At2g24120 SYNGENTA 11913
Genomic Sequence (from TAIR)
aaaaaaccgcagcgtagcgcggatgatcatctaatggctaataataattacccaaacaaaataatattccttctgtatttttagttagtgtttaagagtt ttacacacaaattaaagaatcatttagggagcttattggttcttgcattttttctactgatgataaaacaatcaacatattatatttcgtcaacactaat taatttttacatggtctaaaacatcaactaaaaaatacaaggggatatttaatgttcatattccctatattttgttttttaattaaatgtatttgttttt ctgaatattttataaatcattctagaaatacaatggattttctttttttgatatatttggggaaaaaaacaaaagagtagaggttttagagaggtttgtt ggattgttttgctctcaaaatttctttctcttcttcaaatgttcattggaagaccaataccttatcttctactatcttcaccttccttccATGGCTTCCG CTGCGGCGGCTTCTCCTTCTCTCTCCTTAAACCCAACCTCTCATTTCCAACACCAAACTTCTCTCGTCACCTGGCTTAAACCTCCTCCCTCCTCCGCCCT CTTCCGCCGCAAAACCCTTCCTTTCTTCGAACGCCACTCACTTCCGATTTCAGCTTCTTCTTCTTCTTCTTCTTCCTCTTCTACTTCCCTCTCCGTTCAC GAGAAACCCATTTCGAATTCGGTTCACTTCCACGGCAATCTCATCGAGAGCTTCGAGAATCAGGACTCTTCATACGCTGGAACCATTAAAGGAGCAAGCT TGATTGAGGAGCTTGAGAATCCTGTCGAAAGGAATGGACTTTCTGGTCGGAGAAGACTGTTTATGCAAGACCCACCATGGATCTCTGCTTTGTTTCTCAA GGGTTTGAGTAAAATGGTTGATCAGACTTTGAAAATCGAGCGGAAAGATATCGATAAGAGGAAATTTGATTCCTTGAGGAGACGACAAGTGAAGGAAGAG ACTGAAGCGTGGGAGAGGATGGTTGATGAGTACAGAGATTTGGAGAAGGAGATGTGTGAGAAGAATCTAGCTCCGAATTTGCCTTATGTGAAACATATGT TCTTGGGATGGTTTCAACCTTTGAAAGATGTGATTGAGAGAGAGCAGAAGTTGCAGAAGAATAAGAGCAAGAAGGTTAGAGCAGCTTATGCTCCTCATAT TGAGCTTTTGCCTGCTGATAAAATGGCGGTTATTGTGATGCATAAGATGATGGGTTTGGTTATGTCTGGACATGAAGATGGGTGTATCCAAGTTGTTCAA GCTGCTGTTAGTATTGGCATAGCTATTGAGCAGGAGgtatgaatgagtagtaattcaatttgtttctataaagaaatgatgtgttgagtcgtggttttgg ttgatctcttagGTGAGGATTCATAACTTCTTGAAGAGAACTAGGAAGAACAATGCAGGGGACTCACAAGAGGAATTGAAAGAAAAGCAATTGCTTAGGA AACGTGTTAATAGTTTGATTCGAAGGAAAAGGATTATTGACGCATTAAAAGTGGTGAAAAGTGAA◄GGT►ACCAAACCATGGGGACGAGCTACACAAGCT AAGgtctggctttgataattcgtttgagtgaaattatagtatttgcctttggtattgacacatttcatctttgttgttgggcttatgctaaatttcagCT TGGAAGCCGTCTGCTAGAACTATTGATCGAAGCAGCTTATGTGCAACCTC◄CCTTGACCCAGTCTGGGGACTCTATACCCGAGTTTCGACCTGCATTCAG ACACAGGTTTAAAACTGTGACTAAATATCCAGGgtgagagaaatcctcaaaatgagtacccatctctttatttgtttttctagtcagttgttttatgtat agaaccgtctattgcaagaaagttgtttttttctcaactgggatatatgcttatggtgtagagtttacttatcactggaacttgcagGTCTAAGCTGGTG AGGAGGTATGGAGTTATTGAATGTGACTCGCTCCTTCTTGCAGGACTAGATAAATCTgtgagttaagatgtcttttttatcattccattcatgagctgtt aggtgatcttttattgtttttttgtctcatgcagGCTAAGCATATGTTAATTCCTTATGTTCCGATGTTAGTGCCACCAAAGAGATGGAAAGGgtatgct ttgaaaaactctttcttgttttgctctagattttatccccttatgaatcatgccctattattgagaaccacacattatttttagccatgggtttctcgtg cttacgtatgcaaatgctgtgacattttcttcagATATGACAAGGGTGGTTACTTGTTTTTACCTTCCTATATCATGCGTACTCATGGATCCAAAAAGCA GCAAGATGCACTGAAAGATATTAGTCACAAGACTGCTCATAGAGTATTTGAGgtacattggtatttcgctcttgtaatatatattttgttgttgctctca ggtaatgtattatattaatattccgaaattgaacttgaatagGCATTGGATACACTTGGGAATACCAAGTGGAGGGTGAATAGGAATATACTTGATGTGG TAGAAAGGCTCTGGGCTGATGGAGGCAACATTGCAGGCTTAGTTAATCGTGAAGATgtaagtcactagaaatgttatgagatttctgaacttttaccttt cattgtttcatttcaagagttaattaatctgcatagttataggttttaatggtatgtgtctgacgtatttttgttctctttcttattttatttttgttta gGTTCCCATACCCGAAAAACCATCCTCTGAGGATCCTGAAGAACTCCAGTCCTGGAAATGGAGTGCTCGAAAGGCCAACAAGATTAACAGAGAGAGGCAT TCTCTAAGATGTGATGTTGAGCTCAAACTTTCTgtaagaaatacattcttactgcttaagacttttcgttccgtcttcacttaactaggaaaagatatag actaaaggttatcattgcagGTGGCTAGAAAAATGAAGGACGAAGAAGGATTCTACTACCCTCACAATCTTGACTTTAGAGGCCGTGCATACCCAATGCA TCCTCATCTGAATCATCTGAGTTCTGATCTTTGCCGTGGAACCCTGGAGTTTGCTGAAGGACGACCACTTGGAAAGTCAGGCTTGCATTGGCTGAAAATA CATTTAGCAAACCTCTATGCAGGTGGTGTTGAAAAGCTCTCACATGATGCCCGTCTGGCTTTCGTGGAAAACCATTTGGATGATATAATGGATTCAGCTG AAAATCCTATACATGGAAAACGATGGTGGTTAAAGGCTGAAGATCCGTTTCAGTGTTTAGCTGCATGTGTTATTCTGACACAAGCCTTGAAAAGCCCTTC ACCTTATTCAGTAATTTCCCACTTGCCTATTCATCAGgtaagcaccgtaaacttatatccaaagttatcctactctttttagttacttgacacttgcttt ctgtagaagattctaggttggggaattcagtagactgtttgcttttcccttttgttaagtttttaattggtttcaccagatatggtctttccattgggat ctgaatcaactgtgctatactcttttcaaagaatctgtgaattcttaaacaacactttttccttgaatcatttctatgtgcagGATGGGTCGTGCAATGG TCTACAGCATTATGCAGCTTTAGGAAGAGATAGTgtagcctctcttgtgaacatttataatatgcttttttctcttagtaattttcaatctcatatagtt ctcttcttgtaaactggcttctctcagTTTGAAGCTGCGGCAGTTAATCTAGTTGCAGGAGAAAAACCAGCTGATGTCTACTCTGAAATTTCACGGAGgt atcatatcaattttgaatggagtagctgtcaatttcatttattcgagttggaatcatgtcaggtgtagcttcttatggtttttctctctgtctctctttc tcactcctctcttctttgcttgtgctgagatagAGTTCATGAAATAATGAAGAAGGACAGCAGTAAGGATCCTGAGTCAAACCCAACCGCCGCACTGGCA AAGATCCTTATCACTCAAgtgagtatcaacggtttttgattgaacattatgccacagcaaaagttcttcccagtgatgcaatgttttcttctaatttcag GTCGACAGGAAGCTGGTAAAGCAGACGGTAATGACGTCAGTATATGGTGTCACCTATGTAGGGGCTCGTGAACAAATAAAAAGAAGATTAGAAGAGAAAG GTGTTATCACTGACGAGAGAATGTTATTTGCTGCTGCTTGCTATTCTGCAAAAgtaagaagaatagtggcattcacgcggataaatgttattttgttttt agctatgtactaatgttatacttgaaacatttctcctcagGTGACGCTAGCTGCCCTTGGAGAGATATTTGAAGCGGCACGTGCCATTATGAGTTGGCTT GGTGATTGTGCAAAGgtgtggtcttgtagcatgtttattaactctgctcttctacgtttagtaaatagagacttactagtgttttctttttgacttgtca attttacagATAATTGCTTCCGATAATCATCCAGTGCGATGGATCACCCCTCTTGGGCTTCCTGTTGTGCAACCCTATTGCAGAAGTGAAAGACATCTGg taagtattatccattaagaatccttcatgttatttaaaaatcatctctctgcgagccaataattttgactttgtaatcaaatatggccactgtgattaca gATAAGAACATCTCTTCAGGTTTTGGCTCTGCAGCGAGAGGGTAACACGgtaaagccgatttgtttgtttctttgttttcactgagcaagactatcagtg ggtctttgcttaaagactatcaattcgcagGTCGATGTTAGGAAACAAAGAACTGCATTTCCTCCCAACTTTGTGCACTCGCTGGACGGCACTCACATGA TGATGACTGCTGTTGCATGTCGAGAGGCCGGCCTAAACTTTGCAGgttagttctgtcaattcgactaatggcctaccaacaaaaaaagaagtattatctt cttattgaatgcttgggttctgcagGTGTGCATGACTCATACTGGACCCATGCATGTGACGTTGACACAATGAACAGAATACTTAGAGAGAAATTCGTTG AGCTTTACAACACACCGATCCTTGAAGATgtaagttttcgataactctctagttagaagcttaggactaaacgtctgactttctttttctgcacatctgc caaaacaaatgaatgtggttttcaccagacgattttcaaatcgtatgtgaagtattttccagcttttactgatcacaagtttatacttacgatcacaaga aatcctgaaacaaagctatctttattgaatatcaacattaatgatgatgctctagttagtacttctttctctaactgtatttaggatttgattgaagcgt ttgtatgaattacagcctcgattggcttgttgatattgttgtgttcttgatacagTTGCTCCAAAGTTTCCAAGAATCATACCCGAATCTCGTGTTTCCT CCAGTACCAAAGAGAGGTGATTTCGATTTAAAGGAAGTTCTCAAATCACAGTACTTCTTCAACTGAgtcatgcatgtagcaccagtgaaccatctgaaga agggagcaagtttttgacgcagggatcttccttggtggcctgtaaataacatccaccacctcaaaatgacatggaaagaaccagaaatgtgcaagaaaga caaactgatactgcaacacactaagattctgacataaattatcttgcagcagaagaggaattcagacaaatctacttagagaaattttggcagcattgaa gaagtttctagctcagtaggtaggtcctagacagtcttgaataattgatgtaaggtatgagtcatttgcatcaagcttgtttttggagatgagattagga ttagagttgtgttgtatctgtcattcgtaatgttgtacagagagagacttcatatacaaaacaagaacacaataacgatgatttagtaagtttaaagaaa atttagcaatgaatgggtcatcaggatttcagggcctgagtcccaaagcccattttattataactacgaatctgccgcttttgcgatttAGGGTCATTTT CTC
Border_1 (11913_LB2U)
TTCTGTTTCTATTCCAACTTTTTCTTGATCCGCAGCCATTAACGACTTTTGAATAGATACGCTGACACGCCAAGCCTCGCTAGTCAAAAGTGTACCAAAC
AACGCTTTACAGCAAGAACGGAATGCGCGTGACGCTCGCGGTTACGCCATTTCGCCTTTTCAGAAATGGATAAATAGCCTTGCTTCCTATTATATCTTCC
CAAATTACCAATACATTACACTAGCATCTGAATTTCATAACCAATCTCGATACACCAAATCGAATTCAATTCGGCGTTAATTCAGTATAATTCGACCTTA
GTTGTTCATACTATAATTTCACTTTTCACCACTTTTAATGCGTCAATAATCCTTTTCCTTCGAATCAAACTATTAACACGTTTCCTAAGCAATTGCTTTT
CTTTCAATTCCTCTTGTGAGTCCCCTGCATTGTTCTTCCTAGTTCTCTTCAAGAAGTTATGAATCCTCACCTAAGAGATCAACCAAAACCACGACTCAAC
ACATCATTTCTTTATAGAAACAAATTGAATTACTACTCATTCATACCTCCTGCTCAATAGCTATGCCAATACTAACAGCAGCTTGAACAACTTGGATACA
CCCATCTTCATCTCACTCGACA
| Start of BLAST Alignment: | NT 1258 / Exon 3 of 19 |
| First 15 bp Perfect Match: | NT 1075 / Exon 2 of 19 |
BLAST Details: Query Sequence: 11913_LB2U Length: (622 letters) Database: Genes from AGI, Total Genome (DNA); Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N At2g24120 68415.t02694 DNA-directed RNA polymerase, chlor... 1491 1.0e-61 1 At2g48060 68415.t05482 hypothetical protein 182 0.9991 1 >At2g24120 68415.t02694 DNA-directed RNA polymerase, chloroplast (RPOPT) identical to SP|O24600 DNA-directed RNA polymerase, chloroplast precursor (EC 2.7.7.6) {Arabidopsis thaliana} Length = 5725 Minus Strand HSPs: Score = 1491 (229.8 bits), Expect = 1.0e-61, P = 1.0e-61 Identities = 409/501 (81%), Positives = 409/501 (81%), Strand = Minus / Plus Query: 622 TGTCGAGTGAGATGAAGATGGGTGTATCCAAGTTGTTCAAGCTGCTGTTAGTATTGGCAT 563 |||| | || ||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 884 TGTCT-G-GACATGAAGATGGGTGTATCCAAGTTGTTCAAGCTGCTGTTAGTATTGGCAT 941 Query: 562 AGCTATTGAGCAGGAGGTATGAATGAGTAGTAATTCAATTTGTTTCTATAAAGAAATGAT 503 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 942 AGCTATTGAGCAGGAGGTATGAATGAGTAGTAATTCAATTTGTTTCTATAAAGAAATGAT 1001 Query: 502 GTGTTGAGTCGTGGTTTTGGTTGATCTCTTAGGTGAGGATTCATAACTTCTTGAAGAGAA 443 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 1002 GTGTTGAGTCGTGGTTTTGGTTGATCTCTTAGGTGAGGATTCATAACTTCTTGAAGAGAA 1061 Query: 442 CTAGGAAGAACAATGCAGGGGACTCACAAGAGGAATTGAAAGAAAAGCAATTGCTTAGGA 383 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 1062 CTAGGAAGAACAATGCAGGGGACTCACAAGAGGAATTGAAAGAAAAGCAATTGCTTAGGA 1121 Query: 382 AACGTGTTAATAGTTTGATTCGAAGGAAAAGGATTATTGACGCATTAAAAGTGGTGAAAA 323 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 1122 AACGTGTTAATAGTTTGATTCGAAGGAAAAGGATTATTGACGCATTAAAAGTGGTGAAAA 1181 Query: 322 GTGAAATTATAGTATGAACAACTAAGGTCGAATTATACTGAATTAACGCC--GAATTGA- 266 ||||| || | ||| | | || ||| || || | ||| | | | |||| Sbjct: 1182 GTGAAGGTACC--A--AACCA-TGGGGACGAGCTACACA-AGCTAAGGTCTGGCTTTGAT 1235 Query: 265 -ATTCGATTTG-GTGTA-TCG-AG-ATTGGT-TATGAAATT--CAGATGCTAGTGTAATG 214 ||||| |||| ||| | | || ||| | | || ||| || || | | | || Sbjct: 1236 AATTCG-TTTGAGTGAAATTATAGTATTTGCCTTTGGTATTGACACATTTCA-TCTT-TG 1292 Query: 213 TA-TTGGTAATTTGGGAAGATATAA--TAGGAAGCAAGGCTATTT-ATCCATTTCT-GAA 159 | |||| | || || || | | | |||||| | || | | | ||| | ||| Sbjct: 1293 