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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcctgtacctaacgattttgttatgtttagttgatgccttttgatctttttcaaaataagatctcaccatgatggtctttaacgtgttgttttcttggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g59990.1
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|30228671|gb|CB966561.1|CB966561
EST:     CTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: CTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|38480261|gb|CF964350.1|CF964350
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88321645|gb|CI672786.1|CI672786
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|58604519|gb|CK015047.1|CK015047
EST:     GCAGGACA-TGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88351281|gb|CI623503.1|CI623503
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|58591772|gb|CF990080.1|CF990080
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88576762|gb|CI673287.1|CI673287
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|163922730|gb|EG712201.1|EG712201
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|163929077|gb|EG713022.1|EG713022
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|55434318|gb|CV730280.1|CV730280
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88579651|gb|CI688661.1|CI688661
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88336434|gb|CI649021.1|CI649021
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|14981286|gb|BI305964.1|BI305964
EST:     GAAAA-ATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88351707|gb|CI617432.1|CI617432
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88402814|gb|CI613262.1|CI613262
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88724029|gb|CI749288.1|CI749288
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88330914|gb|CI638322.1|CI638322
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|218481886|gb|FG948632.1|FG948632
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|86908394|gb|CI300774.1|CI300774
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|87018104|gb|CI275918.1|CI275918
EST:     TCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: TCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88350195|gb|CI623133.1|CI623133
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|55439109|gb|CV732856.1|CV732856
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|55434794|gb|CV730521.1|CV730521
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88350259|gb|CI623197.1|CI623197
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|55433285|gb|CV729700.1|CV729700
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|117244000|gb|CT848387.1|CT848387
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|55431287|gb|CV728657.1|CV728657
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88328544|gb|CI676754.1|CI676754
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|163928807|gb|EG711919.1|EG711919
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88327884|gb|CI648283.1|CI648283
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|33806682|gb|CF329222.1|CF329222
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88743518|gb|CI767026.1|CI767026
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88404907|gb|CI685341.1|CI685341
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88577347|gb|CI673923.1|CI673923
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTNAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|33654059|gb|CF276673.1|CF276673
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88571646|gb|CI663019.1|CI663019
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88327281|gb|CI645058.1|CI645058
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|33690835|gb|CF319074.1|CF319074
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|33690719|gb|CF318958.1|CF318958
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|55440029|gb|CV733325.1|CV733325
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88688905|gb|CI732481.1|CI732481
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaataagatctcaccatgatggtctttaacgtgttgttttcttggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG
                         ctttaac  putative branch site (score: 3)
                                      ttttcttg  putative PPT
                        tctttaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcctgtacctaacgattttgttatgtttagttgatgccttttgatctttttcaaaataagatctcaccatgatggtctttaacgtgttgttttcttggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT