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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA

Basic information

species Glycine max
transcript GLYMA17G13850.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 23
------gtaagccttttaaccaagggtattgtgttgtattgattcattgaat------ataa-ctttacta---gctttgttt--cagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
       | ||| | |          ||||||  | || ||||| |||   |      || | |  ||| |   ||    |||  |||||||| || ||| | ||  |||| || || ||||| |||||||| || ||||| ||||||||||| ||||| ||||||||||||||||| |||||||| |
gtatgcttgagcatgtgggttggttttattgtcat-tagtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAAAACGAATTTATGGTGAATTGGGATGGATTACGCACTA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
------------------gtaa-gccttttaaccaagggtattgtgttgtattgattcattgaatataact--ttactagct---------ttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                   ||  |||| | |  ||   |  | |  |  | ||| || ||    |  |  |  |||||  ||         || ||  |||||||  ||||| ||||| | ||||| |||||||| || ||||| || ||||| |||||||||||||| || ||||| |||||||||||  |  | || |
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
-------------------------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataacttt--actagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                           ||  | |||  |  |      |||| ||| ||| ||  | |  |||    ||   || |  |||| | |||||||  ||||||||||| || | |||||||| ||||| ||||| || ||||| || ||||||||||| || |||||||| ||||||||  || | || |
gtaagtaaattgtaattgatcaatcacaacgccttt--ctgaattccctgtgatgt-ttgctttctagtttatcttcttcatcttgtgttgtat-agGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
-------------------------------------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttc-agGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                                     |  |||||   | || |||       | ||    | ||   ||   ||   | | ||  | ||||||  |||||||  ||||||||||  || |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgagga------ggtgggaggctttcctgctcat--ttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
----gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataa---ctttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
    | ||||     |    |   || |      ||  |   || |  |||  |    |||  | |  ||  | ||||| || || ||| | ||  |||| ||||| ||||| |||||||| || ||||| |||||||| |||||||| ||||| |||||||||||||| ||||| |
gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------------------------------------------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttc-agGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                                                                                                                                  |     || |   |||   |||  || || ||   ||| |       |  | | ||  | ||||||  |||||||  ||||||||||  || |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcct---gctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G370521_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------------------------------------------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttc-agGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                                                                                                                                  |     || |   |||    ||  || || ||   ||| |       |  | | ||  | ||||||  |||||||  ||||||||||  || |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
gtacgtactggtctaattaaaggtgcatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatatgtagtttgttgtcaatcccatattgatgcatactttcct---gctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G417650_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------------------------------------------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttc-agGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                                                                                                                                  |     || |   |||    ||  || || ||   ||| |       |  | | ||  | ||||||  |||||||  ||||||||||  || |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  || | || |
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagcattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcccatattgatgcatactttcct---gctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G482077_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------------------------------------------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                                                                                                                                  |     || |   |||    ||  || || ||   ||| |      | | | | |   |||  ||| |||||||  ||||||||||  || |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| |||||||   |  | || |
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttattctgcc--cttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGATCTGAGAACAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 3
----gtaagccttttaaccaagggtattgtgttgtattgattcattgaatat-aactttactagctttgttt-----cagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
    | ||||     |    |   || |      ||  |   || |  |||  |||||   |   ||||  |     ||||| || || ||| | ||  |||| ||||| ||||| |||||||| || ||||| |||||||| |||||||| ||||| |||||||||||||| | ||| |
gtatgcaagcacacaagtttactttagtaatcactaccggcacagtatataccaacttctttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCACACTA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 2
----gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataa----ctttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
    | ||||     |    |   || |      ||  |   || |  |||  |    ||||  | |  ||  |  |||| || || ||| | ||  |||| ||||| ||||| |||||||| || ||||  |||||||| |||||||| ||||| |||||||||||||| ||||| |
gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaacttctttttttgactttctggagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCACAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
----gtaagccttttaa------ccaagggtat---tgtgttgtattgattcattgaatataactttactag----ctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
    || |   | ||||      |  | | |||   | ||   || | | |  | |  ||    || | | |    || | | | |||||||  ||||| ||||| |  | || || ||||| || |||||||||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
gttagtgattttcttaacggtcactgatgatatgcctatgacataataagttgtagcttactcattgatttgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
-------------------------------------------------------------------------gtaagccttttaaccaagggtattgtgt-tgtattgattcattgaatataactttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                                                                         |||     |  | ||     || ||  |   | |    ||||| |   |    ||  |    || ||| |||||||  ||||| ||||  || |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttatt-ttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 14
----gtaagccttttaaccaagggtattgtgttgtattgattcattgaatat-aactttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
    | ||||         |    || |      | ||| | || || | |  |||| |  | |  ||  | ||||| || || ||| | ||  |||| ||||| ||||| |||||||| || ||||| |||||||| |||||||| ||||| |||||||||||  | ||||| |
gtatgcaagcagacaggttacat-tagtaaacactgttggtacagtgtacaccaactgtctttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G438355_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataact---ttacta-gctttg--tttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                                                                   |   || ||       ||    |    ||||||| |||    | |  ||   |||  | ||  |   ||| |||||||  ||||| ||||  ||  ||| |||||  |||| ||||| |||||||| |||||||||||||| |  |||||||| ||||||||  |  | |  |
gtaagttatagtagtgttgtgattcatgtacattttctacttatttcaattgtactaggacaccaccatatttgtagtttgttgt-caattccatattgatgcatactttcttgctcatttatcatgccctagtttttagGTTGATGGCATGCTGGGAAGGCAGGAGAACCCTAGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTCTATGGTGAACTGGGATGGTCTCAGAAGAA

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 23
-----------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
            |||  |||||     |   |||  |||| |  |   ||  ||  |   |  ||  | | || || | ||||||| |||||| |||| |||||||| || ||||| || |||||||||||||| ||||||||||| ||||| ||||| || |||||||| || ||||| |
gtgagcttcatataactctttttgttta---tatattgtt-tgcttcctctctgcttgctatattctttgtttggtcttagGTTGATAGCATGCTGGGCCGGAGGGAGAATCCAGGGGAACATGAGGCCATGCGTAAGATGAAAAACGAATTTATGGTCAACTGGGATGGCTTGCGCACAA

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|21995058|gb|BQ786586.1|BQ786586
EST:     TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG                         GTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
genomic: TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttt ... tttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
EST: gi|16277629|gb|BI942480.1|BI942480
EST:     TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG                         GTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
genomic: TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttt ... tttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
EST: gi|16282350|gb|BI944969.1|BI944969
EST:     TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG                         GTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
genomic: TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttt ... tttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
EST: gi|254327049|gb|GR836658.1|GR836658
EST:     TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG                         GTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
genomic: TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttt ... tttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
EST: gi|298163750|gb|HO012483.1|HO012483
EST:     TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGTG                         GTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
genomic: TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttt ... tttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
EST: gi|15203099|gb|BI425867.1|BI425867
EST:     TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG                         GTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGATGCCATG
genomic: TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttt ... tttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
EST: gi|22522568|gb|BU081379.1|BU081379
EST:     TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG                         GTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG
genomic: TTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttt ... tttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagggtattgtgttgtattgattcattgaatataactttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA
                             atataac  putative branch site (score: 3)
                                            ctttgtttc  putative PPT
                        attgaatataacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG