amtr02g06571 Smso7g00495 Smso29g00642 Taer1g05919 Fro12g02166 Fso2g00453 . Fra11g02343 Fli1g00515
Vivi19g01155 Arla1g00078 Armi1g00088 Sain12g00089 . Cati3g00119 Ccar2g02322 Cien5g03532 . Lssa7g03773 Laca7g03084 Tako4g03031 . Pslu1g20741 Lomi1g00450 Lomi2g04192 Enbr6g03171 Ecan3g00213 Soca5g05372 Glco3g01538 Artr3g10781 . . Aann4g00760 Chma7g07480 . . . Chla6g05636 Chna2g00952 Cind3g02050 . . . . . . . . . . . . . . . . . . . . . Cobi4g02807 Hean11g01547 Bial4g03026 Bial16g02453 Dapi7g00555 Dapi23g00576 . . . Amtr02g06572 Smso7g00494 Smso29g00641 Taer1g05918 Fro12g02167 Fso2g00452 . Fra11g02344 Fli1g00514
Vivi19g01156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01159 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01163 Arla1g00076 . . . Cati3g00117 Ccar2g02324 Cien5g03529 . Lssa7g03771 Laca7g03082 Tako4g03025 . Pslu1g20743 Lomi1g00449 Lomi2g04196 Enbr6g03172 Ecan3g00215 . . Artr3g10785 . . Aann4g00762 Chma7g07478 Chmo13g01111 . Chmo15g00977 Chla6g05639 Chna2g00950 Cind3g02052 . . Hean6g02885 . . . . . . . . . Smso26g01732 . . . . . . Stre9g01545 . Cobi4g02808 Hean11g01548 . . Dapi7g00554 Dapi23g00575 . Hetu31g00954 Hetu33g01079 Amtr02g06573 Smso7g00493 Smso29g00640 Taer1g05917 Fro12g02168 Fso2g00451 Ftr4g03473 Fra11g02345 Fli1g00513
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 49824846 49826231 + chr4g0766331 Aann4g00759 759
4 49826253 49832383 - chr4g0766341 Aann4g00760 760
4 49838068 49839245 + chr4g0766361 Aann4g00762 762
2 119204547 119205823 + AtrifAMIRv0_Chr02g0161671 Amtr02g06571 6571
2 119206165 119211931 - AtrifAMIRv0_Chr02g0161681 Amtr02g06572 6572
2 119214770 119215838 + AtrifAMIRv0_Chr02g0161691 Amtr02g06573 6573
1 1366795 1368546 - evm.model.000012F.96 Arla1g00076 76
1 1373751 1381991 + evm.model.000012F.98 Arla1g00078 78
1 1381967 1384809 - evm.model.000012F.99 Arla1g00079 79
1 1384678 1392478 + AmiAMIRv0_Chr01g0000881 Armi1g00088 88
1 1392982 1395297 - AmiAMIRv0_Chr01g0000891 Armi1g00089 89
3 363513065 363514732 + AtridAMIRv0_Chr03g0415161 Artr3g10780 10780
3 363514900 363520512 - AtridAMIRv0_Chr03g0415171 Artr3g10781 10781
3 363595286 363596763 + AtridAMIRv0_Chr03g0415211 Artr3g10785 10785
4 69265084 69266086 + g42864.t1 Bial4g03025 3025
4 69266444 69270617 - g42865.t1 Bial4g03026 3026
16 63953723 63954725 + g150130.t1 Bial16g02452 2452
16 63955081 63959292 - g150129.t1 Bial16g02453 2453
3 570977 572667 - CtAH03T0006200.1 Cati3g00117 117
3 582371 591677 + CtAH03T0006400.1 Cati3g00119 119
3 592700 594954 - CtAH03T0006500.1 Cati3g00120 120
2 70393823 70405453 + gnl|WGS:LEKV|Ccrd_011372.mRNA.1_mrna Ccar2g02321 2321
2 70395922 70405409 - gnl|WGS:LEKV|Ccrd_011373.mRNA.1_mrna Ccar2g02322 2322
2 70414811 70416209 + gnl|WGS:LEKV|Ccrd_011375.mRNA.1_mrna Ccar2g02324 2324
2 80960312 80961891 - >KAJ9562686.1 Ceso2g03209 3209
6 223436582 223438462 + ClaG1_Chr06g0428821 Chla6g05635 5635
6 223438469 223444296 - ClaG1_Chr06g0428831 Chla6g05636 5636
6 223472170 223474523 + ClaG1_Chr06g0428861 Chla6g05639 5639
7 257156690 257159109 - CmaNakai_Chr07g0697801 Chma7g07478 7478
7 257170334 257176333 + CmaNakai_Chr07g0697821 Chma7g07480 7480
