Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Csa02g00027 ATGCCGGTGCATCTCACGCCCAATGCAATCTCTGCTATTGTCGCTGGCGACGTTAATTCCAAGCCTCTGGTGCAGGTTCTGGATATCAAGCTGATCGGTAACGCGCAGGAGAGGTACAGCCTCTTGATATCCGATGCTGTTTCTGCTGAGCAGGCTATGCTCGCCACTCAGCTTAATGATGTTGTTAAGACTGGACGAGTCAAGAAAGGATCCGTTATCCAGTTGATCGACTATGTCTGCAGTCCCATCAAGAACCGCAAGATTATTGTTGTACTCTGCCTGGAAACTATTATATTGGATTGTGAGATAATTGGGAATCCAAAATCATCTGCTCAATCAGAGAATTTTGCACAAAAGGCAACACCATCTGTAAATTTAGAGCAACCTGCCAAGGTTGGTAATGGTCATTTGAGTGCCAGAAATCCAGTTCATAATGTGCAAAGCTTCCAAGCTACAGTTCAACCTCCATATCAGCCACCTCCAAATTATAAAAATCATGGTGCAATCATTAAGAACGAGGCACCAGCTCGTATAATTCCCATAGCTGCATTGAATCCTTATCAGGGACGATGGGCTATAAAGGCAAGAGTTACTGCAAAGGGTGATCTCCGTCGCTATAACAATGCCAAAGGAGATGGAAAAGTTTTCTCTTTTGACCTCCTTGATTCTGATGGAGGAGAGATACGTGTGACCTGTTTTAATGCTGTTGTGGATCGTTTCTACGAGGTCATAGAAGTTGGTAAAGTTTACTTGATTTCTAAAGGTAGCCTGAAACCTGCACGGAAGGATTTCAATCATCTAAAGAATGAATGGGAGGTTTTCTTGGAGGCATCTTCCACTGTGGAACTGTGCCCAGATGAAGATGATACCATACCAAGACAACAGTTTTCTTTTAAACCTATCAGTGAAATCGAGAATGCTGAAACCAACTCTATTCTGGATGTTATTGGGATTGTAACATCTATCAATCCATCAATCCCTGTTTTGAGAAAAAATGGTATGGAAACTCAAAGAAGAGTTGTGTATTTGAAGGATGCGTCTGGCAGGAGTGTTGAGCTAACAATGTGGGGGGATTTTTGCAACAAGGAAGGCCAAAAATTGCAAGAAATAATTTACTCAGGCCTTTCTCCAGTTTTAGCTGTGAAATCCGGGAAGGTGAGTGATTTCACTGGGAAATCCATTGGGACAATTTCTTCTACTCAGCTTTTCATAAATCCCGATCTTCCTGAGGCTCACATCTTGAGGGAGTGGTACGATGGTGGGGGAAAGAATACTACTTCTCTATCTATTTCTAAAGAAATTGTACCAGGATCTGCCAAGAATGATATTCGGAAGACTGTGTCTCAGATTAAAGATGAAGGACTTGGCAGAGCTGACAAGCCAGATTGGATAACAGTGAAAGCAACAATATCGTTTATCAAAACAGATTCTTTCTGCTACACAGCATGCCCGTTAATGATTGGAGATCGACAATGCAACAAGAAGGTGACTAGATCAGGAAACTCGAAGTGGGTGTGTGACAGGTGCAATCAAGAATTTGAGGATTGCGACTACAGGTATCTTCTTCAAGCCCAAATCCAAGACCATACTGGATTGACATGGGTGACGGCCTTCCAGGAAACTGGTGAAGAGATTCTGGGTGTCTCAGCCAAGGAATTGTACATGTTGAAGTATGAAGAGCAGGATGATGTCAAGTTTGGTGAAATCATCAGAAGTAAAATCTTCGATCAATTTCTGTTTAGGCTCAAAATTAAGGAGGAGGTGTATGGCGATGAACAGAGAGTGAAAAATACTGTAGTCAAGGCAGATAGGGTAAACTATTCTTCAGAAAGCAAATATATGTTGGATTTGCTTTCCAAATTTTCGAGGTAA 1872 42.04 MPVHLTPNAISAIVAGDVNSKPLVQVLDIKLIGNAQERYSLLISDAVSAEQAMLATQLNDVVKTGRVKKGSVIQLIDYVCSPIKNRKIIVVLCLETIILDCEIIGNPKSSAQSENFAQKATPSVNLEQPAKVGNGHLSARNPVHNVQSFQATVQPPYQPPPNYKNHGAIIKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNAKGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEVIEVGKVYLISKGSLKPARKDFNHLKNEWEVFLEASSTVELCPDEDDTIPRQQFSFKPISEIENAETNSILDVIGIVTSINPSIPVLRKNGMETQRRVVYLKDASGRSVELTMWGDFCNKEGQKLQEIIYSGLSPVLAVKSGKVSDFTGKSIGTISSTQLFINPDLPEAHILREWYDGGGKNTTSLSISKEIVPGSAKNDIRKTVSQIKDEGLGRADKPDWITVKATISFIKTDSFCYTACPLMIGDRQCNKKVTRSGNSKWVCDRCNQEFEDCDYRYLLQAQIQDHTGLTWVTAFQETGEEILGVSAKELYMLKYEEQDDVKFGEIIRSKIFDQFLFRLKIKEEVYGDEQRVKNTVVKADRVNYSSESKYMLDLLSKFSR* 624
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
2 279931 285822 + CsaV3_2G001260.1 Csa02g00027 518084

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Csa02g00027 623 TIGRFAM rpa1: replication factor-a protein 1 (rpa1) 4 620 IPR004591 GO:0003677|GO:0005634|GO:0006260|GO:0006281|GO:0006310
Csa02g00027 623 CDD RPA1_DBD_A 180 283 - -
Csa02g00027 623 Gene3D - 431 622 IPR012340 -
Csa02g00027 623 PANTHER REPLICATION FACTOR A 1, RFA1 2 618 IPR004591 GO:0003677|GO:0005634|GO:0006260|GO:0006281|GO:0006310
Csa02g00027 623 CDD RPA1_DBD_B 312 419 - -
Csa02g00027 623 SUPERFAMILY Nucleic acid-binding proteins 1 106 IPR012340 -
Csa02g00027 623 SUPERFAMILY Nucleic acid-binding proteins 444 621 IPR012340 -
Csa02g00027 623 Pfam Replication protein A OB domain 301 405 IPR031657 -
Csa02g00027 623 PANTHER REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT A 2 618 - -
Csa02g00027 623 SUPERFAMILY Nucleic acid-binding proteins 177 291 IPR012340 -
Csa02g00027 623 CDD RPA1_DBD_C 447 620 IPR013955 -
Csa02g00027 623 CDD RPA1N 9 98 IPR007199 GO:0003677|GO:0005634|GO:0006260
Csa02g00027 623 Pfam OB-fold nucleic acid binding domain 192 263 IPR004365 GO:0003676
Csa02g00027 623 Pfam Replication factor-A C terminal domain 463 614 IPR013955 -
Csa02g00027 623 Gene3D - 290 430 IPR012340 -
Csa02g00027 623 Gene3D - 177 287 IPR012340 -
Csa02g00027 623 SUPERFAMILY Nucleic acid-binding proteins 295 425 IPR012340 -
Csa02g00027 623 Pfam Replication factor-A protein 1, N-terminal domain 5 97 IPR007199 GO:0003677|GO:0005634|GO:0006260
Csa02g00027 623 Gene3D - 3 111 IPR012340 -
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Csa02g00027 K07466 RFA1, RPA1, rpa; replication factor A1 - csv:101207583 1233.39
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Csa01g00297 Csa-Chr1:1850827 Csa02g00027 Csa-Chr2:279931 2.74E-102 dispersed
Csa02g00027 Csa-Chr2:279931 Csa03g00107 Csa-Chr3:835283 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
Vvi11g104 . Blo16g00969 . Bda11g01026 . . . . . . . . . . . . . . . . . . . . Cla11g00142 Cam11g0164 Cec11g0165 Cco11g0176 Clacu11g0299 Cmu11g0152 Cre11g0650 . . . . . Csa02g00027 Chy05g01462 . . . . . . Bpe13g01237 . Bma06g00893 Sed04g0901 . . . . . . . . Bhi06g01596 Tan08g0026 Cmetu06g1804 . Hepe08g2687 . . . . . . . . . Lsi11g00167 . . Cme05g02064
       

Syn-Families

Select Gene Event_type S_start S_end Function Ath_gene Identity(%) E-value Score
Csa03g02770 . 107 802 Core DNA Replication Machinery Family AT4G14700 65.9 1.7e-269 925.6
