Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Lsi03g01001 ATGAGGAAGAGTAGAGGCAGGCAAAAGGTGGAGATGGTGAAGATGCCAAATGAGAGCAACCTTCAGGTCACCTTCTCGAAGCGTCGGTCCGGTCTCTTCAAGAAAGCTAGCGAGCTTTGCACGCTCTGCGGTGCCGAGATTGCCATCATCGTCTTCTCGCCTGGGAAGAAGGTCTTCTCCTTTGGCCACCCTTGTGTCGAGGCTCTCATCGAGCGCTTTGTGACACGAAACCCTCCACCGAGCTCTGGTACGTTGCAACTAATCGAAGCTCACCGGAATGCCAATGTTCGAGAACTGAATGTGCAACTTACTCAAGTGCTGAACCAGCTAGAAATGGAGCGGAAGCGCGGCGAAGAGTTGAACAAACTGCGGAAGGCAAGCCAGGCACAATGTTGGTGGGAGCTTCCCATAGAAGAAATGGAAATGCATCAACTAGAACAACTTAAAGCATCGTTGGATGAGCTAAAGAAGAATGTCACACAACAAGCTGATCGGATTTTAATTCAAACTTCTAATGGCAATCCGCCGCCACAGTTCTTCCCGACTCCGTCGACACCGGCAAACCCTAACCAGCAACCCGGCCTTTTCGTCGTCGATCCAAAGAACATCATCTCCCATCTTCCTTACAACTATGGTTCCTATGGATCAAGAGGTTTCTTTTGA 663 49.92 MRKSRGRQKVEMVKMPNESNLQVTFSKRRSGLFKKASELCTLCGAEIAIIVFSPGKKVFSFGHPCVEALIERFVTRNPPPSSGTLQLIEAHRNANVRELNVQLTQVLNQLEMERKRGEELNKLRKASQAQCWWELPIEEMEMHQLEQLKASLDELKKNVTQQADRILIQTSNGNPPPQFFPTPSTPANPNQQPGLFVVDPKNIISHLPYNYGSYGSRGFF 220
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
3 19289582 19291400 - Lsi03G010010.1 Lsi03g01001 658751

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Lsi03g01001 220 CDD MADS_MEF2_like 6 73 IPR033896 GO:0000977|GO:0045944
Lsi03g01001 220 SUPERFAMILY SRF-like 6 78 IPR036879 GO:0003677|GO:0046983
Lsi03g01001 220 SMART madsneu2 5 64 IPR002100 GO:0003677|GO:0046983
Lsi03g01001 220 PRINTS MADS domain signature 27 42 IPR002100 GO:0003677|GO:0046983
Lsi03g01001 220 PRINTS MADS domain signature 7 27 IPR002100 GO:0003677|GO:0046983
Lsi03g01001 220 PRINTS MADS domain signature 42 63 IPR002100 GO:0003677|GO:0046983
Lsi03g01001 220 PANTHER AGAMOUS-LIKE MADS-BOX PROTEIN AGL62 5 183 - -
Lsi03g01001 220 Gene3D - 17 81 IPR036879 GO:0003677|GO:0046983
Lsi03g01001 220 PANTHER MADS BOX PROTEIN 5 183 - -
Lsi03g01001 220 Coils Coil 138 165 - -
Lsi03g01001 220 ProSiteProfiles MADS-box domain profile. 5 65 IPR002100 GO:0003677|GO:0046983
Lsi03g01001 220 Coils Coil 93 120 - -
Lsi03g01001 220 Gene3D - 83 175 - -
Lsi03g01001 220 Pfam SRF-type transcription factor (DNA-binding and dimerisation domain) 16 61 IPR002100 GO:0003677|GO:0046983
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Lsi03g01001 - - - csv:101221957 395.586
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Lsi01g00164 Lsi-Chr1:1641830 Lsi03g01001 Lsi-Chr3:19289582 7.26E-35 dispersed
Lsi03g01001 Lsi-Chr3:19289582 Lsi10g00541 Lsi-Chr10:7768142 9.31E-36 dispersed
Lsi03g01001 Lsi-Chr3:19289582 Lsi02g00875 Lsi-Chr2:8268485 6.11E-37 transposed
       

Deco-Alignment

Select 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
Vvi3g784 . . . . . Bpe12g00730 . . . . . . . . . . . . . . . . . . Cla10g00956 Cam10g0979 Cec10g1010 Cco10g0973 Clacu10g1001 Cmu10g1783 Cre10g1157 . . . . . . . . . . . . . . . . Sed14g1573 Cmo04g00457 . . . . . . Cpe01g00383 Bhi11g01095 Tan01g0599 Cmetu07g0995 . Hepe07g0389 Mch10g0403 . . . . . . . . Lsi03g01001 . . .
       

Syn-Families

Select Gene Event_type S_start S_end Function Ath_gene Identity(%) E-value Score
Lsi03g01001 . 1 165 Type I MADS-box Gene Family AT5G60440 61.9 2.7e-50 196.1
Lsi06g00024 . 1 163 Type I MADS-box Gene Family AT5G48670 64.4 1.9e-54 209.9
Lsi02g01097 . 1 157 Type I MADS-box Gene Family AT5G48670 55.4 4.3e-46 182.2
Lsi03g01001 . 1 165 Type I MADS-box Gene Family AT5G60440 61.9 2.7e-50 196.1
Lsi06g00024 . 1 163 Type I MADS-box Gene Family AT5G48670 64.4 1.9e-54 209.9
Lsi02g01097 . 1 157 Type I MADS-box Gene Family AT5G48670 55.4 4.3e-46 182.2
Lsi03g01001 . 1 165 Type I MADS-box Gene Family AT5G60440 61.9 2.7e-50 196.1
Lsi06g00024 . 1 163 Type I MADS-box Gene Family AT5G48670 64.4 1.9e-54 209.9
Lsi02g01097 . 1 157 Type I MADS-box Gene Family AT5G48670 55.4 4.3e-46 182.2
Lsi03g01001 . 1 165 Type I MADS-box Gene Family AT5G60440 61.9 2.7e-50 196.1
Lsi06g00024 . 1 163 Type I MADS-box Gene Family AT5G48670 64.4 1.9e-54 209.9
Lsi02g01097 . 1 157 Type I MADS-box Gene Family AT5G48670 55.4 4.3e-46 182.2
       

Syn-Orthogroups

Select Orthogroup Bda Bhi Blo Bma Bpe Cam Car Cco Cec Chy Cla Clacu Cma Cme Cmetu Cmo Cmu Cone Cpe Cre Csa HCH Hepe Lac Lcy Lsi Mch Sed Tan Vvi Total
OG0003994 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 2 2 1 7 42
       

Regulatory proteins

Select Gene Hmm_acc Hmm_name Score E-value Regulatory Factors Family
24990 PF00319 SRF-TF 3.50E-24 No_clan Lsi TF
       

Transcriptome

Select Gene Chr Type da1 da2 da3 da4 da5 da6 da7 da8 da9 da10
Lsi03g01001 Lsi_Chr03 FPKM 1.738685 1.813653 1.236105 1.201346 3.973139 4.336094 3.777512 1.479469 1.770953 1.434433