7 257176803 257177997 - CmaNakai_Chr07g0697831 Chma7g07481 7481
13 57159028 57160113 - evm.model.scaffold_1239.62 Chmo13g01111 1111
13 57178003 57179805 - evm.model.scaffold_1239.59 Chmo13g01114 1114
14 51836174 51837910 - evm.model.scaffold_490.4 Chmo14g01033 1033
15 56785100 56787789 - evm.model.scaffold_1049.143 Chmo15g00977 977
15 56844343 56846003 - evm.model.scaffold_1049.148 Chmo15g00982 982
2 72220091 72221380 - Cn1274740 Chna2g00950 950
2 72245423 72251395 + Cn1274710 Chna2g00952 952
2 72251631 72252974 - Cn1274700 Chna2g00953 953
5 81193013 81193978 - KAI3510049.1 Cien5g03529 3529
5 81204748 81209080 + KAI3510052.1 Cien5g03532 3532
5 81209396 81210262 - KAI3510053.1 Cien5g03533 3533
3 311296706 311297960 + D.indicum_Contig21_G00093.t1 Cind3g02049 2049
3 311298444 311303824 - D.indicum_Contig21_G00094.t1 Cind3g02050 2050
3 311313369 311318015 + D.indicum_Contig21_G00096.t1 Cind3g02052 2052
4 75728246 75729104 + h2tg000009l_1.g42473.t1 Cobi4g02806 2806
4 75729429 75734459 - h2tg000009l_1.g42472.t1 Cobi4g02807 2807
4 75737994 75739122 + h2tg000009l_1.g42471.t1 Cobi4g02808 2808
7 11933273 11934370 - h1tg000030l.g77144.t1 Dapi7g00554 554
7 11937579 11942945 + h1tg000030l.g77145.t1 Dapi7g00555 555
7 11943279 11944167 - h1tg000030l.g77146.t1 Dapi7g00556 556
23 12738650 12739779 - h2tg000020l.g165124.t1 Dapi23g00575 575
23 12786509 12791725 + h2tg000020l.g165123.t1 Dapi23g00576 576
23 12792054 12792941 - h2tg000020l.g165122.t1 Dapi23g00577 577
3 2337893 2339369 + XM_043764788.1 Ecan3g00211 211
3 2350078 2356411 - XM_043766382.1 Ecan3g00213 213
3 2367563 2368937 + XM_043763006.1 Ecan3g00215 215
6 115859300 115860506 + evm.model.ctg1851.17 Enbr6g03166 3166
6 115921822 115927784 - evm.model.ctg1851.22 Enbr6g03171 3171
6 115940987 115942114 + evm.model.ctg1851.24 Enbr6g03172 3172
1 10538476 10539746 - FliAMIRv0_Chr01g0005081 Fli1g00513 513
1 10555904 10561151 + FliAMIRv0_Chr01g0005091 Fli1g00514 514
1 10561508 10562382 - FliAMIRv0_Chr01g0005101 Fli1g00515 515
11 77202586 77203480 + FraAMIRv0_Chr11g0223651 Fra11g02343 2343
11 77203844 77209144 - FraAMIRv0_Chr11g0223661 Fra11g02344 2344
11 77214418 77215721 + FraAMIRv0_Chr11g0223671 Fra11g02345 2345
12 29098525 29099437 + FroAMIRv0_Chr12g0217141 Fro12g02166 2166
12 29099800 29105647 - FroAMIRv0_Chr12g0217151 Fro12g02167 2167
12 29111755 29112943 + FroAMIRv0_Chr12g0217161 Fro12g02168 2168
2 5995307 5996577 - FsoAMIRv0_Chr02g0032701 Fso2g00451 451
2 6001962 6007307 + FsoAMIRv0_Chr02g0032711 Fso2g00452 452
2 6007674 6008554 - FsoAMIRv0_Chr02g0032721 Fso2g00453 453
4 117626517 117627733 + FtrAMIRv0_Chr04g0129071 Ftr4g03473 3473
3 99553567 99558842 + GcoAMIRv0_Chr03g0171671 Glco3g01538 1538
3 99559286 99560482 - GcoAMIRv0_Chr03g0171681 Glco3g01539 1539
6 103398912 103400344 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr06g0271291 Hean6g02885 2885
11 47177238 47179374 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484101 Hean11g01546 1546
11 47178497 47184297 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484111 Hean11g01547 1547
11 47187435 47188970 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484121 Hean11g01548 1548
