Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Lsi05g01420 ATGGTTTCCAGTAATCGAGCGACGCATTCGCATCAACAACAAGCACAGTCTTCGAACACGAATACAAGCAATTTGCGATCTCATCGTACAGATTCCATCAGCAAAGCTATAGCGCAGTACACAGTTGATGCTCGTCTTCACGCGGTGTTTGAGCAGTCAGGTGAGTCTGGAAAATCTTTTGACTACTCACAATCTATAAGAACTTCGACTCAATCTGTGCCGGAGCAGCAAATTACTGCTTATTTGTCGAAGATTCAAAGGGGTGGCCATATCCAGCCCTTTGGATGTATGATAGCTATAGAAGAGGCTAGTTTTCGGGTTATTGCATACAGTGAGAACGCTAGGGAATTGCTCGGTCTAACGCCTCAATCAGTGCCGAGTCTTGAAAAACCTGAGATCCTTACAATTGGGACTGATGTACGGAACTTGTTCACTTCCAACAGTGCAATTCTGCTAGAGAAAGCATTTGGGGCTCGAGAAATCACTTTGTTGAACCCGGTTTGGATTCATTCCAAGAATTCTGGGAAACCCTTTTACGCAATTTTGCATAGGATTGATGTGGGAATTGTGATTGATTTGGAGCCTGCAAGAACGGAGGATCCTGCCCTTTCTATTGCTGGAGCAGTGCAATCGCAGAAGCTTGCGGTACGTGCAATTTCTCAGTTACAAGCACTTCCTGGTGGAGATATTAAACTGTTGTGTGATACTGTGGTTGAGAGTGTTAGGGAGCTTACTGGATATGATAGAGTTATGGTGTATAAGTTTCATGAGGATGAGCATGGTGAGGTTGTGGCTGAAAGCAAGAGGCCTGACTTAGAGCCATACATTGGATTGCATTATCCTTCTACCGATATCCCTCAGGCATCAAGGTTTTTGTTTAAGCAAAACCGGGTTAGGATGATTGTTGATTGCCATGCCTCTCCAGTTCGTGTAATTCAGGATGCAGGGCTTATGCAACATCTCTGCTTGGTGGGTTCAACTCTTCGTGCTCCCCATGGCTGCCATGCCCAGTATATGGCCAATATGGGCTCCATTGCTTCGTTAGCAATGGCAGTTGTTATCAATGGTAATGATGATGAAGCTATCGGTGGGCGAAATTCAACGAGGCTTTGGGGTTTGGTTGTATGCCACCATACCTCTGCTCGGTGTATTCCGTTCCCGCTCCGGTATGCGTGTGAGTTTCTAATGCAAGCATTTGGGCTTCAACTGAATATGGAATTGCAGTTGGCTTCACAGATGTCTGAGAAACATGTTTTGAGGACTCAAACTCTCTTGTGTGACATGCTTCTTCGTGATTCCCCAGCTGGCATTGTTACGCAGAGTCCAAGCATCATGGACCTAGTAAAGTGTGATGGGGCAGCTCTTTACTATCAAGGGAAATATTACCCTCTGGGTGTGACGCCAACTGAGGCCCAAATAAAGGATATTGTGGAATGGTTGTTGGCTTTCCATGGAGATTCAACTGGTTTAAGTACAGATAGCTTGGGCGATGCTGGATATCCAGGGGCAGCCTTGCTGGGTGATGCAGTTTGTGGTATGGCTGTTGCTTACATCACAAAAAAGGATTTTCTATTTTGGTTCCGATCTCATACAGCAAAAGAGATCAAGTGGGGTGGTGCAAAGCATCACCCAGAGGATAAGGATGATGGTCAAAGAATGCATCCGCGTTCTTCATTCAAGGCATTCTTGGAAGTGGTAAAATCCCGTAGTTTACCATGGGAGAATGCAGAAATGGATGCAATTCACTCATTGCAGCTTATTCTACGAGATTCATTTAAGGATGATGTGGCAATCAATTCAAAGGCAGTTGTTCACCCTCAACTAGGGGATCTTGACTTGCAAGGGATTGATGAGCTCAGCTCGGTTGCAAGAGAAATGGTCAGGTTGATTGAGACTGCAACTGCTCCTATCTTTGCTGTAGATGCTGATGGTCGTATCAATGGATGGAATGCTAAGATTGCTGAGTTGAGTGGGCTTTCTGTTGAGGAAGCTATGGGGAAATCCTTAGTTCGTGATCTTGTGTACAAAGAATCTGAAGAAACAGTTGACAAACTTGTTTCCCGGGCTTTAAAAGGTGAAGAAGATAAAAATGTAGAGATAAAAATGAGGACATTTGGGCCAGAAGATCAAAGGACGCCAATTTTTGTTGTTGTAAATGCTTGCTCTAGCAGGGACTACACTGATAATATAGTTGGCGTTTGTTTTGTTGGTCAAGATGTTACCTGCCAAAAAGTGTTCATGGACAAATTTGTTAGCATACAAGGTGATTATAAAGCAATTGTTCATAGTCCAAATCCTCTTATCCCTCCAATATTTGCTTCAGACGACAATACATGTTGCTCGGAATGGAATACTGCCATGGAAAAGCTCACTGGATGGTCCAGGGAGGAGATAATTGGAAAAATGCTAGTAGGAGATGTTTTTGGAAGTTGTTGTCGACTTAAGGGTCCAGATGCATTGACCAAATTTATGATTGTCCTGCACGGTGCAATGGGAGGGCAGGACAATGAAAAATACCCGTTTTCTTTTTATGACAAAAAGGGGAAATATGTGCAAGCTCTCTTAACAGCAAATAAGAGGATGAATATGGAGGGTCAGATTGTTGGAGCTTTCTGCTTCTTACAGATAGCTAGTCCTGAATTGCAGCAAACTCTTAGAATGCAGAGGCAACAGGAGAAGAACCGGTTTGCAAGGATGAAAGAGCTGGCTTACATTTGCCAGGAAGTGAAGAGTCCTTTGAGTGGTATACGCTTTACTAACTCACTTTTGGAGGCTACAGATTTGAGTGAAGATCAAAAGCAGTTCCTTGAGACCAGTGTTGCTTGTGAAAAGCAGATGCTAAAAATTATAGAGGATATGGATTTGGAATGTATTGATGATGGGACGATGGAGCTTGAGAAGGGGGAGTTCTTATTGGGAAGTGTTATTAATGCTGTTGTTAGTCAAGTGATGATACTACTCAGAGAAAGAAACTTACAACTGATTCGTGATATACCAGAAGAAGTAAAGACTATGGCTGTCTATGGCGATCAAGTGAGGATTCAACAGGTCTTAGCTGATTTCTTGTTGAATATGGTCCGTTACGCGCCCTCTCCAGAAGGCTGGGTAGAAATACGTGTCTGTCCATTCCTGAAGCAAAACCCGGATGGACTTACTCTTGCACACACTGAATTCAGGATTGTATGCCCTGGGGAAGGTCTACCTCCTGAGTTAGTTCAGGACATGTTTCATAGTGGCAGATGGGTGACTCAAGAAGGGTTAGGCTTGAGCATGTGCAGAAAGATTTTGAAGCTCATGAATGGTGAAGTCCAATACATCAGAGAGTCTGAAAGATGTTATTTCTTGATTACTCTTGAACTCCCCTTGACAGAGAGAGGCTTAAACGATGTCGGTTAG 3396 43.67 MVSSNRATHSHQQQAQSSNTNTSNLRSHRTDSISKAIAQYTVDARLHAVFEQSGESGKSFDYSQSIRTSTQSVPEQQITAYLSKIQRGGHIQPFGCMIAIEEASFRVIAYSENARELLGLTPQSVPSLEKPEILTIGTDVRNLFTSNSAILLEKAFGAREITLLNPVWIHSKNSGKPFYAILHRIDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQALPGGDIKLLCDTVVESVRELTGYDRVMVYKFHEDEHGEVVAESKRPDLEPYIGLHYPSTDIPQASRFLFKQNRVRMIVDCHASPVRVIQDAGLMQHLCLVGSTLRAPHGCHAQYMANMGSIASLAMAVVINGNDDEAIGGRNSTRLWGLVVCHHTSARCIPFPLRYACEFLMQAFGLQLNMELQLASQMSEKHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTEAQIKDIVEWLLAFHGDSTGLSTDSLGDAGYPGAALLGDAVCGMAVAYITKKDFLFWFRSHTAKEIKWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWENAEMDAIHSLQLILRDSFKDDVAINSKAVVHPQLGDLDLQGIDELSSVAREMVRLIETATAPIFAVDADGRINGWNAKIAELSGLSVEEAMGKSLVRDLVYKESEETVDKLVSRALKGEEDKNVEIKMRTFGPEDQRTPIFVVVNACSSRDYTDNIVGVCFVGQDVTCQKVFMDKFVSIQGDYKAIVHSPNPLIPPIFASDDNTCCSEWNTAMEKLTGWSREEIIGKMLVGDVFGSCCRLKGPDALTKFMIVLHGAMGGQDNEKYPFSFYDKKGKYVQALLTANKRMNMEGQIVGAFCFLQIASPELQQTLRMQRQQEKNRFARMKELAYICQEVKSPLSGIRFTNSLLEATDLSEDQKQFLETSVACEKQMLKIIEDMDLECIDDGTMELEKGEFLLGSVINAVVSQVMILLRERNLQLIRDIPEEVKTMAVYGDQVRIQQVLADFLLNMVRYAPSPEGWVEIRVCPFLKQNPDGLTLAHTEFRIVCPGEGLPPELVQDMFHSGRWVTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLITLELPLTERGLNDVG 1131
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
5 22155641 22161365 - Lsi05G014200.1 Lsi05g01420 663912

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Lsi05g01420 1131 SUPERFAMILY ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 972 1121 IPR036890 -
Lsi05g01420 1131 ProSiteProfiles PAS repeat profile. 756 808 IPR000014 -
Lsi05g01420 1131 Pfam PAS fold 756 875 IPR013767 GO:0006355
Lsi05g01420 1131 Pfam PAS fold 625 740 IPR013767 GO:0006355
Lsi05g01420 1131 ProSiteProfiles Phytochrome chromophore attachment site domain profile. 229 397 IPR016132 -
Lsi05g01420 1131 SMART gaf_1 229 417 IPR003018 GO:0005515
Lsi05g01420 1131 PRINTS Phytochrome signature 718 735 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 PRINTS Phytochrome signature 644 659 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 PRINTS Phytochrome signature 555 573 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 PRINTS Phytochrome signature 522 541 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 PRINTS Phytochrome signature 437 457 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 PRINTS Phytochrome signature 625 641 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 PRINTS Phytochrome signature 244 263 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 PRINTS Phytochrome signature 738 758 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 PRINTS Phytochrome signature 144 166 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 PRINTS Phytochrome signature 329 350 IPR001294 GO:0006355|GO:0009584
Lsi05g01420 1131 Gene3D - 878 959 - -
Lsi05g01420 1131 CDD HisKA 897 953 IPR003661 GO:0000155|GO:0007165
Lsi05g01420 1131 Gene3D PAS domain 769 877 - -
Lsi05g01420 1131 Pfam GAF domain 229 407 IPR003018 GO:0005515
Lsi05g01420 1131 Gene3D - 210 568 IPR029016 -
Lsi05g01420 1131 SUPERFAMILY Homodimeric domain of signal transducing histidine kinase 885 953 IPR036097 GO:0000155|GO:0007165
Lsi05g01420 1131 TIGRFAM sensory_box: PAS domain S-box protein 629 743 IPR000014 -
Lsi05g01420 1131 SUPERFAMILY PYP-like sensor domain (PAS domain) 627 736 IPR035965 -
Lsi05g01420 1131 CDD PAS 633 740 IPR000014 -
Lsi05g01420 1131 ProSiteProfiles PAS repeat profile. 622 693 IPR000014 -
Lsi05g01420 1131 CDD HATPase_Phy-like 1008 1120 IPR044767 -
Lsi05g01420 1131 Gene3D - 960 1126 IPR036890 -
Lsi05g01420 1131 Gene3D - 412 585 IPR043150 -
Lsi05g01420 1131 SUPERFAMILY PYP-like sensor domain (PAS domain) 85 199 IPR035965 -
Lsi05g01420 1131 SMART HisKA_10 897 961 IPR003661 GO:0000155|GO:0007165
Lsi05g01420 1131 SUPERFAMILY GAF domain-like 415 592 - -
Lsi05g01420 1131 SUPERFAMILY GAF domain-like 209 404 - -
Lsi05g01420 1131 Gene3D PAS domain 84 332 - -
Lsi05g01420 1131 ProSiteProfiles Histidine kinase domain profile. 904 1124 IPR005467 -
Lsi05g01420 1131 SMART HKATPase_4 1009 1124 IPR003594 -
Lsi05g01420 1131 Pfam Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase 1009 1121 IPR003594 -
Lsi05g01420 1131 Gene3D PAS domain 620 744 - -
Lsi05g01420 1131 Pfam His Kinase A (phospho-acceptor) domain 901 961 IPR003661 GO:0000155|GO:0007165
Lsi05g01420 1131 SUPERFAMILY PYP-like sensor domain (PAS domain) 770 874 IPR035965 -
Lsi05g01420 1131 PIRSF Phytochrome_conventional 12 1129 IPR012129 GO:0006355|GO:0009585|GO:0009881|GO:0017006|GO:0042803
Lsi05g01420 1131 CDD PAS 767 875 IPR000014 -
Lsi05g01420 1131 SMART pas_2 624 691 IPR000014 -
Lsi05g01420 1131 SMART pas_2 755 825 IPR000014 -
Lsi05g01420 1131 Pfam Phytochrome region 420 593 IPR013515 GO:0006355|GO:0009584
Lsi05g01420 1131 PANTHER TWO-COMPONENT HISTIDINE KINASE 7 1125 - -
Lsi05g01420 1131 ProSitePatterns Phytochrome chromophore attachment site signature. 329 338 IPR013516 -
Lsi05g01420 1131 Pfam PAS fold 80 196 IPR013654 GO:0006355
Lsi05g01420 1131 PANTHER PHYTOCHROME 7 1125 - -
Lsi05g01420 1131 MobiDBLite consensus disorder prediction 1 29 - -
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Lsi05g01420 K12121 PHYB; phytochrome B - csv:101212197 2217.58
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Lsi02g00857 Lsi-Chr2:8039562 Lsi05g01420 Lsi-Chr5:22155641 0 dispersed
Lsi05g01420 Lsi-Chr5:22155641 Lsi08g00755 Lsi-Chr8:15879561 0 dispersed
       

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
Vvi5g63 Blo01g00030 . . Bda08g00333 . . . Bma05g00993 . . Cma06g01564 Cma14g01590 Car06g01329 Car14g01399 Sed02g1136 Cpe08g00149 Cpe03g01327 Bhi01g01090 Tan10g1077 Cmetu06g1585 . Hepe05g1374 . Lcy11g1336 . . . . . . . Cone14ag0717 Cone15ag0729 . . Lsi05g01420 . . Cme06g00790 . Blo07g00144 Bda11g00500 . Bpe05g00798 Bpe13g00697 . Bma06g01466 . Cmo06g01560 Cmo14g01619 . . . . . . . . . . . . . Cla05g00707 Cam05g0774 Cec05g0782 Cco05g0775 Clacu05g0764 Cmu05g0730 Cre05g0804 . Csa03g01519 Chy06g00756 .
       

Syn-Families

Select Gene Event_type S_start S_end Function Ath_gene Identity(%) E-value Score
Lsi07g01094 . 30 1319 Histidine Kinase Gene Family AT2G17820 59.8 0.0e+00 1375.9
Lsi09g00708 CCT 175 1195 Histidine Kinase Gene Family AT2G01830 68.3 0.0e+00 1301.2
Lsi11g00010 . 18 923 Histidine Kinase Gene Family AT2G01830 65.2 0.0e+00 1187.9
Lsi09g01720 . 58 1018 Histidine Kinase Gene Family AT2G01830 53.0 6.3e-272 934.1
Lsi10g00055 . 304 1282 Histidine Kinase Gene Family AT2G01830 51.4 2.7e-267 918.7
Lsi04g01364 . 1 992 Histidine Kinase Gene Family AT5G10720 57.6 7.9e-295 1010.0
Lsi08g00755 . 1 1120 Histidine Kinase Gene Family AT1G09570 79.9 0.0e+00 1830.5
Lsi11g01345 . 18 1112 Histidine Kinase Gene Family AT1G09570 55.1 0.0e+00 1214.1
Lsi05g01420 . 34 1120 Histidine Kinase Gene Family AT1G09570 54.8 0.0e+00 1199.5
Lsi08g00758 . 3 377 Histidine Kinase Gene Family AT1G09570 62.6 1.3e-142 504.6
Lsi05g01420 . 13 1061 Histidine Kinase Gene Family AT2G18790 79.2 0.0e+00 1676.8
Lsi02g00857 . 31 1051 Histidine Kinase Gene Family AT2G18790 60.4 0.0e+00 1238.0
Lsi08g00755 . 9 1054 Histidine Kinase Gene Family AT2G18790 52.9 0.0e+00 1087.8
Lsi11g01345 . 26 1069 Histidine Kinase Gene Family AT2G18790 52.5 0.0e+00 1079.3
Lsi11g01345 . 12 1116 Histidine Kinase Gene Family AT5G35840 61.5 0.0e+00 1363.6
Lsi05g01420 . 21 1122 Histidine Kinase Gene Family AT5G35840 53.0 0.0e+00 1153.7
Lsi08g00755 . 9 1114 Histidine Kinase Gene Family AT5G35840 51.7 0.0e+00 1115.5
Lsi05g01420 . 3 1122 Histidine Kinase Gene Family AT4G16250 75.9 0.0e+00 1716.4
Lsi02g00857 . 32 1113 Histidine Kinase Gene Family AT4G16250 58.6 0.0e+00 1281.9
Lsi08g00755 . 8 1115 Histidine Kinase Gene Family AT4G16250 52.6 0.0e+00 1132.9
Lsi11g01345 . 26 1115 Histidine Kinase Gene Family AT4G16250 52.6 0.0e+00 1121.3
Lsi02g00857 . 15 1129 Histidine Kinase Gene Family AT4G18130 62.6 0.0e+00 1372.5
Lsi05g01420 . 38 1120 Histidine Kinase Gene Family AT4G18130 59.0 0.0e+00 1271.9
       

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
OG0004550 2 1 2 2 2 1 2 1 1 1 1 1 2 1 1 2 1 2 2 1 1 1 1 2 1 1 1 3 1 1 42
       

Transcriptome

Select Gene Chr Type da1 da2 da3 da4 da5 da6 da7 da8 da9 da10
Lsi05g01420 Lsi_Chr05 FPKM 5.170251 3.824654 0.730078 0.801721 15.906027 16.570156 14.806625 1.142817 0.800783 0.866276