Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Lsi04g01328 ATGGAACGTAATCCGCTTTCCATGGAACCAAACTACTCTGCACCTGAGGCATACTTGGAGTCTGAACAAGATGTCTCTTTCAAGCAAAACTGGAAATCTATCTCAACTCAGTCAACAGTCTCAGAAGAGGCGAACGGTTGCTTTGATTGCAACATTTGCTTAGACTCAGCAGCTGACCCTGTTGTCACCCTCTGTGGTCACCTCTACTGCTGGCCGTGCATTTACAAATGGCTTCATGTTCAAATCTCCAGCAACGAACATGAAAACACCCAGAACTGCCCTGTTTGTAAGGCTAGCATTACTCCCTCCTCTTTGGTTCCCCTCTATGGTCGTGGCACATCATCGAACTCAGATTCCGAATCCAAGAAATCTCACTTGGGTATGGCTGTACCTCGAAGACCACCACCATCAATGAACACACTGGCCCATTCCATTGCAACCTCTTCATTGCATCCTAGCCAGGAGCTTCATCCAAATTATATTCGCTCGCCCTCACACCCAATCTATCACCAACAATATTTTCCCCAGACGTACGGTGACTTTGCCTCATATACACCGTCTTATCTCGGTAATGCTGTGATAACGAGTCTGCTAAACCCGACGATTGGGATGTTCGGAGAAACAGTTTTCACTAGAATATTCGGTAGCATGGATGGGAACTTATTGCCATATCCGCCATACAACAACTCCATCCCAGGAAATGCCAGTACCAGAATGAGAAGACAGGAAATGCAGCTTGATAAGTCTCTTAATAGAACGGTTAATAAGCTAAGAGCTGAAAACTTGATGGAACTTGGAATTTCAAAAATCAACTTCTTTCATTGGAGTCCAGTGGCGAGAAAATTGATATTCATTGCATACTCAAGTTGA 870 44.6 MERNPLSMEPNYSAPEAYLESEQDVSFKQNWKSISTQSTVSEEANGCFDCNICLDSAADPVVTLCGHLYCWPCIYKWLHVQISSNEHENTQNCPVCKASITPSSLVPLYGRGTSSNSDSESKKSHLGMAVPRRPPPSMNTLAHSIATSSLHPSQELHPNYIRSPSHPIYHQQYFPQTYGDFASYTPSYLGNAVITSLLNPTIGMFGETVFTRIFGSMDGNLLPYPPYNNSIPGNASTRMRRQEMQLDKSLNRTVNKLRAENLMELGISKINFFHWSPVARKLIFIAYSS 289
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
4 21066138 21068746 - Lsi04G013280.1 Lsi04g01328 661377

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Lsi04g01328 289 Pfam Zinc finger, C3HC4 type (RING finger) 50 96 IPR018957 GO:0046872
Lsi04g01328 289 CDD RING-HC_AtRMA_like 48 98 - -
Lsi04g01328 289 SUPERFAMILY RING/U-box 30 103 - -
Lsi04g01328 289 ProSiteProfiles Zinc finger RING-type profile. 50 97 IPR001841 -
Lsi04g01328 289 PANTHER E3 UBIQUITIN-PROTEIN LIGASE RNF5-RELATED 9 253 IPR045103 GO:0005783|GO:0006511|GO:0061630
Lsi04g01328 289 MobiDBLite consensus disorder prediction 111 133 - -
Lsi04g01328 289 SMART ring_2 50 96 IPR001841 -
Lsi04g01328 289 ProSitePatterns Zinc finger RING-type signature. 65 74 IPR017907 -
Lsi04g01328 289 Gene3D Zinc/RING finger domain, C3HC4 (zinc finger) 10 115 IPR013083 -
Lsi04g01328 289 PANTHER E3 UBIQUITIN-PROTEIN LIGASE RMA3-LIKE 9 253 - -
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Lsi04g01328 K10666 RNF5; E3 ubiquitin-protein ligase RNF5 [EC:2.3.2.27] - csv:101206686 465.692
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Lsi01g00319 Lsi-Chr1:2821120 Lsi04g01328 Lsi-Chr4:21066138 3.26E-52 dispersed
Lsi04g01328 Lsi-Chr4:21066138 Lsi10g00893 Lsi-Chr10:13198086 2.12E-45 dispersed
Lsi05g00445 Lsi-Chr5:5713066 Lsi04g01328 Lsi-Chr4:21066138 3.97E-07 transposed
Lsi02g00747 Lsi-Chr2:6854087 Lsi04g01328 Lsi-Chr4:21066138 6.99E-46 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
Vvi19g241 . . Bda07g00293 . . Bpe02g01905 Bma10g00503 . . . . Cma09g00872 Car01g01030 Car09g00785 Sed06g0407 Cpe06g00695 Cpe02g00705 Bhi09g03405 Tan01g4405 Cmetu07g2305 . Hepe01g1379 Mch11g1077 . Cla11g01769 . . Cco11g1863 . . Cre11g2213 Cone3ag1414 Cone10ag1343 . Cone12ag1456 Lsi04g01328 Csa04g02351 Chy07g00084 . . . . . Bpe11g00486 Bpe03g00833 . Bma14g00232 . Cmo01g01258 Cmo09g00861 . . . . . . . . . . . . . . . . . . . . . . . .
       

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
OG0011682 1 1 0 2 2 0 2 1 0 0 1 0 0 1 1 2 0 3 2 1 1 1 1 1 1 1 1 1 1 1 30
       

Transcriptome

Select Gene Chr Type da1 da2 da3 da4 da5 da6 da7 da8 da9 da10
Lsi04g01328 Lsi_Chr04 FPKM 26.288605 27.866529 42.148941 41.118847 38.297894 40.117519 41.473312 44.473392 42.126644 43.517895