31 42642009 42642988 - >Htub.h1tg002121l.g186.t1 Hetu31g00954 954
31 42659546 42660417 - >Htub.h1tg002121l.g189.t1 Hetu31g00957 957
33 45148604 45149582 - >Htub.h1tg001052l.g283.t1 Hetu33g01079 1079
33 45161525 45162407 - >Htub.h1tg001052l.g281.t1 Hetu33g01081 1081
7 145554841 145555945 - CAI9295282.1 Laca7g03082 3082
7 145587886 145593156 + CAI9295284.1 Laca7g03084 3084
7 145593022 145594417 - CAI9295285.1 Laca7g03085 3085
1 4073985 4075200 - LmiAMIRv0_Chr01g0004491 Lomi1g00449 449
1 4084931 4090581 + LmiAMIRv0_Chr01g0004501 Lomi1g00450 450
1 4091093 4091981 - LmiAMIRv0_Chr01g0004511 Lomi1g00451 451
2 47463789 47464678 + LmiAMIRv0_Chr02g0087241 Lomi2g04191 4191
2 47465191 47470814 - LmiAMIRv0_Chr02g0087251 Lomi2g04192 4192
2 47483732 47484988 + LmiAMIRv0_Chr02g0087291 Lomi2g04196 4196
7 198592850 198593924 - >KAJ0194896.1 Lssa7g03771 3771
7 198616044 198621373 + >KAJ0195964.1 Lssa7g03773 3773
7 198621288 198622528 - >KAJ0198334.1 Lssa7g03774 3774
4 15314735 15315632 - PdyAMIRv0_Chr04g0156561 Pdy4g00849 849
1 149597777 149598664 + PluAMIRv0_Chr01g0206491 Pslu1g20740 20740
1 149599154 149604663 - PluAMIRv0_Chr01g0206501 Pslu1g20741 20741
1 149611301 149612365 + PluAMIRv0_Chr01g0206521 Pslu1g20743 20743
12 1141201 1152282 + SinAMIRv0_Chr12g0356541 Sain12g00089 89
12 1152754 1154401 - SinAMIRv0_Chr12g0356551 Sain12g00090 90
7 8227033 8228208 - KAI3810073.1 Smso7g00493 493
7 8250078 8255978 + KAI3810074.1 Smso7g00494 494
7 8256181 8257158 - KAI3810075.1 Smso7g00495 495
26 29519052 29519877 + KAI3695217.1 Smso26g01732 1732
29 9044923 9046173 - KAI3675634.1 Smso29g00640 640
29 9077099 9082859 + KAI3675635.1 Smso29g00641 641
29 9083208 9084104 - KAI3675636.1 Smso29g00642 642
5 73920515 73922056 + transfrag23921.t01 Soca5g05371 5371
5 73922258 73929669 - transfrag23922.t01 Soca5g05372 5372
6 20214747 20216253 - Streb.6G006950.1 Stre6g00695 695
6 20282573 20287066 + Streb.6G006960.1 Stre6g00696 696
6 20287424 20288434 - Streb.6G006970.1 Stre6g00697 697
9 27109465 27110464 - Streb.9G015450.1 Stre9g01545 1545
1 53384346 53385546 - >KAK1440092.1 Taer1g05917 5917
1 53387034 53393600 + >KAK1440093.1 Taer1g05918 5918
1 53393897 53394786 - >KAK1440094.1 Taer1g05919 5919
4 58612981 58614509 - TkA04G230750.1 Tako4g03025 3025
4 58642224 58648967 + TkA04G230840.1 Tako4g03031 3031
4 58648886 58650013 - TkA04G230850.1 Tako4g03032 3032
4 34456809 34458492 - TbA04G052720.1 Tamo4g02121 2121
19 23132272 23133626 + GSVIVT01036740001 Vivi19g01154 1154
19 23135393 23145621 - GSVIVT01036739001 Vivi19g01155 1155
19 23172291 23185359 - GSVIVT01036737001 Vivi19g01156 1156
19 23186037 23190813 + GSVIVT01036736001 Vivi19g01157 1157
19 23190824 23190979 - GSVIVT01036735001 Vivi19g01158 1158
19 23194272 23195684 + GSVIVT01036734001 Vivi19g01159 1159
19 23206320 23207782 + GSVIVT01036732001 Vivi19g01160 1160
19 23215254 23216894 + GSVIVT01036731001 Vivi19g01161 1161
19 23237784 23238509 + GSVIVT01036729001 Vivi19g01162 1162
19 23265199 23266600 + GSVIVT01036726001 Vivi19g01163 1163
       
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