Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Lsi04g01812 ATGCTGACTCCCCCCACCGCGAAGACAACGAATATTAGGAGAGAAAACACAAAGAGGCGGAAAGGATTCGAAATGAAAGGCGGTAAATCGAAGTCGGAGTCGAAGAAAGCAGACACCAAGCTATCAGTGAAAAAAGGTGCAGCCAACGCGGGCAAGAAAGGAAGTAAGAAGGCAGGGAAAGATCCTAACAAACCTAAGAGGCCTGCCAGTGCCTTCTTCGTTTTTATGGAAGAGTTCAGGAAGAAGTTCAATGAGGAGAATCCGAATAACAAAGCAGTGTCTGCTGTTGGTAAAGCTGCTGGACAGAAATGGAAATCATTGTCGGATGCTGAAAAAGCACCTTACATTGCTAAGGCTGACAAGAGGAAGGTTGAATATGAAAAAAATATGAAGGCCTATAACAAGAAACAGGCCAGTGGAGCCAATGCTGCAGAAGAAGATGAATCTGAGAAGTCAATGTCTGAGGTGAATGATGATGAGGATGGAGATGAGGGCAGCGAAGAGGTTAGCTTCCTTAAGGAGAGGATGACGACGAGTGATGAAGATGTAGATGATGCTCTTCTGTCTCTGAATTTATTTTCATTCTCTTATCTGAAAAGAAGGACTGTTCCATTCAGTGTAGCTAATTACAGGGACATGCGAGTAAACGGTAGCTTAATCATACGCATTATGGGGGAGCATCAATCTGGCTTGCCGAAAGCCACAAGATCAGTGATACCATTTGCAATCACCAGCGACAATGAAGTTTCCCTTGAATGCCTCTCATGGATGCTTTACTCTTTTCCTCTCGTGTTTGTGGAAGTGTCTTGCCGGCTTGTATGGCGTTTCTGGCTGCAAGACGGAATCTCCTCAGGCGGGAGTGGCGACGGCTTGTCTGTTGGTGCTTCACCATTTGGCTTATAG 903 45.51 MLTPPTAKTTNIRRENTKRRKGFEMKGGKSKSESKKADTKLSVKKGAANAGKKGSKKAGKDPNKPKRPASAFFVFMEEFRKKFNEENPNNKAVSAVGKAAGQKWKSLSDAEKAPYIAKADKRKVEYEKNMKAYNKKQASGANAAEEDESEKSMSEVNDDEDGDEGSEEVSFLKERMTTSDEDVDDALLSLNLFSFSYLKRRTVPFSVANYRDMRVNGSLIIRIMGEHQSGLPKATRSVIPFAITSDNEVSLECLSWMLYSFPLVFVEVSCRLVWRFWLQDGISSGGSGDGLSVGASPFGL 300
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
4 25344166 25347018 + Lsi04G018120.1 Lsi04g01812 661861

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Lsi04g01812 300 SUPERFAMILY HMG-box 52 139 IPR036910 -
Lsi04g01812 300 MobiDBLite consensus disorder prediction 1 69 - -
Lsi04g01812 300 SMART hmgende2 64 135 IPR009071 -
Lsi04g01812 300 PANTHER HIGH MOBILITY GROUP B PROTEIN 4-RELATED 25 170 IPR031061 -
Lsi04g01812 300 MobiDBLite consensus disorder prediction 151 167 - -
Lsi04g01812 300 PANTHER HIGH MOBILITY GROUP B PROTEIN 2-RELATED 25 170 - -
Lsi04g01812 300 MobiDBLite consensus disorder prediction 136 170 - -
Lsi04g01812 300 Pfam HMG (high mobility group) box 65 134 IPR009071 -
Lsi04g01812 300 Gene3D High mobility group box domain 48 152 IPR036910 -
Lsi04g01812 300 Coils Coil 116 136 - -
Lsi04g01812 300 ProSiteProfiles HMG boxes A and B DNA-binding domains profile. 65 134 IPR009071 -
Lsi04g01812 300 CDD HMGB-UBF_HMG-box 65 131 - -
Lsi04g01812 300 MobiDBLite consensus disorder prediction 84 104 - -
Lsi04g01812 300 MobiDBLite consensus disorder prediction 12 42 - -
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Lsi04g01812 K25507 HMGBP; high mobility group B protein, plant - csv:101203891 246.514
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Lsi04g01812 Lsi-Chr4:25344166 Lsi10g00137 Lsi-Chr10:2155643 3.49E-27 dispersed
Lsi01g01542 Lsi-Chr1:13559242 Lsi04g01812 Lsi-Chr4:25344166 2.37E-41 transposed
Lsi03g01461 Lsi-Chr3:25491155 Lsi04g01812 Lsi-Chr4:25344166 1.51E-07 transposed
Lsi01g00162 Lsi-Chr1:1618724 Lsi04g01812 Lsi-Chr4:25344166 1.64E-11 transposed
Lsi09g00846 Lsi-Chr9:9743698 Lsi04g01812 Lsi-Chr4:25344166 2.21E-23 transposed
Lsi04g01812 Lsi-Chr4:25344166 Lsi07g01055 Lsi-Chr7:15922525 2.15E-43 wgd
       

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
Vvi18g85 . Blo12g00851 . Bda03g00323 Bpe02g00306 Bpe04g00284 Bma04g00290 . . . Cma01g02021 Cma09g00049 Car01g01588 . . Cpe06g00019 . . . . . . . . . . . . . . . Cone4ag2024 Cone7ag1941 Cone17ag1458 . Lsi04g01812 Csa04g02709 . . . . Bda11g00975 . . . . . Sed01g2431 Cmo01g02078 Cmo09g00052 . . . Car09g00041 . . Bhi09g02874 Tan01g5116 Cmetu06g2583 . . Mch11g0052 . Cla11g01828 Cam11g1895 Cec11g1920 Cco11g1929 Clacu11g2059 Cmu11g1864 Cre11g2271 . . Chy07g00398 .
       

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
OG0002005 3 3 2 2 2 0 4 1 0 2 2 1 3 2 2 3 0 5 2 1 2 2 2 2 2 2 2 2 1 2 59
       

Regulatory proteins

Select Gene Hmm_acc Hmm_name Score E-value Regulatory Factors Family
25228 PF00505 HMG_box 1.30E-23 CL0114 Lsi TR
       

Transcriptome

Select Gene Chr Type da1 da2 da3 da4 da5 da6 da7 da8 da9 da10
Lsi04g01812 Lsi_Chr04 FPKM 8.40114 9.174554 10.880254 9.178579 7.804862 7.063106 7.636622 7.521465 7.290996 8.744202