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AGRP

Asteraceae Genomic Research Platform

Gene Search

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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
Vivi19g00984 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00986 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00987 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00988 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00989 Arla1g00114 Armi1g00133 Sain12g00128 Ceso2g03241 Cati3g00171 Ccar2g02290 Cien5g03610 . Lssa7g03835 Laca7g03135 . . Pslu1g06409 . Lomi2g04166 . Ecan3g00161 Soca5g05310 . . Aary5g02683 . Aann4g00683 . . . . . Chna2g02176 . Pdy4g00894 . . . . . . . . . . . . . . . . . . . . . Hean11g01467 . . . . Hetu32g01094 Hetu31g01056 Hetu33g01156 Amtr02g06502 . . . . . . . .
Vivi19g00990 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00991 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00993 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 46336541 46343839 - chr4g0763511 Aann4g00683 683
5 155645470 155651492 + Aargg5g26830.1 Aary5g02683 2683
2 117511366 117512283 - AtrifAMIRv0_Chr02g0160981 Amtr02g06502 6502
1 2509964 2518104 + evm.model.000012F.148 Arla1g00114 114
1 2665119 2672239 + AmiAMIRv0_Chr01g0001331 Armi1g00133 133
3 1321462 1331165 + CtAH03T0009600.1 Cati3g00171 171
2 69952822 69960861 - gnl|WGS:LEKV|Ccrd_011341.mRNA.1_mrna Ccar2g02290 2290
2 81590248 81598258 + >KAJ9562736.1 Ceso2g03241 3241
2 228956547 228957971 + Cn0816730 Chna2g02176 2176
5 82538073 82542136 + KAI3510130.1 Cien5g03610 3610
3 1488348 1495986 - XM_043763639.1 Ecan3g00161 161
11 43087095 43094786 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0483081 Hean11g01467 1467
31 47602376 47608783 - >Htub.h2tg000229l.g7.t1 Hetu31g01056 1056
32 51677844 51685161 - >Htub.h1tg000795l.g345.t1 Hetu32g01094 1094
33 49530648 49536988 - >Htub.h1tg003380l.g193.t1 Hetu33g01156 1156
7 147915390 147920172 + CAI9295338.1 Laca7g03135 3135
2 47206117 47212485 - LmiAMIRv0_Chr02g0086991 Lomi2g04166 4166
7 203258232 203262637 + >KAJ0195256.1 Lssa7g03835 3835
17 47749031 47762691 + KAD3067173.1 Mimi17g00851 851
4 17004711 17011406 + PdyAMIRv0_Chr04g0157011 Pdy4g00894 894
1 43989982 43995360 + PluAMIRv0_Chr01g0063851 Pslu1g06409 6409
12 2216421 2223287 + SinAMIRv0_Chr12g0356931 Sain12g00128 128
5 72996841 73003642 - transfrag23861.t01 Soca5g05310 5310
19 19222699 19224725 - GSVIVT01020450001 Vivi19g00984 984
19 19247390 19265696 - GSVIVT01020448001 Vivi19g00985 985
19 19293518 19296332 - GSVIVT01020446001 Vivi19g00986 986
19 19354126 19365820 + GSVIVT01020441001 Vivi19g00987 987
19 19433699 19434875 - GSVIVT01020439001 Vivi19g00988 988
19 19442860 19461262 - GSVIVT01020437001 Vivi19g00989 989
19 19485257 19493771 + GSVIVT01020436001 Vivi19g00990 990
19 19501041 19517554 - GSVIVT01020434001 Vivi19g00991 991
19 19529948 19532156 + GSVIVT01020432001 Vivi19g00992 992
19 19539045 19540048 - GSVIVT01020431001 Vivi19g00993 993
       
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