Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Csa03g00107 ATGGCAGCGTCAATGGCGTCGTCTAAGCTAACGGAAGGAGCAGTGATGGTGATATGCAAGAGGGAATCGTCTGCTGAGACGTTCCAGCCGATTCTACAAGTGATTGATTTGAAATTGGTTAACACTTCGCAACAATCAGGTAGCGAGAGGTTCAGATTGTTGGTTTCTGATGGAACCCATTTCCAGCAAGGAATGCTGGGCACTCAGCTCAACGAATTGGTTAAGTCTGGGAAGTTACAGAAAGGTTCTATCGTTCGACTGCGGCAGTATGTTTGTAACCCCGTTCAAGAACGCCTGATTATAATTGTCATTGAGTTGGATGTGATAGAGGAAATGTGTGACATTATTGGTGAACCTGTATCAGCCACAAGATCGTCAGCTAATGCATTAAGTGGAAACCCCCTACCCTCTGTGGGGGGTCTGGGGGCTTCACCTGGTAGTGGAATGATTGGTAAGGGAAATGTATCGAGTGCGTCTTTTGAACAGCCTAAAGTGAATCAATCACATGTACCACACATGGGATCTTATTCTAATCCTCCTGAGACTGGAAGATTCTCTGCATCAATTGCGCCTCCTTCTTACTCTAAGACAGATTCTGGATCAAGATTTAATGGGCCATCTCCTTTAACTGGATCATATGGTGATCAGAAGATGGCATATCACAACAGCGGGTCAGATATTCCCAGGCCACCTCTAAATTCTAATGCCTATGCCCGTCCTCAGCCAATATATCAGCAGCCTCCTTCAATGTACAGTAACAGAGGACCAATAGCAAAAAATGAAGCTGCCCCAAGGATAATGCCTATTTCTGCTCTGAACCCTTACCAAGGTAGGTGGACAATAAAGGCTCGAGTTACTTCAAAAGGAGAACTTAGACACTACAACAATCCTCGTGGTGACGGGAAAGTATTTTCATTTGATTTACTCGATGCTTACCGTGGAGAAATACGAGTAACATGCTTCAATACAGTAGCTGATCAGTTTTACAACCAAATTGAATCTGGTAAAGTCTACTTCATTTCTAAAGGAAGCCTGAAACCTGCTCAAAAGAACTTTAACCATCTCAAAAATGACTATGAAATATTTCTTGAAAACACATCAACAATCCAACCTTGCTTTGAGGATGACCAATCAATCCCCCAGCAGCAGTTTCATTTCCATCAGATTGGTGAGATTGAAGGCATGGACAGCAACAGTGTTGTAGATGTAATTGGTGTTGTTTCTTCCATTAATCCTGCAACTTCTTTGATGAGAAAAAATGGTACTGAGACTCAGAAGAGATCCCTTCAGTTGAAAGATATGTCTGGCCGAAGTGTTGAATTGACTCTTTGGGGGAACTTCTGTCAAGCGGAAGGGCAAAGATTGCAAAATATGTGTGACTCGGGGTTGTTCCCAGTTTTGGCCGTGAAATCTAGTAGAGTAAGCGACTTCAATGGGAAGGCAGTGGGAACCATTTCAACAAGTCAGCTCTTTATAGAGCCAGATTTCCCCGAGGCTCATTCACTGAGAGAGTGGTTTGAAAGGGAAGGGAGGAGTACTCTTTCTGTCTCTATATCCAGGGAAGTTGCTAGTGTGGGTAGGACAGATGTCAGGAAGACCATATCTCAAATTAAAGATGAGAGGTTAGGAACCTCTGAGAAGCCAGATTGGATCACGGTTAGTGCAACTGTTTCATTTATTAAGGTTGACAGTTTCTGCTACACAGCATGTCCTATCATGATCGGGGACCGACAATGTAGCAAAAAAGTTACAAATAATGGAGATGGAAAATGGAGATGTGACAGGTGTGATCAGTCTGTTGACGAATGTGACTACAGGTACATACTCCAGCTGCAAATACAGGATCATACTGGCTTAACTTGGGTAACTGCCTTTCAAGAAGGTGGTGAGGAGATCATGGGCATACCTGCAAAAAGATTGTATTATTTGAAGTATGAAGAGCAAGATGATGAGAAATTTGCAGAAATCATCCGGAAGGTTCTTTTTACAAAATTTATAATGAAGTTGAAAATAAAGGAAGAGACTTTTAGTGATGAACAGAGAGTAAGATCAACAGTGGTAAAAGCAGAAAGCATTAATTTTTCAAGCGAATCCAGGTTTCTTCTAAATTTGATGGAAAAACTCAAGCCAGAGAACAGTAGTTCTGCTACCCCAAAAGCAGAAAGCACCATACATAATTTCGGTTTTCGTGACACTGCTTCTGAAAATATTGGTGGTGGACAGTTCGTGTCACCCATTCGAAATAGTACCAATTTCAGCAGAGAATATGGTACACCCAACCAAGGTGTTCAGTATGGGAACCAGTACAGTAGCTCTAGGCCTTCTCCATCCACACCGCTTAACTCGAACACATACTGCAACAGCTGTGGGGGTTCTGGCCACAGCTCAACGAACTGCCCGAGTATCATGAGTGGTCCTGCACTGTCTGTTGGAGGTGGGATGTATTCAAATCAAGCTTCTGGCCCTTCGGGTGGTACCTCCGGTGAATGCTTCAAATGCCATCAAACTGGGCATTGGGCTAGGGATTGCCCTGGCTTGGCCAATGTCCCTCCAGCTTATGGTAACCGTGGCTTCACGGCTAGGTGA 2586 43.58 MAASMASSKLTEGAVMVICKRESSAETFQPILQVIDLKLVNTSQQSGSERFRLLVSDGTHFQQGMLGTQLNELVKSGKLQKGSIVRLRQYVCNPVQERLIIIVIELDVIEEMCDIIGEPVSATRSSANALSGNPLPSVGGLGASPGSGMIGKGNVSSASFEQPKVNQSHVPHMGSYSNPPETGRFSASIAPPSYSKTDSGSRFNGPSPLTGSYGDQKMAYHNSGSDIPRPPLNSNAYARPQPIYQQPPSMYSNRGPIAKNEAAPRIMPISALNPYQGRWTIKARVTSKGELRHYNNPRGDGKVFSFDLLDAYRGEIRVTCFNTVADQFYNQIESGKVYFISKGSLKPAQKNFNHLKNDYEIFLENTSTIQPCFEDDQSIPQQQFHFHQIGEIEGMDSNSVVDVIGVVSSINPATSLMRKNGTETQKRSLQLKDMSGRSVELTLWGNFCQAEGQRLQNMCDSGLFPVLAVKSSRVSDFNGKAVGTISTSQLFIEPDFPEAHSLREWFEREGRSTLSVSISREVASVGRTDVRKTISQIKDERLGTSEKPDWITVSATVSFIKVDSFCYTACPIMIGDRQCSKKVTNNGDGKWRCDRCDQSVDECDYRYILQLQIQDHTGLTWVTAFQEGGEEIMGIPAKRLYYLKYEEQDDEKFAEIIRKVLFTKFIMKLKIKEETFSDEQRVRSTVVKAESINFSSESRFLLNLMEKLKPENSSSATPKAESTIHNFGFRDTASENIGGGQFVSPIRNSTNFSREYGTPNQGVQYGNQYSSSRPSPSTPLNSNTYCNSCGGSGHSSTNCPSIMSGPALSVGGGMYSNQASGPSGGTSGECFKCHQTGHWARDCPGLANVPPAYGNRGFTAR* 862
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
3 835283 839951 + CsaV3_3G001070.1 Csa03g00107 521012

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Csa03g00107 861 CDD RPA1_DBD_A 268 371 - -
Csa03g00107 861 SMART c2hcfinal6 829 845 IPR001878 GO:0003676|GO:0008270
Csa03g00107 861 SMART c2hcfinal6 785 801 IPR001878 GO:0003676|GO:0008270
Csa03g00107 861 CDD RPA1_DBD_C 534 707 IPR013955 -
Csa03g00107 861 Gene3D - 378 515 IPR012340 -
Csa03g00107 861 Gene3D - 516 708 IPR012340 -
Csa03g00107 861 SUPERFAMILY Nucleic acid-binding proteins 265 378 IPR012340 -
Csa03g00107 861 CDD RPA1N 13 109 IPR007199 GO:0003677|GO:0005634|GO:0006260
Csa03g00107 861 Gene3D - 781 849 - -
Csa03g00107 861 ProSiteProfiles Zinc finger CCHC-type profile. 786 801 IPR001878 GO:0003676|GO:0008270
Csa03g00107 861 MobiDBLite consensus disorder prediction 748 780 - -
Csa03g00107 861 ProSiteProfiles Zinc finger CCHC-type profile. 830 844 IPR001878 GO:0003676|GO:0008270
Csa03g00107 861 Pfam Replication protein A OB domain 389 492 IPR031657 -
Csa03g00107 861 TIGRFAM rpa1: replication factor-a protein 1 (rpa1) 243 707 IPR004591 GO:0003677|GO:0005634|GO:0006260|GO:0006281|GO:0006310
Csa03g00107 861 PANTHER REPLICATION PROTEIN A SUBUNIT 9 743 - -
Csa03g00107 861 CDD RPA1_DBD_B 400 507 - -
Csa03g00107 861 Pfam Replication factor-A C terminal domain 550 701 IPR013955 -
Csa03g00107 861 Pfam OB-fold nucleic acid binding domain 279 364 IPR004365 GO:0003676
Csa03g00107 861 MobiDBLite consensus disorder prediction 150 219 - -
Csa03g00107 861 Pfam Zinc knuckle 829 844 IPR001878 GO:0003676|GO:0008270
Csa03g00107 861 PANTHER REPLICATION FACTOR A 1, RFA1 9 743 IPR004591 GO:0003677|GO:0005634|GO:0006260|GO:0006281|GO:0006310
Csa03g00107 861 MobiDBLite consensus disorder prediction 140 228 - -
Csa03g00107 861 SUPERFAMILY Retrovirus zinc finger-like domains 811 850 IPR036875 GO:0003676|GO:0008270
Csa03g00107 861 SUPERFAMILY Nucleic acid-binding proteins 8 117 IPR012340 -
Csa03g00107 861 Pfam Replication factor-A protein 1, N-terminal domain 10 110 IPR007199 GO:0003677|GO:0005634|GO:0006260
Csa03g00107 861 SUPERFAMILY Nucleic acid-binding proteins 531 708 IPR012340 -
Csa03g00107 861 Gene3D - 265 374 IPR012340 -
Csa03g00107 861 SUPERFAMILY Nucleic acid-binding proteins 384 511 IPR012340 -
Csa03g00107 861 Gene3D - 8 123 IPR012340 -
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Csa03g00107 K07466 RFA1, RPA1, rpa; replication factor A1 - csv:101211358 1732.23
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
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
Vvi2g886 . . . . . Bpe07g00251 . . Cmo06g00609 Cmo16g01260 . . . . . Cpe14g01003 . . . . . . . . Cla10g00108 Cam10g0103 Cec10g0110 Cco10g0112 Clacu10g0107 Cmu10g0955 Cre10g0366 . . . . Lsi07g01137 . . Cme06g02413 . . . . . . . Bma12g00253 . . . Cma06g00602 Cma16g01216 Car06g00537 Car16g01142 . . . . . . . . . . . . . . . . . Csa03g00107 Chy06g02198 .
       

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
OG0008728 0 2 1 1 1 1 2 1 1 1 1 1 2 1 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1 35
       

Transcriptome

Select Gene Chr Type da1 da2 da3 da4 da5 da6 da7 da8 da9 da10
Csa03g00107 Csa_Chr03 FPKM 1.736388 1.738645 1.726261 1.744925 3.259202 3.829242 3.630352 6.655306 6.2642 6.999573