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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
Vivi19g01144 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01147 Arla1g00082 Armi1g00093 Sain12g00095 Ceso2g03212 Cati3g00127 Ccar2g02318 Cien5g03537 . Lssa7g03781 Laca7g03088 Tako4g02937 Tamo4g02124 Pslu1g20728 Lomi1g00454 Lomi2g04187 Enbr6g03159 Ecan3g00206 Soca5g05365 Glco3g01555 Artr3g10772 . . Aann4g00753 . Chmo13g01120 Chmo14g01038 Chmo15g00987 Chla6g05525 Chna2g00957 Cind3g02042 Pdy4g00853 . . . . . . . . . . . . . . . . . . . . Cobi4g02802 Hean11g01541 . . Dapi7g00560 Dapi23g00581 . . . Amtr02g06566 Smso7g00498 Smso29g00647 Taer1g05924 Fro12g02162 Fso2g00461 Ftr4g03469 Fra11g02339 Fli1g00521
Vivi19g01148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01149 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01150 Arla1g00081 Armi1g00091 Sain12g00093 Ceso2g03211 Cati3g00123 Ccar2g02319 Cien5g03535 Cich4g04849 Lssa7g03776 Laca7g03086 Tako4g03036 Tamo4g02123 Pslu1g20731 Lomi1g00453 Lomi2g04189 Enbr6g03163 Ecan3g00208 Soca5g05367 Glco3g01543 Artr3g10773 . . Aann4g00755 . Chmo13g01118 Chmo14g01036 Chmo15g00985 . Chna2g00955 Cind3g02045 Pdy4g00851 . Hean6g02887 . . . . Hetu17g02320 Hetu16g02407 Hetu18g02594 . . . . Fro2g01339 Fso6g01695 Ftr15g00571 Fra10g00395 Fli14g01585 Stre9g01547 . . . . . . . . . . . . . . . . . . .
Vivi19g01151 Arla1g00080 Armi1g00090 Sain12g00092 Ceso2g03210 Cati3g00121 Ccar2g02320 Cien5g03534 Cich4g04848 Lssa7g03775 . Tako4g03033 Tamo4g02122 Pslu1g20732 Lomi1g00452 Lomi2g04190 Enbr6g03165 Ecan3g00210 Soca5g05368 Glco3g01542 Artr3g10774 . . Aann4g00756 Chma7g07483 Chmo13g01116 Chmo14g01035 Chmo15g00984 Chla6g05632 Chna2g00954 Cind3g02046 Pdy4g00850 . . . . . . . . . . . . . . . . . . . . Cobi4g02805 Hean11g01545 Bial4g03024 Bial16g02451 . . . Hetu31g00958 Hetu33g01082 . . . . . . . . .
Vivi19g01152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01153 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 49668175 49673963 + chr4g0766221 Aann4g00753 753
4 49691968 49697722 - chr4g0766261 Aann4g00755 755
4 49744991 49750517 + chr4g0766301 Aann4g00756 756
2 119159002 119179214 + AtrifAMIRv0_Chr02g0161621 Amtr02g06566 6566
1 1386152 1392531 - evm.model.000012F.100 Arla1g00080 80
1 1443304 1448826 + evm.model.000012F.102 Arla1g00081 81
1 1450589 1465724 - evm.model.000012F.103_evm.model.000012F.104 Arla1g00082 82
8 690322 693209 - evm.model.000077F.414 Arla8g00008 8
1 1396880 1402256 - AmiAMIRv0_Chr01g0000901 Armi1g00090 90
1 1422766 1427971 + AmiAMIRv0_Chr01g0000911 Armi1g00091 91
1 1439916 1446528 - AmiAMIRv0_Chr01g0000931 Armi1g00093 93
8 99877949 99880666 + AmiAMIRv0_Chr08g0297281 Armi8g02897 2897
3 363276133 363310038 + AtridAMIRv0_Chr03g0415081 Artr3g10772 10772
3 363317945 363322475 - AtridAMIRv0_Chr03g0415091 Artr3g10773 10773
3 363333130 363336017 + AtridAMIRv0_Chr03g0415101 Artr3g10774 10774
4 69259589 69261972 + g42863.t1 Bial4g03024 3024
16 63947331 63950824 + g150131.t1 Bial16g02451 2451
3 596962 600419 - CtAH03T0006600.1 Cati3g00121 121
3 610039 614496 + CtAH03T0006700.2 Cati3g00123 123
3 616861 633530 - CtAH03T0006800.5 Cati3g00127 127
7 72768992 72780115 - CtAH07T0261900.1 Cati7g03575 3575
2 70353462 70369434 + gnl|WGS:LEKV|Ccrd_011369.mRNA.1_mrna Ccar2g02318 2318
2 70371008 70377586 - gnl|WGS:LEKV|Ccrd_011370.mRNA.1_mrna Ccar2g02319 2319
2 70388602 70393142 + gnl|WGS:LEKV|Ccrd_011371.mRNA.1_mrna Ccar2g02320 2320
2 80963738 80967405 - >KAJ9562687.1 Ceso2g03210 3210
2 80982270 80987524 + >KAJ9562684.1 Ceso2g03211 3211
2 80990296 81002255 - >KAJ9562716.1 Ceso2g03212 3212
6 217898976 217903980 - ClaG1_Chr06g0427721 Chla6g05525 5525
6 223377882 223380981 + ClaG1_Chr06g0428791 Chla6g05632 5632
7 257221621 257224916 - CmaNakai_Chr07g0697851 Chma7g07483 7483
13 57306403 57310152 - evm.model.scaffold_1239.53 Chmo13g01116 1116
13 57510820 57516476 + evm.model.scaffold_1239.43 Chmo13g01118 1118
13 57527470 57532378 - evm.model.scaffold_1239.41 Chmo13g01120 1120
14 51881020 51884525 - evm.model.scaffold_490.1 Chmo14g01035 1035
14 52490378 52496209 + evm.model.scaffold_797.21 Chmo14g01036 1036
14 52550638 52555475 - evm.model.scaffold_797.25 Chmo14g01038 1038
15 56883442 56887088 - evm.model.scaffold_1049.150 Chmo15g00984 984
15 56934978 56939592 + evm.model.scaffold_1049.155 Chmo15g00985 985
15 57088365 57093397 - evm.model.scaffold_1049.164 Chmo15g00987 987
24 326703941 326706404 + evm.model.scaffold_857.19 Chmo24g05757 5757
2 72504201 72507735 - Cn1274690 Chna2g00954 954
2 72682743 72688551 + Cn1274640 Chna2g00955 955
2 72707221 72712234 - Cn1274620 Chna2g00957 957
5 1836152 1838741 - Cn0259140 Chna5g00042 42
4 137242558 137245524 - KAI3753983.1 Cich4g04848 4848
4 137258874 137260769 + KAI3753984.1 Cich4g04849 4849
5 81210298 81213926 - KAI3510054.1 Cien5g03534 3534
5 81221661 81223533 + KAI3510055.1 Cien5g03535 3535
5 81233185 81235852 - KAI3510057.1 Cien5g03537 3537
3 310993644 310998297 + D.indicum_Contig21_G00086.t1 Cind3g02042 2042
3 311043825 311049035 - D.indicum_Contig21_G00089.t1 Cind3g02045 2045
3 311216357 311220314 + D.indicum_Contig21_G00090.t1 Cind3g02046 2046
4 75676916 75680071 + h2tg000009l_1.g42477.t1 Cobi4g02802 2802
4 75720008 75722982 + h2tg000009l_1.g42474.t1 Cobi4g02805 2805
7 11965971 11969017 - h1tg000030l.g77150.t1 Dapi7g00560 560
23 12817580 12820800 - h2tg000020l.g165118.t1 Dapi23g00581 581
3 2303934 2309332 + XM_043764705.1 Ecan3g00206 206
3 2316311 2320610 - XM_043764815.1 Ecan3g00208 208
3 2334277 2335785 + XM_043766786.1 Ecan3g00210 210
5 33669678 33672841 + XM_043773324.1 Ecan5g02029 2029
6 115803583 115810607 + evm.model.ctg1851.10 Enbr6g03159 3159
6 115826184 115829122 - evm.model.ctg1851.14 Enbr6g03163 3163
6 115854570 115857209 + evm.model.ctg1851.16 Enbr6g03165 3165
8 109258479 109261106 - evm.model.ctg51.11 Enbr8g03400 3400
1 10653491 10656433 - FliAMIRv0_Chr01g0005161 Fli1g00521 521
14 49874834 49879155 - FliAMIRv0_Chr14g0327301 Fli14g01585 1585
10 12340188 12344707 + FraAMIRv0_Chr10g0185601 Fra10g00395 395
11 77169682 77172636 + FraAMIRv0_Chr11g0223611 Fra11g02339 2339
2 16647431 16652119 - FroAMIRv0_Chr02g0027261 Fro2g01339 1339
12 29063109 29065951 + FroAMIRv0_Chr12g0217101 Fro12g02162 2162
2 6060363 6063224 - FsoAMIRv0_Chr02g0032801 Fso2g00461 461
6 39253256 39259929 - FsoAMIRv0_Chr06g0148601 Fso6g01695 1695
4 117586740 117590477 + FtrAMIRv0_Chr04g0129031 Ftr4g03469 3469
15 18527294 18532277 + FtrAMIRv0_Chr15g0424641 Ftr15g00571 571
3 99622937 99625843 - GcoAMIRv0_Chr03g0171711 Glco3g01542 1542
3 99659244 99664894 + GcoAMIRv0_Chr03g0171721 Glco3g01543 1543
3 100327286 100331638 - GcoAMIRv0_Chr03g0171841 Glco3g01555 1555
6 103422863 103426209 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr06g0271311 Hean6g02887 2887
11 47060871 47064279 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484041 Hean11g01541 1541
