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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggaactattgcctttcttctttgcaccttccctttttgcctggccatttgtttctgatcatagaatatctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATTCACCATTGCGCTGCTTGGACCCCCTTGGGCCATTTGTATCGTTTTGGTT

Basic information

species Oryza sativa
transcript LOC_Os12g01170.1
intron # 7
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|89187213|gb|CI047280.1|CI047280
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88544420|gb|CI472517.1|CI472517
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88531358|gb|CI459827.1|CI459827
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|13165397|gb|AU174194.1|AU174194
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88217599|gb|CI217448.1|CI217448
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88441589|gb|CI554813.1|CI554813
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|86500721|gb|CI143354.1|CI143354
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88846847|gb|CI005826.1|CI005826
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|86503159|gb|CI145792.1|CI145792
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88441245|gb|CI538688.1|CI538688
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|86524884|gb|CI165090.1|CI165090
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88542597|gb|CI471936.1|CI471936
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88382263|gb|CI521263.1|CI521263
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88297334|gb|CI547812.1|CI547812
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88531076|gb|CI459517.1|CI459517
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|58693613|gb|CK082300.1|CK082300
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88225398|gb|CI225314.1|CI225314
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|58595847|gb|CK006375.1|CK006375
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|86525225|gb|CI165431.1|CI165431
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|58680893|gb|CK069580.1|CK069580
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88976248|gb|CI024465.1|CI024465
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|3766627|gb|AU030737.1|AU030737
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|86600690|gb|CI356447.1|CI356447
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCCCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGGCGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88558963|gb|CI489497.1|CI489497
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|66914385|gb|CX101233.1|CX101233
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88545107|gb|CI474645.1|CI474645
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|218486436|gb|FG966615.1|FG966615
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|157651056|gb|EX450690.1|EX450690
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|86261453|gb|CI017195.1|CI017195
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88530451|gb|CI458846.1|CI458846
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|29678195|gb|CB674470.1|CB674470
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88981104|gb|CI021187.1|CI021187
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|86504868|gb|CI147501.1|CI147501
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|58685986|gb|CK074673.1|CK074673
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88964616|gb|CI069964.1|CI069964
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88271644|gb|CI387697.1|CI387697
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|86870305|gb|CI319411.1|CI319411
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
EST: gi|88557348|gb|CI487745.1|CI487745
EST:     GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAG                         GCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT
genomic: GAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 71 (downstream exon)
Score: 118

ATGATGCTGATGATATCTCTGAAGAAGTGTTGCGAGCATCAAGTGCTCTAGAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaacta ... ctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATTCACCATTGCGCTGCTTGGACCCCCTTGGGCCATTTGTATCGTTTTGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccttccctttttgcctggccatttgtttctgatcatagaatatctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATTCACCATTGCGCTGCTTGGACCCCCTTGGGCCATTTGTATCGTTTTGGTT
                            ttctgat  putative branch site (score: 118)
                                            tctgtttcc  putative PPT
                                    atagaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggaactattgcctttcttctttgcaccttccctttttgcctggccatttgtttctgatcatagaatatctgtttccagGCATCCAGGCGACGGTGCTGAGTAAAATCGGAAGGTGGGATGGGTCCAATTCACCATTGCGCTGCTTGGACCCCCTTGGGCCATTTGTATCGTTTTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT