Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Cma16g01216 ATGGCAGCATCAATGGCGCCTTTTAAGCTGACGGAAGGAGCAGTGATGGTGATATGCAAGCGAGAATCGTCGGAAGAGACGTTCCAGCCGGTTGTACAAGTAATTGACTTAAAATTTGTTAACACTACGCAACAATCGGGCAGCGAGAGGTACAGATTGTTGCTTTCTGATGGAACTCATTACCAGCAAGGAATGCTGGGCACTCAGCTCAATGGATTGGTTAAGTCCGGGAAGTTACAGAAAGGTTCCATCGTTCAATTGCGGCAGTATGTTTGTAATCCCGTTCAAGAACGCCTAATTATAATCGTCATTGAGTTGGATGTGATAAAGGAAATGTGTGACTTTATTGGCGAGCCTGTTCCAGCAACAAGATCAGTATCAGCCGCATTTAGTGGAAACCCTCAATCCTCTGTGGGGGCTTCATCCGGCAGCGGAATAGTTGGTAATGTGAATGTATCTGGTGCGTCTTTTGAACAGCCTAAAGTGAATCAATCACAAGTACCGCATGTGGGATTTCATTTTAATACTCCTAATTCTGGAACAAGGTTTAATGGTTCATCTCCTGTAACTGGGTCATATGGTGATCAGAAGATGGCATACCACAACAATGGATCGGATATTCCCAGGTCACCTCTAAATGCTTATGCTTATGCCCCTCCTCAGCCAATACATCAGCAGCCACCTTCAATGTACAGTAATAGGGGAGGACCGGTAGCAAAAAATGAAGCTCCCCCAAGGATAATGCCTATTACTGCTCTGAACCCTTACCAAGGAAGGTGGACAATAAAGGCTCGAGTTACTTCGAAAGGAGAACTTAGAGACTACAATAATCCTCGTGGAGATGGGAAAGTGTTTTCATTTGATCTACTTGATGCATACGGTGGAGAAATACGAGCAACATGCTTCGATATGGTAGCTGATCAGTTTTACAACCAGATTGAATCGGGTAACGTATACTTCATTTCTAAAGGAAGCTTGAAACCTGCACAGAAGAACTATAACCATCTCAATAATGACTTTGAAATATTTCTTGAAAACACATCAACAATCCAACCTTGCTTTGAGGATGACCAATCAATCCCCCATCAGCAGTTTCATTTCCATCACATTAGTGAGATTGAGGGCATGGACAGCAACAGTGTTGTAGATGTAATTGGTGTTGTTTCTTCCATTAATCCTGCAACGTCTCTCATGAGAAAAAATGGTACTGAGACTCAGAAGAGATCCCTTCAGTTGAAAGATATGTCTGGCCGAAGTGTTGAATTGACTCTTTGGGGAAACTTTTGTCAAGCAGAAGGGCAAAAATTGCAAAACATGTGCGACTCGGGGTTGTTCCCAGTTTTGGCTGTGAAATCTGGTAGAGTGAGCAACTTCAATGGGAAGGCGGTGGGAACCATTTCAACAAGTCAGCTTTTCGTAGAGCCAGATTTCCCCGAGGCTCGTACATTAAGAGGGTGGTTCGAAAAGGAAGGAAGGAGCACTCCTTCTGTCTCCATATCCAGGGAAGTTGCTACCGTGGGTAGGACAGATGCCCGTCAGACCATATCTCAAATAAAAGATGAGAGGTTAGGAACCTCTGAGAAGCCAGATTGGATCACTGTTAGTGCAACTGTTTCATTCATTAAGGTTGATAATTTCTGTTACACAGCATGTCCTATCATGATCGGGGATCGTCAATGCAGCAAAAAGGTTACAAATAACGGAGATGGAAAATGGAGATGCGACCGGTGTGATCAGTCTGTCGACGAATGTGACTACAGGTACATATTGCAGCTGCAAATACAGGATCATACTGGCTTAACTTGGGTGACAGCATTTCAAGAAGGCGGTGAGGAGATCATGGGCATACCTGCAAAAAGATTGTACTATTTGAAATACGAAGAACAAGATGATGAAAAATTTGCAGAAATCATCCGTAAAGTTCTTTTTACAAAATTTATTATGAAGTTGAAAGTAAAGGAAGAGACTTTTAGTGATGAACAGAGTGAAATCAACGGTCATGAAAGCAGAAAGCATTAA 2019 42.69 MAASMAPFKLTEGAVMVICKRESSEETFQPVVQVIDLKFVNTTQQSGSERYRLLLSDGTHYQQGMLGTQLNGLVKSGKLQKGSIVQLRQYVCNPVQERLIIIVIELDVIKEMCDFIGEPVPATRSVSAAFSGNPQSSVGASSGSGIVGNVNVSGASFEQPKVNQSQVPHVGFHFNTPNSGTRFNGSSPVTGSYGDQKMAYHNNGSDIPRSPLNAYAYAPPQPIHQQPPSMYSNRGGPVAKNEAPPRIMPITALNPYQGRWTIKARVTSKGELRDYNNPRGDGKVFSFDLLDAYGGEIRATCFDMVADQFYNQIESGNVYFISKGSLKPAQKNYNHLNNDFEIFLENTSTIQPCFEDDQSIPHQQFHFHHISEIEGMDSNSVVDVIGVVSSINPATSLMRKNGTETQKRSLQLKDMSGRSVELTLWGNFCQAEGQKLQNMCDSGLFPVLAVKSGRVSNFNGKAVGTISTSQLFVEPDFPEARTLRGWFEKEGRSTPSVSISREVATVGRTDARQTISQIKDERLGTSEKPDWITVSATVSFIKVDNFCYTACPIMIGDRQCSKKVTNNGDGKWRCDRCDQSVDECDYRYILQLQIQDHTGLTWVTAFQEGGEEIMGIPAKRLYYLKYEEQDDEKFAEIIRKVLFTKFIMKLKVKEETFSDEQSEINGHESRKH 672
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
16 9204013 9206444 - CmaCh16G012160.1 Cma16g01216 311814

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Cma16g01216 672 Gene3D - 246 355 IPR012340 -
Cma16g01216 672 Gene3D - 8 123 IPR012340 -
Cma16g01216 672 SUPERFAMILY Nucleic acid-binding proteins 246 359 IPR012340 -
Cma16g01216 672 PANTHER REPLICATION FACTOR A 1, RFA1 6 665 IPR004591 GO:0003677|GO:0005634|GO:0006260|GO:0006281|GO:0006310
Cma16g01216 672 Pfam Replication factor-A C terminal domain 531 661 IPR013955 -
Cma16g01216 672 Gene3D - 359 497 IPR012340 -
Cma16g01216 672 CDD RPA1_DBD_A 249 352 - -
Cma16g01216 672 Pfam Replication protein A OB domain 370 473 IPR031657 -
Cma16g01216 672 SUPERFAMILY Nucleic acid-binding proteins 365 493 IPR012340 -
Cma16g01216 672 PANTHER REPLICATION PROTEIN A SUBUNIT 6 665 - -
Cma16g01216 672 Pfam OB-fold nucleic acid binding domain 260 341 IPR004365 GO:0003676
Cma16g01216 672 Gene3D - 498 667 IPR012340 -
Cma16g01216 672 CDD RPA1_DBD_B 381 488 - -
Cma16g01216 672 CDD RPA1_DBD_C 515 661 IPR013955 -
Cma16g01216 672 SUPERFAMILY Nucleic acid-binding proteins 8 117 IPR012340 -
Cma16g01216 672 SUPERFAMILY Nucleic acid-binding proteins 512 661 IPR012340 -
Cma16g01216 672 Pfam Replication factor-A protein 1, N-terminal domain 10 111 IPR007199 GO:0003677|GO:0005634|GO:0006260
Cma16g01216 672 TIGRFAM rpa1: replication factor-a protein 1 (rpa1) 236 661 IPR004591 GO:0003677|GO:0005634|GO:0006260|GO:0006281|GO:0006310
Cma16g01216 672 CDD RPA1N 13 110 IPR007199 GO:0003677|GO:0005634|GO:0006260
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Cma16g01216 K07466 RFA1, RPA1, rpa; replication factor A1 - csv:101211358 1150.96
       

WGDs- Genes

Select Gene_1 Gene_2 Event_name
Cma06g00602 Cma16g01216 CST
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Cma05g01409 Cma-Chr5:10498054 Cma16g01216 Cma-Chr16:9204013 0 dispersed
Cma11g00209 Cma-Chr11:1047706 Cma16g01216 Cma-Chr16:9204013 1.53E-78 dispersed
Cma16g01216 Cma-Chr16:9204013 Cma06g00602 Cma-Chr6:2913219 0 transposed
       

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
Cma09g01213 . 106 793 Core DNA Replication Machinery Family AT4G14700 67.2 9.8e-271 930.2
Cma09g01213 . 73 793 Core DNA Replication Machinery Family AT4G12620 67.7 1.1e-282 969.9
Cma12g00526 . 2 361 Core DNA Replication Machinery Family AT2G37560 67.2 1.3e-142 503.4
Cma04g01092 . 9 418 Core DNA Replication Machinery Family AT2G01120 65.5 4.2e-156 548.5
Cma17g00438 . 92 588 Core DNA Replication Machinery Family AT4G29910 58.3 3.6e-163 572.4
Cma05g00856 . 1 261 Core DNA Replication Machinery Family AT1G26840 67.8 3.7e-92 335.5
Cma06g01701 CST 1031 1774 Core DNA Replication Machinery Family AT1G79150 56.9 8.6e-230 794.3
Cma06g01755 . 218 1156 Core DNA Replication Machinery Family AT1G44900 75.4 0.0e+00 1344.3
Cma14g01060 . 9 939 Core DNA Replication Machinery Family AT1G44900 75.2 0.0e+00 1337.0
Cma07g00117 CST 1 572 Core DNA Replication Machinery Family AT5G46280 81.5 3.2e-268 921.4
Cma03g01388 CST 1 224 Core DNA Replication Machinery Family AT5G46280 54.4 9.2e-66 248.8
Cma19g00684 . 20 884 Core DNA Replication Machinery Family AT2G16440 75.1 0.0e+00 1149.4
Cma11g01087 . 107 738 Core DNA Replication Machinery Family AT2G16440 64.9 3.9e-262 901.7
Cma12g01169 . 1 735 Core DNA Replication Machinery Family AT2G07690 78.6 0.0e+00 1116.3
Cma07g00004 . 523 1345 Core DNA Replication Machinery Family AT5G44635 72.8 0.0e+00 1189.9
Cma17g01031 . 8 719 Core DNA Replication Machinery Family AT4G02060 85.8 0.0e+00 1221.8
Cma08g00472 . 11 690 Core DNA Replication Machinery Family AT4G02060 85.3 0.0e+00 1152.9
Cma20g00352 . 30 509 Core DNA Replication Machinery Family AT2G29680 59.8 1.1e-158 557.4
Cma20g00352 . 30 479 Core DNA Replication Machinery Family AT1G07270 59.1 2.4e-144 509.6
Cma08g00225 . 238 830 Core DNA Replication Machinery Family AT3G25100 76.1 4.4e-260 894.4
Cma17g01271 . 241 833 Core DNA Replication Machinery Family AT3G25100 76.6 2.2e-256 882.1
Cma06g00352 . 39 805 Core DNA Replication Machinery Family AT3G09660 74.4 0.0e+00 1109.7
Cma19g00466 . 16 642 Core DNA Replication Machinery Family AT2G14050 78.3 1.0e-286 983.0
Cma20g00753 . 1 398 Core DNA Replication Machinery Family AT2G20980 55.0 8.3e-114 407.9
Cma09g00770 . 7 968 Core DNA Replication Machinery Family AT1G77320 50.1 6.7e-261 897.9
Cma08g00461 CST 25 146 Core DNA Replication Machinery Family AT4G02110 56.5 4.5e-38 157.9
Cma08g00673 . 1 192 Core DNA Replication Machinery Family AT1G80190 66.5 5.2e-72 268.1
Cma07g01186 . 1 145 Core DNA Replication Machinery Family AT3G12530 72.4 3.1e-61 231.9
Cma04g02907 . 1103 1270 Core DNA Replication Machinery Family AT1G19080 61.3 1.7e-53 206.5
Cma04g02907 . 1103 1270 Core DNA Replication Machinery Family AT3G55490 61.3 1.7e-53 206.5
Cma14g02049 . 15 164 Core DNA Replication Machinery Family AT5G49010 66.7 5.7e-52 201.4
Cma02g00514 . 1 1546 Core DNA Replication Machinery Family AT5G67100 60.4 0.0e+00 1763.4
Cma18g00719 . 2 620 Core DNA Replication Machinery Family AT1G67630 63.8 1.8e-224 776.2
Cma08g00169 . 498 940 Core DNA Replication Machinery Family AT1G67320 65.3 1.8e-182 636.3
Cma09g01290 . 39 477 Core DNA Replication Machinery Family AT5G41880 65.3 1.1e-175 613.6
Cma07g00817 . 1 1086 Core DNA Replication Machinery Family AT5G63960 81.1 0.0e+00 1807.7
Cma14g00418 . 1 438 Core DNA Replication Machinery Family AT2G42120 75.6 1.7e-205 712.6
Cma08g00169 . 498 940 Core DNA Replication Machinery Family AT1G67320 65.3 1.8e-182 636.3
Cma02g01335 . 1 2094 Core DNA Replication Machinery Family AT1G08260 70.4 0.0e+00 2946.0
Cma02g01335 . 9 2200 Core DNA Replication Machinery Family AT2G27120 67.4 0.0e+00 2919.4
Cma01g00753 . 529 1044 Core DNA Replication Machinery Family AT5G22110 65.8 1.5e-192 669.8
Cma02g01296 . 1 928 Core DNA Replication Machinery Family AT5G22010 62.4 3.1e-305 1045.0
Cma20g00138 CCT,ECH 67 182 Core DNA Replication Machinery Family AT5G22010 64.1 7.2e-36 150.2
Cma16g01020 . 1 333 Core DNA Replication Machinery Family AT1G63160 89.5 7.3e-172 600.5
Cma03g00215 . 1 335 Core DNA Replication Machinery Family AT5G27740 83.3 1.7e-166 582.8
Cma01g01369 . 1 336 Core DNA Replication Machinery Family AT1G21690 80.7 6.4e-152 534.3
Cma15g00666 . 1 363 Core DNA Replication Machinery Family AT1G77470 75.3 6.5e-153 537.7
Cma04g02374 . 1 363 Core DNA Replication Machinery Family AT1G77470 73.0 2.1e-148 522.7
Cma05g01409 . 26 604 Core DNA Replication Machinery Family AT2G06510 68.8 1.8e-245 845.9
Cma06g00602 CST 34 701 Core DNA Replication Machinery Family AT2G06510 52.2 6.2e-201 698.0
Cma16g01216 CST 34 661 Core DNA Replication Machinery Family AT2G06510 52.1 9.3e-189 657.5
Cma11g00209 . 1 623 Core DNA Replication Machinery Family AT5G08020 67.3 3.8e-243 838.2
Cma06g00602 CST 10 808 Core DNA Replication Machinery Family AT5G45400 51.1 6.3e-228 788.1
Cma16g01216 CST 10 661 Core DNA Replication Machinery Family AT5G45400 54.5 1.0e-206 717.6
Cma11g00209 . 1 618 Core DNA Replication Machinery Family AT5G61000 65.4 3.6e-236 815.1
Cma06g00602 CST 5 822 Core DNA Replication Machinery Family AT4G19130 53.1 2.1e-230 796.2
Cma16g01216 CST 5 661 Core DNA Replication Machinery Family AT4G19130 58.8 2.8e-214 742.7
Cma11g01183 . 1 376 Core DNA Replication Machinery Family AT5G26680 85.7 1.6e-184 642.9
Cma14g01944 . 1 1102 Core DNA Replication Machinery Family AT1G08840 51.8 8.7e-296 1013.8
Cma14g01473 . 1 297 Core DNA Replication Machinery Family AT2G25100 67.3 2.4e-115 412.5
Cma20g00522 . 44 804 Core DNA Replication Machinery Family AT1G08130 68.3 1.2e-292 1003.0
Cma20g00522 . 204 804 Core DNA Replication Machinery Family AT1G49250 68.4 8.0e-239 823.9
       

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
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
Cma16g01216 Cma_Chr16 FPKM 0.099458 0.202743 1.164146 1.625275 3.654716 3.082812 4.42729 1.391888 1.528245 1.48042