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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAACACCGGTGCTCCTTGTTCTCCCTGTTGTAACCTTTTATTTCTATAAATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctcatctcagaatcagtttatcatgccactatgtattttaagtttttatctattaaaccttagcttgtgaaataaaaaacaatattaaaattct...

Basic information

species Oryza sativa
transcript LOC_Os01g35050.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g35050.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G064189_T01 (Zea mays), 5'ss of exon 4
GTCAACACCGGTGCTCCTTGTTCTCCCTGTTGTAACCTTTTATTTCTATAAATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctcatctcagaatcagtttatcatgccactatgtattttaagttt--ttatctattaaaccttagcttgtgaaataaaaaacaatattaaaattct----------------------------------------------
||||||||| |||||||||||||| ||||| || ||||| |||||| | || |||||||| || |||||  ||||  |||||||| |||  ||||| ||||||    || |   | | || |           | | |||    ||| |    |||  |  | ||   | || |   ||||  ||| ||   ||||||   |                                              
GTCAACACCTGTGCTCCTTGTTCTTCCTGTAGTGACCTTCTATTTCCACAAGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttccttcaaaactctgggaggtgaataaatgtgtgacctaaatacagttagatcattaaaaatggcat---aaattcaaaccatgtttaaaacggttgcaccatggagcatgactaccaacacatttccatttcgttaccag

upper sequence: LOC_Os01g35050.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G021194_T01 (Zea mays), 5'ss of exon 11
GTCAACACCGGTGCTCCTTGTTCTCCCTGTTGTAACCTTTTATTTCTATAAATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctcatctcagaatcagtttatcatgccactatgtattttaagtt---tttatctattaaaccttagcttgtgaaataaaaaacaatattaaaattct---------------------------
||||||||| |||||||||||||| ||||| || ||||| |||||| | || |||||||| || |||||  | ||  |||||||| |||  ||||| ||||||    || |   | |||| |           | | |||    ||| |    ||     ||||||    |  ||   ||       || ||     |   ||                           
GTCAACACCTGTGCTCCTTGTTCTTCCTGTAGTGACCTTCTATTTCCACAAGTACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAGgtatgtttccttctaaaatctgggaggtgaataaatgtgtgacctaaatacagttagatcattaaaaaccatgtttaaaacggtcgcaccatggagcatgactaccaacacatttccatttcgttaccag
















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|86833482|gb|CI336271.1|CI336271
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|29623286|gb|CB628297.1|CB628297
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88243126|gb|CI244248.1|CI244248
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88543277|gb|CI473272.1|CI473272
EST:     ATACTGCAAGAATCGCTATGAGCCTGCTTTTTTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: ATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88258873|gb|CI359263.1|CI359263
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88375895|gb|CI528199.1|CI528199
EST:     GCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: GCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86835561|gb|CI348018.1|CI348018
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|218495655|gb|FG950469.1|FG950469
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTAGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGATTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|87007249|gb|CI277324.1|CI277324
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|89179078|gb|CI043583.1|CI043583
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86853189|gb|CI326284.1|CI326284
EST:     TGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGGCAGGGTTCGAC
genomic: TGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88252315|gb|CI350743.1|CI350743
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|58592543|gb|CF990851.1|CF990851
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86853732|gb|CI330583.1|CI330583
EST:     TGCTTTTTTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGGACGCGCAAGAGAGCCAGGGTTCGAC
genomic: TGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86822527|gb|CI358041.1|CI358041
EST:     CTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAA-GATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: CTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88286267|gb|CI522567.1|CI522567
EST:     CTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: CTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86597881|gb|CI276667.1|CI276667
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|218496990|gb|FG950833.1|FG950833
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCT
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCT
EST: gi|86874445|gb|CI316811.1|CI316811
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86869150|gb|CI335717.1|CI335717
EST:     TCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: TCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|58599561|gb|CK010089.1|CK010089
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTAGGG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGNTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88971739|gb|CI388980.1|CI388980
EST:     AATCGCTATGACCCTGCTTTTTTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88464480|gb|CI544941.1|CI544941
EST:     ATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: ATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86908662|gb|CI318977.1|CI318977
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88508795|gb|CI436301.1|CI436301
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGGCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88409488|gb|CI561974.1|CI561974
EST:     GAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: GAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86600754|gb|CI356511.1|CI356511
EST:     ATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: ATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88283652|gb|CI405098.1|CI405098
EST:     CCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: CCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|89185595|gb|CI052121.1|CI052121
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88256336|gb|CI358724.1|CI358724
EST:     TGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: TGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86528225|gb|CI168431.1|CI168431
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88265544|gb|CI376446.1|CI376446
EST:     TATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGGCCAGGGTTCGA
genomic: TATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGA-GCCAGGGTTCGA
EST: gi|88507740|gb|CI435246.1|CI435246
EST:     CTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: CTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86881530|gb|CI322585.1|CI322585
EST:     AATACGGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88427973|gb|CI554481.1|CI554481
EST:     TTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: TTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|33798947|gb|CF325331.1|CF325331
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|88449442|gb|CI534001.1|CI534001
EST:     GAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: GAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
EST: gi|86881762|gb|CI324077.1|CI324077
EST:     AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAG                         GATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC
genomic: AATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGAC

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: 26 (upstream exon), 50 (downstream exon)
Score: 1

GTCAACACCGGTGCTCCTTGTTCTCCCTGTTGTAACCTTTTATTTCTATAAATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctca ... ccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGACCTCAAAGGATACCTGATGAATGCCTACATCCACCCGGTGTTCAAAGGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAACACCGGTGCTCCTTGTTCTCCCTGTTGTAACCTTTTATTTCTATAAATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctcatctcagaatcagtttatcatgccactatgtattttaagtttttatctattaaaccttagcttgtgaaataaaaaacaatattaaaattct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA