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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGACGCCGCAGCCGCAGCCGTAGCCGGAGTCCAAGGTACCGCGGTCGTAGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaagttattgtcttcaaacaggctctgtagatatgagtaatgacaaaatgatatcttggcatccctagattctttcttgttggccagccaaat...

Basic information

species Oryza sativa
transcript LOC_Os02g39720.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39720.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G107896_T01 (Zea mays), 5'ss of exon 4
GAAGACGCCGCAGCCGCAGCCGTAGCCGGAGTCCAAGGTACCGCGGTCGTAGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaagttattgtcttcaaacaggctctgtagatatgagtaatgacaaaatgatatcttggcatccctagattctttcttgttggccagccaaat----
| ||  |  |  | |||||||| || |  ||     |   |||  | || ||||||||||| ||||||||| | || ||||||||||||||||| |||||||||| |   | || || |  ||| |   |  |  |   ||| | | |     | |  ||  |  |  |    | |      || |    ||    |  |    
GTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGGAGCCGAAGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaattt---gctaatgacaccaatcgaccaatccat-catgtgcattccattagttttaattaagggttgggaaacatcacctagaaatcccaaaacttttga

upper sequence: LOC_Os02g39720.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G027105_T04 (Zea mays), 5'ss of exon 4
GAAGACGCCGCAGCCGCAGCCGTAGCCGGAGTCCAAGGTACCGCGGTCGTAGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgt---aaagttattgtcttcaaacaggctct------gtagatatgagtaatgacaaaatgatat--cttggcatccctagattctttcttgttggccagccaaat
|     |  |  |  |  | || ||||| ||||| || || ||| | || || |||||||||||||||||||| || ||||||||||||||| | |||||||||| |   || |  |     |    ||| |   |      |||| | | | ||| |        | |   | | | |  |||| |   |||      |           
GCTTGGGTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGCAGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgctaatgacaccaattcaccacatgtattcatccagtagttttaattaagggttgggaaacacgacctagaaatcctaaaacttttgagaacg-----------
















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|86530292|gb|CI170498.1|CI170498
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|87031507|gb|CI263880.1|CI263880
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|86495002|gb|CI137635.1|CI137635
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|86906238|gb|CI320169.1|CI320169
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|32948206|gb|BP184778.1|BP184778
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|32948206|gb|BP184778.1|BP184778
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|32948206|gb|BP184778.1|BP184778
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|32948206|gb|BP184778.1|BP184778
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|32948206|gb|BP184778.1|BP184778
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|32948206|gb|BP184778.1|BP184778
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|32948206|gb|BP184778.1|BP184778
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|33692937|gb|CF321176.1|CF321176
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGGAGTTACAG                 
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGT------AG--A-AGgtaatgtaaa ... gg
EST: gi|86545716|gb|CI185922.1|CI185922
EST:     ATTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGGAGTTACAG                 
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGT------AG--A-AGgtaatgtaaa ... gg
EST: gi|88206414|gb|CI206263.1|CI206263
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGGAGTTACAG                 
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGT------AG--A-AGgtaatgtaaa ... gg
EST: gi|88210718|gb|CI210567.1|CI210567
EST:     AGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|29643918|gb|CB648925.1|CB648925
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|87034991|gb|CI189615.1|CI189615
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|86531202|gb|CI171408.1|CI171408
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGGAGTTACAG                 
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGT------AG--A-AGgtaatgtaaa ... gg
EST: gi|88206373|gb|CI206222.1|CI206222
EST:     ATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGTTACAGCAGGTCGCCACCACC
genomic: ATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|29658266|gb|CB654541.1|CB654541
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|87018220|gb|CI265512.1|CI265512
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGGAGTTACAG                 
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGT------AG--A-AGgtaatgtaaa ... gg
EST: gi|86435370|gb|CI106603.1|CI106603
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|33657441|gb|CF280055.1|CF280055
EST:     GCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: GCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|87033033|gb|CI187657.1|CI187657
EST:     CGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGCAGAAGGAGTTACAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCAC
genomic: CGCAGCCCAAGATACCGGAGGAGCCCAAGCTAT----G--GTAG--A-AGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCAC
EST: gi|38475200|gb|CF959333.1|CF959333
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|88852217|gb|CI373985.1|CI373985
EST:     GTCGCAGCCGCAGCCCAAGATAGCCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: GTCGCAGCCGCAGCCCAAGATA-CCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|29660883|gb|CB657158.1|CB657158
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|29660883|gb|CB657158.1|CB657158
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|29660883|gb|CB657158.1|CB657158
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|29660883|gb|CB657158.1|CB657158
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|29660883|gb|CB657158.1|CB657158
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|29660883|gb|CB657158.1|CB657158
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|29660883|gb|CB657158.1|CB657158
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         G
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacag-
EST: gi|38482929|gb|CF966731.1|CF966731
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|325493520|gb|JG458044.1|JG458044
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCG
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCG
EST: gi|88201589|gb|CI201944.1|CI201944
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|33664155|gb|CF295122.1|CF295122
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGTTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|86596340|gb|CI268640.1|CI268640
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|89168547|gb|CI038901.1|CI038901
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|86524080|gb|CI164286.1|CI164286
EST:     AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
genomic: AGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC
EST: gi|88217821|gb|CI217670.1|CI217670
EST:     CAAGATACCGGAGGAGCCCAAGCTATGGTAGAAG                         CCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCCCCACC
genomic: CAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACC

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: 74 (upstream exon), 71 (downstream exon)
Score: 52

GAAGACGCCGCAGCCGCAGCCGTAGCCGGAGTCCAAGGTACCGCGGTCGTAGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaa ... ggagttacagCCCACGGGATCGTTCTCCAAAGAGGCGCAGCTACAGCAGGTCGCCACCACCAGCTCGTGCACGAAGCTACAGCCGATCACCTCCACCTCCTCGTGAGCGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGACGCCGCAGCCGCAGCCGTAGCCGGAGTCCAAGGTACCGCGGTCGTAGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaagttattgtcttcaaacaggctctgtagatatgagtaatgacaaaatgatatcttggcatccctagattctttcttgttggccagccaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT