Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Cma05g00948 ATGTCTACCTCTAGACCTAGTCAGTCTTCTAGCAACTCTGGGCGGTCCAGACATAGCACTAGAATTATTGCTCAAACATCTGTTGATGCAAAGCTGCAAGCTGATTTCGAGGAATCTGGGAATTCGTTCGACTACTCAAGTTCAGTGCGTGTCACTAGTGATGTTAGCGGAGATCAACAGCCTAGGTCAGACAAAGTTACTACAGCTTATCTCCATCATATTCAGAAAGGCAAACTTATCCAACCATTTGGTTGCTTGTTGGCTTTAGATGACAAAACATTCAAGGTTATTGCGTATAGTGAAAATGCCCCTGAAATGTTGACCATGGTGAGCCATGCTGTCCCAAGCATGGGGGATTACCCTGTTCTTGGCATTGGCACAGATGTAAGGACTATTTTCACCGCACCAAGTGCTTCTGCACTGTTGAAGGCCTTGGGCTTTGGAGAGGTTACTCTTCTTAATCCTATCCTGGTGCATTGCAAGACTTCTGGAAAACCCTTCTATGCAATTGTTCATCGTGTTACTGGAAGCTTAATCATTGACTTTGAGCCTGTGAAGCCTTATGAAGGTCCAGTGACTGCAGCTGGAGCTCTACAGTCATATAAACTTGCCGCCAAAGCAATTACTAGATTGCAGTCTTTGCCTAGTGGAAGCATGGCTAGGCTTTGTGACACAATGGTTCAAGAAGTTTTTGAACTAACAGGTTATGATCGAGTTATGGCTTATAAATTCCATGATGATGATCACGGGGAAGTGATCTCTGAAGTCACAAAGCCTGGCCTTCAGCCATATCTTGGTTTGCATTATCCAGCAACTGACATTCCTCAAGCTGCACGTTTTTTGTTCATGAAAAATAAGGTCCGCATGATTGTTGATTGTCGTGCAAAACATTTAAAAGTACTCCAAGATGAGAAATTACAGTTTGATCTAACTTTATGTGGTTCAACTTTAAGGGCTCCACACAGTTGCCATTTACAGTATATGGAAAACATGAACTCTATAGCCTCTTTGGTTATGGCAGTTGTAGTTAATGAAGGGGATGAAGAAAGTGAAGGCCCTGCTTTGCAGCAACAAAAGAGAAAGAGATTATGGGGCTTGGTAGTATGTCATAATTTAAGTCCCAGATTTGTTCCGTTTCCTCTTAGGTATGCTTGTGAGTTCCTAGCTCAAGTATTTGCTATTCATGTGAACAAGGAATTAGAGTTGGAAAATCAAATTATAGAAAAGAATATTCTGCGTACGCAAACACTCTTGTGCGACATGCTAATGCGTGATGCTCCTGTAGGTATTGTGTCAAGGAGTCCTAACATAATGGATCTTGTCAAATCTGATGGGGCTGCCTTGTTATATAAGAAAAAAATTTGGCGATTAGGATTGACACCTAATGACTTCCAGTTGCTGGACATAGCTTCGTGGCTTTCCGAGTATCATATGGATTCAACGGGGTTGAGTACTGACAGTTTGTATGATGCAGGATACCCTGGAGCTATTGCTTTAGGTGATGAAGTGTGTGGGATGGCAGCTGTGAGGATAACTAATAATGACATGATTTTTTGGTTTCGATCTCACACTGCTTCAGAGATTCGATGGGGTGGAGCAAAGCATGAACATGGTCAAAAGGATGATGCCAGAAAAATGCATCCAAGATCATCTTTCAAGGCTTTCCTTGAAGTAGTCAAGACAAGAAGTTTGCCCTGGAAGGACTATGAGATGGATGCAATCCACTCTTTACAACTTATCCTTAGAAATACTTTTAAGGATACAGATGCAACTGAAATAAATAGAAAATCAATTCAAACAACACTTGGTGACCTAAAAATTGAAGGGAGGCAAGAATTGGAATCAGTAACAAGTGAGATGGTCCGGTTAATCGAGACAGCTACTGTACCGATTTTAGCTGTTGATTTAGATGGGTTAATTAATGGGTGGAATACAAAAATTGCTGAATTGACTGGACTGCCTGTGGATAAAGCTATCGGCAAGCATTTACTTACGTTAGTGGAAGATTCATCTGTAGAAGTTGTCAGGAAGATGTTGTTCTTGGCATTGCAAGGACAAGAAGAGCAAAACGTTCAATTCGAGATCAAGACACATGGTTCTCACATTGAGGTTGGCTCCATCAGCCTAGTTGTAAATGCTTGTGCAAGTAGGGACTTGCGTGAAAATGTCGTGGGTGTGTGTTTTGTAGCACAAGATATCACTGGTCAGAAGATGGTTATGGACAAGTTCACTCGATTAGAAGGCGATTACAAAGCCATTGTACAAAATCCCAATCCATTGATCCCTCCAATATTTGGATCAGATGAATTTGGATGGTGCTCAGAGTGGAATCCTGCAATGGCGAAATTAACTGGGTGGTCACGTGAAGAAGTAATCGATAAGATGCTTTTGGGAGAGGTTTTTGGTGTTCACAAATCATGTTGTCGTTTAAAGAATCAAGAAGCTTTTGTTAACCTTGGGATTGTCTTGAACAATGCCATGTGTGGTCAAGATCCTGAAAAGGCTTCCTTTGGTTTCTTAGCTCGGAACGGGATGTACGTGGAATGTCTTCTATGTGTCAATAAGATCTTGGATAAAGATGGCTCGGTTACAGGGTTCTTTTGCTTTTTGCAGCTTCCTAGTCATGAGTTGCAACAAGCACTAAATATCCAACGCTTATGTGAGCAAACTGCATTGAAGAGATTGAGAGCATTGGGATACATAAAAAGACAGATACAAAATCCTCTTTCTGGGATAATCTTTTCAAGAAGATTATTGGAGCGCACCGAGTTGGGAGTAGAACAAAAAGAACTTCTGCGTACTAGCGGACTCTGTCAAAAGCAGATCTCCAAGGTTCTCGATGAGTCAGACATCGATAAAATTATTGATGGGTTTATTGATTTAGAAATGGACGAGTTTACATTGCATGAAGTATTGATGGTATCAATTAGTCAAGTGATGCTAAAGATTAAAGGAAAGGGTATCCAGATAGTTAATGAGACTCCAGAAGAGGCTATGTCCGAGACCTTATATGGAGATAGTTTAAGGCTTCAACAAGTCTTGGCGAACTTTCTATTGATATCAGTTAGTTATGCGCCTTCAGGAGGCCAACTAACAATTTCAACCAATGTGACCAAGAATCAATTAGGAAAGTCGGTCCATCTGGTGCATTTGGAGTTCAGGATAACATATGCTGGAGGAGGTATACCGGAGTCGTTGCTGAACGAGATGTTTGGAAGTGAGGAGGACACGTCCGAAGAGGGTTTCAGTCTGCTCATCAGTAGAAAGCTGGTGAAGCTGATGAATGGAGATGTACGATATATGAGGGAAGCCGGTAAGTCGAGCTTCATCATAACTGTTGAGCTTGCTGCAGCTCACAAGGCAAGGACAACGTAG 3375 41.51 MSTSRPSQSSSNSGRSRHSTRIIAQTSVDAKLQADFEESGNSFDYSSSVRVTSDVSGDQQPRSDKVTTAYLHHIQKGKLIQPFGCLLALDDKTFKVIAYSENAPEMLTMVSHAVPSMGDYPVLGIGTDVRTIFTAPSASALLKALGFGEVTLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEGPVTAAGALQSYKLAAKAITRLQSLPSGSMARLCDTMVQEVFELTGYDRVMAYKFHDDDHGEVISEVTKPGLQPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRAKHLKVLQDEKLQFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNEGDEESEGPALQQQKRKRLWGLVVCHNLSPRFVPFPLRYACEFLAQVFAIHVNKELELENQIIEKNILRTQTLLCDMLMRDAPVGIVSRSPNIMDLVKSDGAALLYKKKIWRLGLTPNDFQLLDIASWLSEYHMDSTGLSTDSLYDAGYPGAIALGDEVCGMAAVRITNNDMIFWFRSHTASEIRWGGAKHEHGQKDDARKMHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNTFKDTDATEINRKSIQTTLGDLKIEGRQELESVTSEMVRLIETATVPILAVDLDGLINGWNTKIAELTGLPVDKAIGKHLLTLVEDSSVEVVRKMLFLALQGQEEQNVQFEIKTHGSHIEVGSISLVVNACASRDLRENVVGVCFVAQDITGQKMVMDKFTRLEGDYKAIVQNPNPLIPPIFGSDEFGWCSEWNPAMAKLTGWSREEVIDKMLLGEVFGVHKSCCRLKNQEAFVNLGIVLNNAMCGQDPEKASFGFLARNGMYVECLLCVNKILDKDGSVTGFFCFLQLPSHELQQALNIQRLCEQTALKRLRALGYIKRQIQNPLSGIIFSRRLLERTELGVEQKELLRTSGLCQKQISKVLDESDIDKIIDGFIDLEMDEFTLHEVLMVSISQVMLKIKGKGIQIVNETPEEAMSETLYGDSLRLQQVLANFLLISVSYAPSGGQLTISTNVTKNQLGKSVHLVHLEFRITYAGGGIPESLLNEMFGSEEDTSEEGFSLLISRKLVKLMNGDVRYMREAGKSSFIITVELAAAHKARTT 1124
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
5 7645389 7651777 - CmaCh05G009480.1 Cma05g00948 295066

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Cma05g00948 1124 SMART gaf_1 218 410 IPR003018 GO:0005515
Cma05g00948 1124 Pfam PAS fold 69 185 IPR013654 GO:0006355
Cma05g00948 1124 Gene3D PAS domain 74 321 - -
Cma05g00948 1124 SUPERFAMILY GAF domain-like 198 397 - -
Cma05g00948 1124 ProSiteProfiles PAS repeat profile. 616 686 IPR000014 -
Cma05g00948 1124 MobiDBLite consensus disorder prediction 39 64 - -
Cma05g00948 1124 Pfam Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase 1005 1115 IPR003594 -
Cma05g00948 1124 SUPERFAMILY ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 952 1112 IPR036890 -
Cma05g00948 1124 SMART HisKA_10 893 954 IPR003661 GO:0000155|GO:0007165
Cma05g00948 1124 PRINTS Phytochrome signature 133 155 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 PRINTS Phytochrome signature 233 252 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 PRINTS Phytochrome signature 318 339 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 PRINTS Phytochrome signature 430 450 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 PRINTS Phytochrome signature 515 534 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 PRINTS Phytochrome signature 548 566 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 PRINTS Phytochrome signature 619 635 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 PRINTS Phytochrome signature 638 653 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 PRINTS Phytochrome signature 711 728 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 PRINTS Phytochrome signature 731 751 IPR001294 GO:0006355|GO:0009584
Cma05g00948 1124 ProSiteProfiles Phytochrome chromophore attachment site domain profile. 218 390 IPR016132 -
Cma05g00948 1124 ProSiteProfiles Histidine kinase domain profile. 900 1119 IPR005467 -
Cma05g00948 1124 TIGRFAM sensory_box: PAS domain S-box protein 623 739 IPR000014 -
Cma05g00948 1124 CDD HATPase_Phy-like 1004 1115 IPR044767 -
Cma05g00948 1124 Pfam PAS fold 619 733 IPR013767 GO:0006355
Cma05g00948 1124 Pfam PAS fold 749 871 IPR013767 GO:0006355
Cma05g00948 1124 SMART pas_2 748 817 IPR000014 -
Cma05g00948 1124 SMART pas_2 618 684 IPR000014 -
Cma05g00948 1124 ProSitePatterns Phytochrome chromophore attachment site signature. 318 327 IPR013516 -
Cma05g00948 1124 PANTHER PHYTOCHROME A 1 1119 - -
Cma05g00948 1124 Gene3D - 405 578 IPR043150 -
Cma05g00948 1124 SMART HKATPase_4 1005 1117 IPR003594 -
Cma05g00948 1124 ProSiteProfiles PAS repeat profile. 749 801 IPR000014 -
Cma05g00948 1124 SUPERFAMILY PYP-like sensor domain (PAS domain) 74 186 IPR035965 -
Cma05g00948 1124 SUPERFAMILY PYP-like sensor domain (PAS domain) 622 729 IPR035965 -
Cma05g00948 1124 Pfam GAF domain 219 400 IPR003018 GO:0005515
Cma05g00948 1124 MobiDBLite consensus disorder prediction 1 24 - -
Cma05g00948 1124 PANTHER TWO-COMPONENT HISTIDINE KINASE 1 1119 - -
Cma05g00948 1124 Gene3D - 199 561 IPR029016 -
Cma05g00948 1124 Pfam Phytochrome region 413 587 IPR013515 GO:0006355|GO:0009584
Cma05g00948 1124 Coils Coil 397 417 - -
Cma05g00948 1124 CDD PAS 627 733 IPR000014 -
Cma05g00948 1124 CDD PAS 760 871 IPR000014 -
Cma05g00948 1124 Gene3D - 961 1123 IPR036890 -
Cma05g00948 1124 SUPERFAMILY GAF domain-like 408 585 - -
Cma05g00948 1124 SUPERFAMILY PYP-like sensor domain (PAS domain) 763 869 IPR035965 -
Cma05g00948 1124 Gene3D PAS domain 611 748 - -
Cma05g00948 1124 PIRSF Phytochrome_conventional 1 1124 IPR012129 GO:0006355|GO:0009585|GO:0009881|GO:0017006|GO:0042803
Cma05g00948 1124 Gene3D PAS domain 763 875 - -
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Cma05g00948 K12120 PHYA; phytochrome A - csv:101208491 2081.99
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Cma05g00948 Cma-Chr5:7645389 Cma06g01564 Cma-Chr6:9793752 0 dispersed
Cma19g00854 Cma-Chr19:8014444 Cma05g00948 Cma-Chr5:7645389 0 transposed
Cma12g00705 Cma-Chr12:3888331 Cma05g00948 Cma-Chr5:7645389 0 wgd
Cma12g00705 Cma-Chr12:3888331 Cma05g00948 Cma-Chr5:7645389 0 wgd
       

Syn-Families

Select Gene Event_type S_start S_end Function Ath_gene Identity(%) E-value Score
Cma06g00120 . 5 1218 Histidine Kinase Gene Family AT2G17820 63.3 0.0e+00 1425.2
Cma16g01243 . 102 1255 Histidine Kinase Gene Family AT2G17820 64.9 0.0e+00 1414.8
Cma04g00016 . 28 1012 Histidine Kinase Gene Family AT2G01830 70.5 0.0e+00 1325.8
Cma15g00887 CST 20 979 Histidine Kinase Gene Family AT2G01830 72.0 0.0e+00 1303.5
Cma04g02142 CST 23 992 Histidine Kinase Gene Family AT2G01830 69.8 0.0e+00 1276.9
Cma17g01443 . 102 1060 Histidine Kinase Gene Family AT2G01830 52.7 7.7e-276 947.6
Cma11g01285 . 280 1223 Histidine Kinase Gene Family AT2G01830 53.8 1.9e-274 943.0
Cma20g00673 . 302 1245 Histidine Kinase Gene Family AT2G01830 52.9 7.7e-268 921.0
Cma08g00179 . 51 983 Histidine Kinase Gene Family AT2G01830 52.5 3.8e-267 918.7
Cma02g00221 . 329 1267 Histidine Kinase Gene Family AT2G01830 50.7 7.8e-260 894.4
Cma01g01683 CCT 1 992 Histidine Kinase Gene Family AT5G10720 57.2 4.8e-290 994.6
Cma09g00387 CCT 1 996 Histidine Kinase Gene Family AT5G10720 56.2 2.0e-288 989.2
Cma05g00948 . 1 1120 Histidine Kinase Gene Family AT1G09570 79.4 0.0e+00 1817.7
Cma12g00705 . 1 1114 Histidine Kinase Gene Family AT1G09570 71.0 0.0e+00 1617.8
Cma19g00854 . 18 1087 Histidine Kinase Gene Family AT1G09570 53.8 0.0e+00 1171.0
Cma14g01590 CST 35 1078 Histidine Kinase Gene Family AT1G09570 53.6 0.0e+00 1155.2
Cma06g01564 CST 29 1123 Histidine Kinase Gene Family AT1G09570 52.5 0.0e+00 1155.2
Cma14g01590 CST 13 1041 Histidine Kinase Gene Family AT2G18790 77.1 0.0e+00 1620.1
Cma06g01564 CST 28 1064 Histidine Kinase Gene Family AT2G18790 77.2 0.0e+00 1610.9
Cma13g00567 CST 3 1047 Histidine Kinase Gene Family AT2G18790 59.2 0.0e+00 1227.6
Cma18g00452 CST 31 1051 Histidine Kinase Gene Family AT2G18790 59.3 0.0e+00 1224.5
Cma05g00948 . 21 1054 Histidine Kinase Gene Family AT2G18790 53.4 0.0e+00 1087.0
Cma19g00854 . 26 1068 Histidine Kinase Gene Family AT2G18790 51.9 1.4e-313 1073.2
Cma12g00705 . 18 1048 Histidine Kinase Gene Family AT2G18790 50.8 6.5e-305 1044.3
Cma19g00854 . 12 1087 Histidine Kinase Gene Family AT5G35840 61.2 0.0e+00 1334.7
Cma06g01564 CST 29 1125 Histidine Kinase Gene Family AT5G35840 51.7 0.0e+00 1120.1
Cma05g00948 . 9 1114 Histidine Kinase Gene Family AT5G35840 51.8 0.0e+00 1111.7
Cma14g01590 CST 21 1080 Histidine Kinase Gene Family AT5G35840 50.8 0.0e+00 1092.8
Cma12g00705 . 9 1105 Histidine Kinase Gene Family AT5G35840 50.6 0.0e+00 1080.9
Cma06g01564 CST 32 1125 Histidine Kinase Gene Family AT4G16250 74.3 0.0e+00 1649.0
Cma14g01590 CST 30 1080 Histidine Kinase Gene Family AT4G16250 74.2 0.0e+00 1616.3
Cma13g00567 CST 29 1109 Histidine Kinase Gene Family AT4G16250 57.6 0.0e+00 1261.9
Cma18g00452 CST 38 1113 Histidine Kinase Gene Family AT4G16250 57.6 0.0e+00 1257.7
Cma05g00948 . 8 1115 Histidine Kinase Gene Family AT4G16250 53.1 0.0e+00 1137.1
Cma12g00705 . 11 1109 Histidine Kinase Gene Family AT4G16250 50.5 0.0e+00 1082.8
Cma19g00854 . 26 1087 Histidine Kinase Gene Family AT4G16250 51.5 1.9e-312 1069.3
Cma13g00567 CST 12 1110 Histidine Kinase Gene Family AT4G18130 62.9 0.0e+00 1367.8
Cma18g00452 CST 15 1130 Histidine Kinase Gene Family AT4G18130 61.5 0.0e+00 1356.3
Cma06g01564 CST 40 1123 Histidine Kinase Gene Family AT4G18130 57.2 0.0e+00 1244.6
Cma14g01590 CST 38 1078 Histidine Kinase Gene Family AT4G18130 57.3 0.0e+00 1215.3
       

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
OG0002826 1 3 1 1 1 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 1 3 2 1 56
       

Transcriptome

Select Gene Chr Type da1 da2 da3 da4 da5 da6 da7 da8 da9 da10
Cma05g00948 Cma_Chr05 FPKM 28.562943 29.584635 45.152134 45.354801 45.577221 47.97826 50.079739 26.834023 24.663805 27.141232