TTGTTGGGCTTATGCTAA-ATTTCAGCTTGGAAGCC-GTCTGCTAGAACTATTGATCGAA 1350 Query: 158 AAGGCGAAATGGCGTAACCGC 138 || | || | |||| | Sbjct: 1351 GCAGCTTA-TGT-GCAACCTC 1369 >At2g48060 68415.t05482 hypothetical protein Length = 4587 Minus Strand HSPs: Score = 182 (33.4 bits), Expect = 7.0, P = 0.9991 Identities = 112/178 (62%), Positives = 112/178 (62%), Strand = Minus / Plus
Border_2 (11913_LB1D)
GCCTTTTCAGAAATGGATAAATAGCCTTGCTTCCTATTATATCTTCCCAAATTACCAATACATTACACTAGCATCTGAATTTCATAACCAATCTCGATAC
ACCAAATCGAATTCAATTCGGCGTTAATTCAGTACATTAAAAACGTCCGCAATGTGTTATTAAGTTGTCTAAGCGTCAATTTGTTTACACCACAATATAT
CCTGAAACCAAACCATGGGGACGAGCTACACAAGCTAAGGTCTGGCTTTGATAATTCGTTTGAGTGAAATTATAGTATTTGCCTTTGGTATTGACACATT
TCATCTCTGATGCTACACAT
| Start of BLAST Alignment: | NT 1078 / Exon 2 of 19 |
| First 15 bp Perfect Match: | NT 1078 / Exon 2 of 19 |
BLAST Details: Query Sequence: 11913_LB1D Length: (320 letters) Database: Genes from AGI, Total Genome (DNA); Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N At2g24120 68415.t02694 DNA-directed RNA polymerase, chlor... 513 2.3e-17 1 At5g28415 68418.t03144 copia-like retrotransposon family ... 173 0.69 1 At3g61260 68416.t06335 DNA-binding family protein / remor... 161 0.9992 1 At3g24180 68416.t02737 expressed protein contains Pfam do... 162 0.9994 1 >At2g24120 68415.t02694 DNA-directed RNA polymerase, chloroplast (RPOPT) identical to SP|O24600 DNA-directed RNA polymerase, chloroplast precursor (EC 2.7.7.6) {Arabidopsis thaliana} Length = 5725 Plus Strand HSPs: Score = 513 (83.0 bits), Expect = 2.3e-17, P = 2.3e-17 Identities = 105/108 (97%), Positives = 105/108 (97%), Strand = Plus / Plus Query: 207 ACCAAACCATGGGGACGAGCTACACAAGCTAAGGTCTGGCTTTGATAATTCGTTTGAGTG 266 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 1190 ACCAAACCATGGGGACGAGCTACACAAGCTAAGGTCTGGCTTTGATAATTCGTTTGAGTG 1249 Query: 267 AAATTATAGTATTTGCCTTTGGTATTGACACATTTCATCTCTGATGCT 314 |||||||||||||||||||||||||||||||||||||||| || || | Sbjct: 1250 AAATTATAGTATTTGCCTTTGGTATTGACACATTTCATCTTTGTTGTT 1297 >At5g28415 68418.t03144 copia-like retrotransposon family has a 1.2e-302 P-value blast match to dbj|BAA78425.1| polyprotein [Arabidopsis thaliana] (AtRE1) (Ty1_Copia-element) Length = 4427 Plus Strand HSPs: Score = 173 (32.0 bits), Expect = 1.2, P = 0.69 Identities = 177/304 (58%), Positives = 177/304 (58%), Strand = Plus / Plus