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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
Vivi19g01004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01007 Arla1g00110 Armi1g00125 Sain12g00125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01009 Arla1g00107 Armi1g00122 Sain12g00122 Ceso2g03238 Cati3g00165 Ccar2g02297 Cien5g03598 Cich4g04901 Lssa7g03828 Laca7g03126 . . Pslu1g06390 . Lomi2g04170 Enbr6g01679 Ecan3g00165 Soca5g05320 Glco3g01622 Artr3g10657 Aary5g02677 Aary13g03107 Aann4g00690 Chma7g07256 Chmo13g01190 Chmo14g01090 Chmo15g01041 Chla6g05465 Chna2g01020 Cind3g01988 Pdy4g00888 . . . . . . . . . . . . . . . . . . . . Cobi4g02761 Hean11g01479 Bial4g02989 Bial16g02425 Dapi7g00584 Dapi23g00606 Hetu32g01086 Hetu31g01048 Hetu33g01144 . Smso7g00534 Smso29g00689 Taer1g05953 Fro12g02141 Fso2g00482 Ftr4g03442 Fra11g02314 Fli1g00551
Vivi19g01010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01012 Arla1g00105 . Sain12g00120 . . . . . . . . . . . . . . . . . . . . Chma7g07248 Chmo13g01187 Chmo14g01088 Chmo15g01032 Chla6g05476 Chna2g01016 Cind3g01992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 46757242 46758981 + chr4g0763831 Aann4g00690 690
5 155091702 155093019 - Aargg5g26770.1 Aary5g02677 2677
13 182869112 182870564 - Aargg13g31070.1 Aary13g03107 3107
1 2290950 2307185 + evm.model.000012F.137 Arla1g00105 105
1 2369503 2371030 - evm.model.000012F.139 Arla1g00107 107
1 2413751 2417569 - evm.model.000012F.142 Arla1g00110 110
1 2473433 2474913 - AmiAMIRv0_Chr01g0001221 Armi1g00122 122
1 2540874 2541281 - AmiAMIRv0_Chr01g0001251 Armi1g00125 125
3 359335160 359336544 - AtridAMIRv0_Chr03g0413931 Artr3g10657 10657
4 68654291 68655840 + g55980.t1 Bial4g02989 2989
16 63381226 63383330 + g150157.t1 Bial16g02425 2425
3 1227530 1235203 - CtAH03T0009100.1 Cati3g00165 165
2 70048185 70049576 + gnl|WGS:LEKV|Ccrd_011348.mRNA.1_mrna Ccar2g02297 2297
2 81503675 81506109 - >KAJ9562567.1 Ceso2g03238 3238
6 215405243 215406647 + ClaG1_Chr06g0427121 Chla6g05465 5465
6 215762724 215768374 - ClaG1_Chr06g0427231 Chla6g05476 5476
7 248755163 248757904 + CmaNakai_Chr07g0695501 Chma7g07248 7248
7 249113144 249114377 - CmaNakai_Chr07g0695581 Chma7g07256 7256
13 62066983 62074452 + evm.model.scaffold_4060.187 Chmo13g01187 1187
13 62220918 62222567 - evm.model.scaffold_4060.177 Chmo13g01190 1190
14 56877379 56882426 + evm.model.scaffold_5062.4 Chmo14g01088 1088
14 57108115 57109758 - evm.model.scaffold_5062.12 Chmo14g01090 1090
15 59770055 59775063 + evm.model.scaffold_6625.2 Chmo15g01032 1032
15 59969758 59971388 - evm.model.scaffold_122.8 Chmo15g01041 1041
2 80496627 80501411 + Cn0815130 Chna2g01016 1016
2 80693961 80695475 - Cn0815210 Chna2g01020 1020
4 138943285 138944503 - KAI3754036.1 Cich4g04901 4901
5 82384123 82385336 - KAI3510118.1 Cien5g03598 3598
3 307286287 307287666 + D.indicum_Contig21_G00032.t1 Cind3g01988 1988
3 307459607 307462386 - D.indicum_Contig21_G00036.t1 Cind3g01992 1992
4 74884926 74886265 + h2tg000009l_1.g42518.t1 Cobi4g02761 2761
7 12607460 12610584 - h1tg000030l.g77174.t1 Dapi7g00584 584
23 13466995 13467546 - h2tg000020l.g165093.t1 Dapi23g00606 606
3 1583576 1584870 + XM_043765575.1 Ecan3g00165 165
6 59277211 59278428 + evm.model.ctg291.7 Enbr6g01679 1679
1 11367572 11368575 - FliAMIRv0_Chr01g0005461 Fli1g00551 551
11 76812449 76813480 + FraAMIRv0_Chr11g0223371 Fra11g02314 2314
12 28737878 28738889 + FroAMIRv0_Chr12g0216891 Fro12g02141 2141
2 6448363 6449366 - FsoAMIRv0_Chr02g0033011 Fso2g00482 482
4 117070619 117071597 + FtrAMIRv0_Chr04g0128761 Ftr4g03442 3442
3 105945947 105947150 - GcoAMIRv0_Chr03g0172511 Glco3g01622 1622
11 43882503 43884045 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0483251 Hean11g01479 1479
31 46958887 46960035 - >Htub.h2tg002323l.g77.t1 Hetu31g01048 1048
32 51166292 51167509 - >Htub.h1tg000795l.g335.t1 Hetu32g01086 1086
33 48921548 48922749 - >Htub.h1tg003380l.g180.t1 Hetu33g01144 1144
7 147362168 147363500 - CAI9295329.1 Laca7g03126 3126
2 47256367 47258242 + LmiAMIRv0_Chr02g0087031 Lomi2g04170 4170
7 202904631 202906054 - >KAJ0195790.1 Lssa7g03828 3828
4 16802797 16804025 - PdyAMIRv0_Chr04g0156951 Pdy4g00888 888
1 43856421 43857422 - PluAMIRv0_Chr01g0063661 Pslu1g06390 6390
12 1894595 1897708 + SinAMIRv0_Chr12g0356851 Sain12g00120 120
12 2008543 2009860 - SinAMIRv0_Chr12g0356871 Sain12g00122 122
12 2072496 2072903 - SinAMIRv0_Chr12g0356901 Sain12g00125 125
7 8985239 8986271 - KAI3810114.1 Smso7g00534 534
29 10088410 10090028 - KAI3675683.1 Smso29g00689 689
5 73101419 73103189 + augustus35912.t01 Soca5g05320 5320
6 21871848 21873858 - Streb.6G007360.1 Stre6g00736 736
1 53710740 53711679 - >KAK1440128.1 Taer1g05953 5953
19 19813960 19816800 + GSVIVT01020415001 Vivi19g01004 1004
19 19846206 19847357 + GSVIVT01020414001 Vivi19g01005 1005
19 19894727 19903429 + GSVIVT01020411001 Vivi19g01006 1006
19 19906333 19906912 + GSVIVT01020410001 Vivi19g01007 1007
19 19907421 19915676 + GSVIVT01020409001 Vivi19g01008 1008
19 19941484 19950657 - GSVIVT01020407001 Vivi19g01009 1009
19 19951146 19968808 - GSVIVT01020406001 Vivi19g01010 1010
19 19970563 19972299 + GSVIVT01020405001 Vivi19g01011 1011
19 19972384 19975720 - GSVIVT01020404001 Vivi19g01012 1012
19 20024722 20025572 - GSVIVT01020402001 Vivi19g01013 1013
       
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