11 47147423 47148146 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484081 Hean11g01545 1545
16 124822719 124825593 + >Htub.h1tg000461l.g431.t1 Hetu16g02407 2407
17 119148210 119150821 + >Htub.h2tg000417l.g147.t1 Hetu17g02320 2320
18 125068881 125071501 + >Htub.h1tg000740l.g3.t1 Hetu18g02594 2594
31 42739437 42743307 - >Htub.h1tg002121l.g190.t1 Hetu31g00958 958
33 45228153 45237621 - >Htub.h1tg001052l.g280.t1 Hetu33g01082 1082
7 145596966 145600161 + CAI9295286.1 Laca7g03086 3086
7 145608845 145611983 - CAI9295288.1 Laca7g03088 3088
1 4096186 4098758 - LmiAMIRv0_Chr01g0004521 Lomi1g00452 452
1 4101817 4105737 + LmiAMIRv0_Chr01g0004531 Lomi1g00453 453
1 4112788 4116240 - LmiAMIRv0_Chr01g0004541 Lomi1g00454 454
2 47441503 47445938 + LmiAMIRv0_Chr02g0087201 Lomi2g04187 4187
2 47452225 47456076 - LmiAMIRv0_Chr02g0087221 Lomi2g04189 4189
2 47459907 47462685 + LmiAMIRv0_Chr02g0087231 Lomi2g04190 4190
5 30011101 30011596 - LmiAMIRv0_Chr05g0175041 Lomi5g01855 1855
11 26289784 26292107 - LmiAMIRv0_Chr11g0337671 Lomi11g01796 1796
7 198623747 198625624 - >KAJ0196862.1 Lssa7g03775 3775
7 198663451 198667914 + >KAJ0197602.1 Lssa7g03776 3776
7 198683908 198687357 - >KAJ0197022.1 Lssa7g03781 3781
17 44027636 44031384 + KAD3067126.1 Mimi17g00804 804
4 15319787 15322194 - PdyAMIRv0_Chr04g0156571 Pdy4g00850 850
4 15506630 15512267 + PdyAMIRv0_Chr04g0156581 Pdy4g00851 851
4 15522081 15525460 - PdyAMIRv0_Chr04g0156601 Pdy4g00853 853
1 149535809 149541278 + PluAMIRv0_Chr01g0206371 Pslu1g20728 20728
1 149552357 149556199 - PluAMIRv0_Chr01g0206401 Pslu1g20731 20731
1 149571872 149574299 + PluAMIRv0_Chr01g0206411 Pslu1g20732 20732
3 114347296 114349715 - PluAMIRv0_Chr03g0557191 Pslu3g15892 15892
12 1170247 1176150 - SinAMIRv0_Chr12g0356571 Sain12g00092 92
12 1201644 1206354 + SinAMIRv0_Chr12g0356581 Sain12g00093 93
12 1221295 1229582 - SinAMIRv0_Chr12g0356601 Sain12g00095 95
13 139482921 139485796 + SinAMIRv0_Chr13g0402741 Sain13g02718 2718
7 8280804 8283515 - KAI3810078.1 Smso7g00498 498
29 9119808 9122526 - KAI3675641.1 Smso29g00647 647
2 91450378 91456117 + transfrag28205.t01 Soca2g04676 4676
5 73860665 73865798 + augustus35965.t01 Soca5g05365 5365
5 73877461 73882462 - asmbl_4245.p1 Soca5g05367 5367
5 73886229 73888290 + augustus35968.t01 Soca5g05368 5368
6 20740435 20743640 - Streb.6G007080.1 Stre6g00708 708
9 27134444 27139745 + Streb.9G015470.1 Stre9g01547 1547
1 53418432 53421358 - >KAK1440099.1 Taer1g05924 5924
4 53731623 53737054 - TkA04G209810.2 Tako4g02937 2937
4 58650262 58655621 - TkA04G230860.1 Tako4g03033 3033
4 58738662 58741811 + TkA04G231320.1 Tako4g03036 3036
4 34458506 34463236 - TbA04G052710.1 Tamo4g02122 2122
4 34477628 34481019 + TbA04G052690.1 Tamo4g02123 2123
4 34498481 34502098 - TbA04G052680.1 Tamo4g02124 2124
19 22939141 22943152 + GSVIVT01036757001 Vivi19g01144 1144
19 22972848 22973241 - GSVIVT01036755001 Vivi19g01145 1145
19 22999084 22999621 - GSVIVT01036752001 Vivi19g01146 1146
19 23001165 23010177 + GSVIVT01036751001 Vivi19g01147 1147
19 23010943 23012091 + GSVIVT01036750001 Vivi19g01148 1148
19 23036858 23037511 - GSVIVT01036748001 Vivi19g01149 1149
19 23045181 23055363 - GSVIVT01036747001 Vivi19g01150 1150
19 23086959 23090029 + GSVIVT01036746001 Vivi19g01151 1151
19 23090087 23092179 + GSVIVT01036745001 Vivi19g01152 1152
19 23111233 23122962 - GSVIVT01036742001 Vivi19g01153 1153
       
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