Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactggtttacgatctccgtccatgataacctcttccgaaatgaatgttttagtcaaggtttatcgttttgctcattgttctttcctgatcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATTTCTACCATGCTGGCGAAAGGCTTTATTCTTGGGAAAGATGCCGTCTCTA

Basic information

species Physcomitrella patens
transcript PP1S9_32V6.1
intron # 4
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|208359056|gb|DC957804.1|DC957804
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTNGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208370262|gb|DC952084.1|DC952084
EST:     AGAGAT-AAGCA-TTGGAAATGAT-GG                         GGC-TTGCTNGACCAAGCTCACATACTCC-AACCCAGCGGTTGATGTTATT
genomic: AGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100378310|gb|BY949787.1|BY949787
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGGCCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTGTT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208359261|gb|DC939070.1|DC939070
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|18342157|gb|BJ174192.1|BJ174192
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCC
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCC
EST: gi|208373441|gb|DC941052.1|DC941052
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100358635|gb|BY965746.1|BY965746
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100387784|gb|BY970529.1|BY970529
EST:     TNCAAGCATCAACTCCATTCCCAGAGATAAAGCATTTTGGAAATGATGGG                         GGCTTTGCTGGGACCAAGCTCACATACTCCAAAACCAAGCGGTTGATGTTA
genomic: TCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTT-GGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGG-ACCAAGCTCACATACTCCAAA-CCAAGCGGTTGATGTTA
EST: gi|208368227|gb|DC931453.1|DC931453
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100388020|gb|BY988493.1|BY988493
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|162265878|gb|FC442465.1|FC442465
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208357096|gb|DC942730.1|DC942730
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208393431|gb|DC942515.1|DC942515
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208391878|gb|DC945957.1|DC945957
EST:     AGAGATAAAGCA-TTGGAAATGATGGG                         GGC-TTGCTGGACCCAGCTCACATACTCCAAACCAAGCNGTTGATGTTATT
genomic: AGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208396861|gb|DC908181.1|DC908181
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|162265877|gb|FC442464.1|FC442464
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100397943|gb|BY954009.1|BY954009
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|162225889|gb|FC402181.1|FC402181
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|162280268|gb|FC456285.1|FC456285
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208387672|gb|DC937237.1|DC937237
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100444933|gb|BY982761.1|BY982761
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGNACCA-GCTCACATACTCCAAACCAAGCGGTTGATGTTAT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGG-ACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTAT
EST: gi|162240163|gb|FC418290.1|FC418290
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208384457|gb|DC911543.1|DC911543
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100405823|gb|BY973872.1|BY973872
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208368003|gb|DC951014.1|DC951014
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100417073|gb|BY957153.1|BY957153
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|162230915|gb|FC406754.1|FC406754
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|162240162|gb|FC418289.1|FC418289
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100374498|gb|BY985807.1|BY985807
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208400060|gb|DC908623.1|DC908623
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|162280269|gb|FC456286.1|FC456286
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208391737|gb|DC937955.1|DC937955
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100399961|gb|BY990708.1|BY990708
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|162230914|gb|FC406753.1|FC406753
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208375442|gb|DC940496.1|DC940496
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|208386854|gb|DC953507.1|DC953507
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100449088|gb|CJ973387.1|CJ973387
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100385442|gb|BY969779.1|BY969779
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
EST: gi|100436109|gb|BY979384.1|BY979384
EST:     CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGG                         GGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT
genomic: CTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATT

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: 33 (upstream exon), 34 (downstream exon)
Score: 16

CACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAATTATCTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATGATGGGgtactggttt ... tcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATTTCTACCATGCTGGCGAAAGGCTTTATTCTTGGGAAAGATGCCGTCTCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttttagtcaaggtttatcgttttgctcattgttctttcctgatcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATTTCTACCATGCTGGCGAAAGGCTTTATTCTTGGGAAAGATGCCGTCTCTA
                                       tcctgat  putative branch site (score: 16)
                                  ttctttcctgatctt  CT-rich tract
                                               ttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactggtttacgatctccgtccatgataacctcttccgaaatgaatgttttagtcaaggtttatcgttttgctcattgttctttcctgatcttgtttagGGCTTTGCTGGACCAAGCTCACATACTCCAAACCAAGCGGTTGATGTTATTTCTACCATGCTGGCGAAAGGCTTTATTCTTGGGAAAGATGCCGTCTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG