Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Chy03g00990 ATGTCATCAACAAGTAGACCAAGCCAAGCTTCCAGGAACACAGGAGGAGGATCTTCTTCTTCCTCACAATCAAGACACAGCTCCAGAATCCTCACTCAAACCTCCATAGATGCAAAGCTTCAATCCCACTTTGAGCAATCCGGTTTTTCCTTCGACTACTCCACTTCAATCCATCTCACCAACAACCCAACTGCCGCACCGCCTGCCGCCACCACCACAGCATACCTTCAACAAATCCAAATATCCAACCTTATCCAACCCTTTGGCTGCCTCTTAGCCCTCCACCCCACCACCCTCAAACTCATTGCCTTCAGCCAAAATGCTCCTGAAATGCTCACCACCGTCGCCCACACCGTCCCTGACGGCGACAACCACCCTCTCCTCGCCATCGGCACCGACCTCCGAGGCATCTTCACCGCCCCCACGGCCACCGCCCTCCTCAAGGCCCTTGCCTTCCCCGACGTCACCCTCCTCAACCCTATTCTCGTCCACTCCAAGTCCTCAGGGAAGCCCTTTTACGCCATTCTTCATCGCGTCACCGGTAGCCTTATCATCGACTTTGAACCTCTCAAACCTGACCAAGTCCCCGTCACTGCTGCAGGAGCTCTCCAATCCTATAAGCTCGCGGCCAAAGCCATCACTCGTCTCCAGGCTCTCCCCAGTGGGAGTCTGGTTAGACTGTGTGACACTATGGTTCAAGAAGTGTTTGAGTTGACGGGTTACGATAGAGTGATGGCTTATAAGTTTCATGATGATGATCATGGAGAGGTTTTTTCCGAGGTTACAAAGCCTGGCCTCGAACCTTATCTTGGTTTGCATTATCCAGCCACTGACATTCCTCAGGCTGCAAGATTTTTGTTCATGAAGAACAAGGTTAGAATGATTGTGGATTGTAGAGCCAAACATGTGAAGGTCATTCAAGATCAAAATCTTGATTTTGATTTGACTTTGTGTGGCTCAACTTTAAGAGCTCCTCATTGTTGCCATTTGCAATATATGGAGAATATGGACTCTATTGCCTCATTGGTTATGGCCATTGTGGTAAATGAAGAAGAAGAAGAAGAGAATTTTGATCAAAACAACAACAACGATGCTTCTTTGCAAAAACATAAGAGGAAAAGATTGTGGGGTTTGGTAGTTTGTCACAACACAACTCCTAGATTTGTCCCTTTTCCTCTTAGATATGCTTGTGAATTTCTAGCTCAAGTTTTTGCCATTCATGTCAGCAAGGAATTGGAGTTAGAGAATCAAATTTTGGAGAAAAATATCTTGAGAACTCAAACACTTTTATGTGACATGTTAATGCGTGATGCTCCTTTAGGGATTGTGTCAAGAACTCCTAATATAATGGATCTTGTCAAATCTGACGGAGCTGCATTATTGTACAATAACAAGGTATGGAGATTAGGGATAACCCCTACTGATTTTCATCTTCAAGATATTGCTTCGTGGATTTTGGAGTTTCATATGGATTCCACTGGTTTGAGTACTGATAGCTTGTACGATGCCGGGTACCCCGGCGCGCTTGCACTTGGCGACGTGGTGTGTGGGATGGCTGCTGTGAGGATATCTTCCAACGACATGATTTTCTGGTTTCGATCGCACACTGCGTCGGAGATTCGGTGGGGTGGAGCGAAGCATGTGCCGGGTGAGAAGGATGATGGAAGGAAAATGCATCCAAGATCATCTTTTAAGGCTTTTCTTGAAGTGGTTAAGACAAGGAGTTTGCCATGGAAGGACTTTGAAATGGATGCAATTCATTCTTTGCAACTTATACTAAGAAATACTTTTAAAGATAGAAATGATCATATGAGTGAGATTCATAGAAAATCAATACAAACAACACTTAGTGATCTCAAAATTCTTGATGGGAGGCAAGAATTGGAATCAGTAACAAGTGAAATGGTTAGGTTGATTGAAACAGCCACAGTTCCAATTTTGGCTGTTGATGTTGATGGGCTTGTGAATGGTTGGAACTCAAAAATTGCTGAATTGACTGGACTTTCGGTTGACAAAGCCATTGGCAAGAATTTGCTCACATTAGTGGAAGATTCTTCTGTTGAAATGGTCAAGAAGATGTTGGTCTTGGCATTGCAAGGTCAAGAGGAAAAAAACGTTCAATTTGAGATAAAAACACACAACGTGGACATCAATTCGGGCTCGATAAGCCTAATAGTAAATGCTTGTGCAAGCAAAGACTTAAGTGAAAATGTGGTGGGAGTATGCTTTGTAGCACAAGACATAACATGTCAAAAGATAGTAATGGACAAATTCACAAAACTACAAGGTGATTACAAAGCCATAGTACAAAACCCTAACCCACTAATCCCTCCAATATTTGGGTTAGATGAATTTGGTTGGTGCACAGAATGGAACTTGGCAATGACAAAACTAAGCGGATGGACTCGTGAATCAGTTGTCAACAAAATGCTTTTAGGAGAAGTTTTTGGAACACAATTAAACAACTCGTCATCATGTTGTTGCCAACTCAAGAATCAAGAAGCATTTGTGAATCTTGGGATTGTGTTGAACAATGCAATGAGTGGGCAAGATCCTGAAAAGAATATTTCATTTGGTTTTTATGGAAGAAATGGGATGTTTGTGGAATGTCTATTATGTGTCAATAAGATATTGGATAGAGATGGTGGAGTTATTGGGGTTTTTTGTTTCTTACAACTTGCAAGTCAAGAATTGCAACAAGCTTTGAGTATTCAAAAATTGTGTGAGAGAACTGCATCGAATAGGTTGAAGGCATTGGGATATCTGAAGAGGCAGATTCAAAATCCACTGAGCGGGATTATTTTTTCAAGGAAAATGTTGCAACAAACTCAATTGGGAGTGGAACAGAAGCAACTTTTGATTAATAGTGTTAATTGTCAAAGGCAAATCTCCAAGGTTCTTGATGAGTCTCATGATCTTGATCATATTATTCAAGGAGTGATTGAATTAGAAATGGTTGAGTTTTCATTATATGAAGTATTGGTGGTAGCAATAAGTCAAGTGATGATGAAGAGCAAAGGGAAAGGCATTCAAATAGAAAATGAAGTTGGAGAAGAGATAATGTGTGAGACATTATATGGAGACAATTTGAGACTTCAGCAAATAATGGCTGATTTCTTGTTGATATCAGTTCATTATGCACCAACAGGTGGCCAACTTATGCTTTCAACAACTTTTACTAATAAGGATCATTTTGGGAACTCACTACATCTTCTTCATCTTGAATTCAGGATAACATATGTTGGAGGAGGCATACCAGAATCATTGTTGAATGAGATGTTTGGAAATGATATGGATCGTGAGGATTCATCTGAAGAAGGTTATAGCCTTTTCATAAGTAGAAAACTTGTGAAGATGATGAATGGAGATGTGAGATATGTGAGAGAAGCTGCCAAATCAACCTTCATTATAACTCTTCAACTTGCTGCTGCTGCTGCTCATAAGTAA 3447 41.51 MSSTSRPSQASRNTGGGSSSSSQSRHSSRILTQTSIDAKLQSHFEQSGFSFDYSTSIHLTNNPTAAPPAATTTAYLQQIQISNLIQPFGCLLALHPTTLKLIAFSQNAPEMLTTVAHTVPDGDNHPLLAIGTDLRGIFTAPTATALLKALAFPDVTLLNPILVHSKSSGKPFYAILHRVTGSLIIDFEPLKPDQVPVTAAGALQSYKLAAKAITRLQALPSGSLVRLCDTMVQEVFELTGYDRVMAYKFHDDDHGEVFSEVTKPGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRAKHVKVIQDQNLDFDLTLCGSTLRAPHCCHLQYMENMDSIASLVMAIVVNEEEEEENFDQNNNNDASLQKHKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVSKELELENQILEKNILRTQTLLCDMLMRDAPLGIVSRTPNIMDLVKSDGAALLYNNKVWRLGITPTDFHLQDIASWILEFHMDSTGLSTDSLYDAGYPGALALGDVVCGMAAVRISSNDMIFWFRSHTASEIRWGGAKHVPGEKDDGRKMHPRSSFKAFLEVVKTRSLPWKDFEMDAIHSLQLILRNTFKDRNDHMSEIHRKSIQTTLSDLKILDGRQELESVTSEMVRLIETATVPILAVDVDGLVNGWNSKIAELTGLSVDKAIGKNLLTLVEDSSVEMVKKMLVLALQGQEEKNVQFEIKTHNVDINSGSISLIVNACASKDLSENVVGVCFVAQDITCQKIVMDKFTKLQGDYKAIVQNPNPLIPPIFGLDEFGWCTEWNLAMTKLSGWTRESVVNKMLLGEVFGTQLNNSSSCCCQLKNQEAFVNLGIVLNNAMSGQDPEKNISFGFYGRNGMFVECLLCVNKILDRDGGVIGVFCFLQLASQELQQALSIQKLCERTASNRLKALGYLKRQIQNPLSGIIFSRKMLQQTQLGVEQKQLLINSVNCQRQISKVLDESHDLDHIIQGVIELEMVEFSLYEVLVVAISQVMMKSKGKGIQIENEVGEEIMCETLYGDNLRLQQIMADFLLISVHYAPTGGQLMLSTTFTNKDHFGNSLHLLHLEFRITYVGGGIPESLLNEMFGNDMDREDSSEEGYSLFISRKLVKMMNGDVRYVREAAKSTFIITLQLAAAAAHK* 1149
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
3 13429003 13433250 + Chy3G059700.1 Chy03g00990 223151

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Chy03g00990 1148 SMART pas_2 763 835 IPR000014 -
Chy03g00990 1148 SMART pas_2 633 699 IPR000014 -
Chy03g00990 1148 SUPERFAMILY GAF domain-like 420 600 - -
Chy03g00990 1148 PIRSF Phytochrome_conventional 7 1148 IPR012129 GO:0006355|GO:0009585|GO:0009881|GO:0017006|GO:0042803
Chy03g00990 1148 TIGRFAM sensory_box: PAS domain S-box protein 638 751 IPR000014 -
Chy03g00990 1148 SMART gaf_1 223 422 IPR003018 GO:0005515
Chy03g00990 1148 PRINTS Phytochrome signature 238 257 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 PRINTS Phytochrome signature 527 546 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 PRINTS Phytochrome signature 634 650 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 PRINTS Phytochrome signature 138 160 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 PRINTS Phytochrome signature 323 344 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 PRINTS Phytochrome signature 442 462 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 PRINTS Phytochrome signature 726 743 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 PRINTS Phytochrome signature 746 766 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 PRINTS Phytochrome signature 560 578 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 PRINTS Phytochrome signature 653 668 IPR001294 GO:0006355|GO:0009584
Chy03g00990 1148 SUPERFAMILY ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 972 1139 IPR036890 -
Chy03g00990 1148 SUPERFAMILY PYP-like sensor domain (PAS domain) 778 889 IPR035965 -
Chy03g00990 1148 Pfam Phytochrome region 425 600 IPR013515 GO:0006355|GO:0009584
Chy03g00990 1148 Coils Coil 409 429 - -
Chy03g00990 1148 Pfam GAF domain 224 412 IPR003018 GO:0005515
Chy03g00990 1148 PANTHER PHYTOCHROME A 15 1145 - -
Chy03g00990 1148 SMART HKATPase_4 1027 1143 IPR003594 -
Chy03g00990 1148 Gene3D - 958 1137 IPR036890 -
Chy03g00990 1148 Pfam PAS fold 74 189 IPR013654 GO:0006355
Chy03g00990 1148 Gene3D PAS domain 627 762 - -
Chy03g00990 1148 SUPERFAMILY GAF domain-like 203 408 - -
Chy03g00990 1148 ProSiteProfiles PAS repeat profile. 764 816 IPR000014 -
Chy03g00990 1148 SUPERFAMILY PYP-like sensor domain (PAS domain) 637 744 IPR035965 -
Chy03g00990 1148 Gene3D - 417 590 IPR043150 -
Chy03g00990 1148 Gene3D PAS domain 78 326 - -
Chy03g00990 1148 SUPERFAMILY PYP-like sensor domain (PAS domain) 78 193 IPR035965 -
Chy03g00990 1148 CDD PAS 642 748 IPR000014 -
Chy03g00990 1148 CDD PAS 775 892 IPR000014 -
Chy03g00990 1148 ProSiteProfiles PAS repeat profile. 631 701 IPR000014 -
Chy03g00990 1148 Gene3D - 77 573 IPR029016 -
Chy03g00990 1148 PANTHER TWO-COMPONENT HISTIDINE KINASE 15 1145 - -
Chy03g00990 1148 ProSiteProfiles Histidine kinase domain profile. 921 1143 IPR005467 -
Chy03g00990 1148 Pfam Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase 1027 1141 IPR003594 -
Chy03g00990 1148 ProSiteProfiles Phytochrome chromophore attachment site domain profile. 223 402 IPR016132 -
Chy03g00990 1148 ProSitePatterns Phytochrome chromophore attachment site signature. 323 332 IPR013516 -
Chy03g00990 1148 Pfam PAS fold 764 892 IPR013767 GO:0006355
Chy03g00990 1148 Pfam PAS fold 634 748 IPR013767 GO:0006355