Csa06g03859 . 83 557 Core DNA Replication Machinery Family AT4G14700 62.1 9.4e-172 600.9
Csa03g02770 . 107 802 Core DNA Replication Machinery Family AT4G12620 67.8 4.4e-278 954.1
Csa06g03859 . 83 557 Core DNA Replication Machinery Family AT4G12620 64.7 3.2e-180 629.0
Csa02g01983 . 2 360 Core DNA Replication Machinery Family AT2G37560 65.2 6.3e-141 497.3
Csa05g00861 . 9 418 Core DNA Replication Machinery Family AT2G01120 65.2 7.7e-157 550.4
Csa06g00062 . 3 417 Core DNA Replication Machinery Family AT4G29910 57.1 1.5e-131 466.8
Csa02g00864 . 1 274 Core DNA Replication Machinery Family AT1G26840 63.6 8.3e-91 330.5
Csa07g01193 . 4 799 Core DNA Replication Machinery Family AT1G79150 59.1 2.3e-245 845.5
Csa03g02982 . 12 939 Core DNA Replication Machinery Family AT1G44900 75.7 0.0e+00 1347.4
Csa06g03777 . 1 575 Core DNA Replication Machinery Family AT5G46280 80.5 1.4e-267 918.7
Csa07g00021 . 1 845 Core DNA Replication Machinery Family AT2G16440 75.2 0.0e+00 1154.0
Csa02g00251 . 1 736 Core DNA Replication Machinery Family AT2G07690 78.5 0.0e+00 1115.9
Csa06g03933 . 7 840 Core DNA Replication Machinery Family AT5G44635 71.7 0.0e+00 1189.5
Csa07g01905 . 4 722 Core DNA Replication Machinery Family AT4G02060 84.7 0.0e+00 1214.5
Csa06g01433 . 38 504 Core DNA Replication Machinery Family AT2G29680 61.5 4.2e-162 568.2
Csa06g01433 . 5 465 Core DNA Replication Machinery Family AT1G07270 55.8 2.3e-138 489.2
Csa07g01526 . 1 594 Core DNA Replication Machinery Family AT3G25100 76.2 1.2e-256 882.5
Csa03g03246 . 12 792 Core DNA Replication Machinery Family AT3G09660 73.1 0.0e+00 1098.2
Csa07g00576 . 10 642 Core DNA Replication Machinery Family AT2G14050 77.6 5.4e-287 983.4
Csa02g01390 . 18 420 Core DNA Replication Machinery Family AT2G20980 55.9 1.6e-116 416.4
Csa04g01776 . 7 180 Core DNA Replication Machinery Family AT1G77320 71.3 8.0e-72 269.2
Csa02g00004 . 1 141 Core DNA Replication Machinery Family AT1G77320 56.0 6.0e-43 173.3
Csa04g02777 . 2 146 Core DNA Replication Machinery Family AT1G77320 52.4 4.4e-38 157.1
Csa07g02169 . 1 201 Core DNA Replication Machinery Family AT1G80190 68.5 1.1e-76 283.1
Csa04g00968 . 1 145 Core DNA Replication Machinery Family AT3G12530 71.7 1.8e-60 228.8
Csa06g00183 . 5 190 Core DNA Replication Machinery Family AT1G19080 67.2 5.9e-69 257.3
Csa06g00183 . 5 190 Core DNA Replication Machinery Family AT3G55490 67.2 5.9e-69 257.3
Csa03g00879 . 1 164 Core DNA Replication Machinery Family AT5G49010 62.7 8.2e-50 193.7
Csa02g01434 . 1 1545 Core DNA Replication Machinery Family AT5G67100 60.0 0.0e+00 1746.1
Csa01g00615 . 26 649 Core DNA Replication Machinery Family AT1G67630 61.9 1.5e-217 752.7
Csa06g00817 . 20 466 Core DNA Replication Machinery Family AT1G67320 64.5 3.2e-183 638.3
Csa05g03138 . 7 451 Core DNA Replication Machinery Family AT5G41880 65.8 1.3e-178 622.9
Csa06g02735 . 1 1091 Core DNA Replication Machinery Family AT5G63960 78.3 0.0e+00 1726.5
Csa03g03577 . 1 438 Core DNA Replication Machinery Family AT2G42120 74.7 2.1e-202 701.8
Csa06g00817 . 20 466 Core DNA Replication Machinery Family AT1G67320 64.5 3.2e-183 638.3
Csa05g00569 . 1 126 Core DNA Replication Machinery Family AT1G09815 61.1 2.3e-37 151.8
Csa06g01291 . 1 2096 Core DNA Replication Machinery Family AT1G08260 71.2 0.0e+00 2980.7
Csa06g01291 . 25 2203 Core DNA Replication Machinery Family AT2G27120 67.6 0.0e+00 2940.6
Csa01g02219 . 7 486 Core DNA Replication Machinery Family AT5G22110 68.7 6.8e-189 657.1
Csa06g02480 . 1 921 Core DNA Replication Machinery Family AT5G22010 63.8 6.4e-310 1060.1
Csa03g00353 . 1 332 Core DNA Replication Machinery Family AT1G63160 90.7 6.0e-173 603.6
Csa04g02134 . 1 355 Core DNA Replication Machinery Family AT5G27740 84.2 5.6e-177 617.1
Csa04g01779 . 1 331 Core DNA Replication Machinery Family AT1G21690 81.9 9.9e-152 533.1
Csa06g02139 . 1 364 Core DNA Replication Machinery Family AT1G77470 76.1 4.8e-155 544.3
Csa02g00027 . 26 618 Core DNA Replication Machinery Family AT2G06510 68.0 1.0e-250 862.8
Csa03g00107 . 32 705 Core DNA Replication Machinery Family AT2G06510 51.0 3.7e-200 694.9
Csa01g00297 . 1 623 Core DNA Replication Machinery Family AT5G08020 67.6 8.1e-245 843.2
Csa03g00107 . 10 814 Core DNA Replication Machinery Family AT5G45400 52.4 1.7e-235 812.8
Csa01g00297 . 1 618 Core DNA Replication Machinery Family AT5G61000 65.9 1.4e-239 825.9
Csa03g00107 . 5 800 Core DNA Replication Machinery Family AT4G19130 54.2 1.3e-229 793.1
Csa01g02708 . 1 404 Core DNA Replication Machinery Family AT5G26680 82.2 4.8e-188 654.1
Csa03g01027 . 1 1103 Core DNA Replication Machinery Family AT1G08840 53.0 1.6e-301 1032.3
Csa04g00346 . 1 298 Core DNA Replication Machinery Family AT2G25100 67.8 1.5e-116 416.0
Csa06g01233 . 1 802 Core DNA Replication Machinery Family AT1G08130 66.7 1.3e-298 1022.3
Csa06g01233 . 201 802 Core DNA Replication Machinery Family AT1G49250 69.2 3.1e-242 834.7
       

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
OG0010255 1 3 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 32
       

Transcriptome

Select Gene Chr Type da1 da2 da3 da4 da5 da6 da7 da8 da9 da10
Csa02g00027 Csa_Chr02 FPKM 3.544625 3.989118 2.20066 3.022688 6.530751 7.120124 5.032996 5.72977 4.954306 4.286638