Chy03g00990 1148 MobiDBLite consensus disorder prediction 1 29 - -
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Chy03g00990 K12120 PHYA; phytochrome A - csv:101219585 2177.9
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Chy03g00990 Chy-Chr3:13429003 Chy06g00756 Chy-Chr6:5211189 0 dispersed
Chy03g00986 Chy-Chr3:13388886 Chy03g00990 Chy-Chr3:13429003 0 proximal
       

Syn-Families

Select Gene Event_type S_start S_end Function Ath_gene Identity(%) E-value Score
Chy06g02240 . 5 1196 Histidine Kinase Gene Family AT2G17820 65.3 0.0e+00 1457.2
Chy10g00085 . 20 1004 Histidine Kinase Gene Family AT2G01830 71.7 0.0e+00 1350.9
Chy11g01787 . 58 1002 Histidine Kinase Gene Family AT2G01830 53.3 2.9e-274 941.8
Chy11g00704 . 304 1259 Histidine Kinase Gene Family AT2G01830 52.1 2.2e-269 925.6
Chy07g00300 . 1 995 Histidine Kinase Gene Family AT5G10720 57.3 3.3e-290 994.6
Chy03g00986 . 35 1154 Histidine Kinase Gene Family AT1G09570 79.7 0.0e+00 1822.4
Chy03g00990 . 3 1144 Histidine Kinase Gene Family AT1G09570 71.1 0.0e+00 1617.4
Chy06g00756 . 34 1121 Histidine Kinase Gene Family AT1G09570 54.6 0.0e+00 1192.9
Chy01g00529 . 18 952 Histidine Kinase Gene Family AT1G09570 57.0 0.0e+00 1082.8
Chy06g00756 . 13 1062 Histidine Kinase Gene Family AT2G18790 78.8 0.0e+00 1665.6
Chy12g00013 . 21 1043 Histidine Kinase Gene Family AT2G18790 59.6 0.0e+00 1239.9
Chy03g00986 . 55 1088 Histidine Kinase Gene Family AT2G18790 53.2 0.0e+00 1085.9
Chy03g00990 . 22 1077 Histidine Kinase Gene Family AT2G18790 50.9 1.8e-306 1048.9
Chy01g00529 . 26 952 Histidine Kinase Gene Family AT2G18790 56.0 8.2e-299 1023.5
Chy01g00529 . 18 954 Histidine Kinase Gene Family AT5G35840 64.1 0.0e+00 1223.8
Chy06g00756 . 21 1123 Histidine Kinase Gene Family AT5G35840 53.1 0.0e+00 1150.2
Chy03g00986 . 43 1148 Histidine Kinase Gene Family AT5G35840 51.7 0.0e+00 1114.4
Chy01g00528 . 1 160 Histidine Kinase Gene Family AT5G35840 52.4 9.3e-37 152.9
Chy06g00756 . 3 1123 Histidine Kinase Gene Family AT4G16250 75.9 0.0e+00 1712.2
Chy12g00013 . 22 1105 Histidine Kinase Gene Family AT4G16250 57.7 0.0e+00 1283.5
Chy03g00986 . 42 1149 Histidine Kinase Gene Family AT4G16250 52.7 0.0e+00 1137.9
Chy01g00529 . 26 952 Histidine Kinase Gene Family AT4G16250 54.4 1.2e-292 1003.0
Chy12g00013 . 31 1119 Histidine Kinase Gene Family AT4G18130 63.2 0.0e+00 1375.5
Chy06g00756 . 38 1121 Histidine Kinase Gene Family AT4G18130 58.9 0.0e+00 1271.5
Chy01g00529 . 27 952 Histidine Kinase Gene Family AT4G18130 50.1 3.2e-255 878.6
       

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
Chy03g00990 Chy_Chr03 FPKM 248.072571 245.629898 1.742867 1.667241 0.0 0.0 0.166629 0.636884 0.807149 0.654079