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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccatattatttggtctttgtcaggcagggtgtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA

Basic information

species Zea mays
transcript GRMZM2G032505_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 2
---ttccatattatttggtctttgtcaggcagggtgtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
    |    |  | ||| | |||  |    |  ||| |      ||  ||       ||  |  ||      |||  |  |    ||||||||||| ||| ||||  ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||
gctattaccagaaattgctgtttccctattaatgtgacctattgtt--ttggaacaattgcgtattgtaaccatatggtttctgcttttctcaactgttt-agATTCTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAATATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACTTCCA

upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
---------------------------------------------ttccatattatttggtctttgtcaggcagggtgtctgtacattatttatttt---gtttctgggttactcatatacagcctgccttttt--ctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
                                             ||    | | ||   |||   ||     |  ||  || | |  | || |||     ||| |       |   ||  |   || | |  |   |       ||||||| |||||||||||||| || || |||||||| || |||||||| || |||||| | |||||||||||||| ||||| |||||||| || ||||| || |
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
----------------------------------------------ttccatattatttggtctttgtcaggcagggtgtctgtaca--------ttatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
                                              ||      | |    |||   ||  |  |  ||  || | |        || || ||||| | ||   |||  |    ||   | ||     || |    |   |||||| |||||||||||||| || || |||||||| || |||||||| || |||||| | |||||||||||||| ||||| |||||||| || ||||| || |
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcat---ttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
ttccatattatttggtctttgtcaggcagggtgtctgtac--attatttattttgtttctgggttactcatatac---agcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
      |||   ||  || |   |      |   |||||    | ||| | ||  ||| |   |  || || | |   |  ||| | |  | |      ||| |||| |||||||| || || || |||||||| || || |||||| | ||||||||| | ||||| ||||||||||||||||||||||| || ||||| || |
-----aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttttcattccctaatgttccaaattctgacatgatatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA

upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 2
-ttccatattatttggtctttgtcaggcagggtgtctgtacattatttattttgtttctgggtt-actcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
 |     | || ||    | | | |     ||| | |    |     | ||   | | ||  || | |  ||       ||      | |||    | |||||| ||||| ||||| || || ||||| |||||||| |||||||| || |||||| | ||||| ||| |||||||||||||||||||  |||| || || |
gtattcaactagttttcttatcttatttttggtattttcctacagagtcttacctatttgatttgaattctaactgttgtgttaccatatcatgc-tattagATTTTGGAGATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTA

upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
ttccatattatttggtctttgt-caggcagggt---gtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
    |||  | |||||   ||  |||||    |     ||| |  |    ||  ||| ||||   |   |  | |     ||   || |  | ||   ||||||||||||||||||||||| |||||||| || ||||| |||||||| || |||||| | ||||| || ||||| ||||||||||||||| |||| || || |
----ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA

upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 3
-----ttccatattatttggtctttgtcaggcagggtgtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
      |   |  ||||   |  ||  ||  ||| || | |||  ||  |||||||| | | |  | ||   || ||    || |  |||  |    | |||||||| |||||||||||||| || ||||||||||| || ||||| |||||| ||||| | ||||| ||||| |||||||||||||| ||  |||| ||||| |
ctcctgttgctgctattgctttattaacacccagcgtatttgtttatattttattttttatttttggtaaatattta---actacagtttgttgg--tgttttagATTTTGGAAATGAACCCAGAAGATGAAGCTGAAGAAGATGGCGCTAACGTTGATCTTGACTCCCAAAGAAAAGGAAAATGTGTCGTGTTGAAAACCTCTA

upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
ttccatatta--tttggtctttgtcaggcagggtgtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattt-tagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
    | | ||  | | || ||| |    ||  |  |   | | |  |||   |||   | || |   ||| |||     |   ||  | ||       |  |||| |||||  | || || || ||||||||||| ||||||||||||||  ||||||| ||||| ||||||| |||||| ||||| ||  ||||||| ||||
cgagaaagtagctctcgtgtttttattccacagc-ttaattcctgtttttcgttgcaaccggttg--tcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA

upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 2
ttccatattatttggtctttgtcaggcagggtgtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
                                    |||  | |    | || | ||||  ||  | | | |      | ||| |  ||      | |||||||||||  | || |||||||||||||||||||| || ||||| ||  | ||| | || || ||||| ||||||||||| || || || ||||||||||
------------------------------------gtatgtcaagagtgttttctctgcatttttgagagat--ttcgtcttatcttccgtg--tctagATCTTGGATGTAAATCCTGAGGATGAAGCTGAGGAAGACGGTGCCAATGTCGATCTCGATTCTCAAAGAAAAGGAAAATGCGTCGTGCTCAAGACCTCCA

upper sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 2
ttccatattatttggtctttgtcaggcagggtgtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
                                    |||  | |      || | ||||  ||  |   | |      | ||| |  ||      | |||||||||||  | || |||||||||||||||||||| || ||||| ||  | ||| | || || ||||| ||||||||||| || || || ||||||||||
------------------------------------gtatgtcaagagagttttctctgcatttttgggagat--ttcgtcttatcttccgtg--tctagATCTTGGATGTAAATCCTGAGGATGAAGCTGAGGAAGACGGTGCCAATGTCGATCTCGATTCTCAAAGAAAAGGAAAATGCGTCGTGCTCAAGACCTCCA

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|149101527|gb|EE187650.2|EE187650
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|148951330|gb|EC897040.2|EC897040
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|22473221|gb|BU037701.1|BU037701
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|22715443|gb|BU197766.1|BU197766
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|149109720|gb|EE293507.2|EE293507
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|149085416|gb|EE174922.2|EE174922
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|22473395|gb|BU037875.1|BU037875
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|211077789|gb|FL088742.1|FL088742
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|148979721|gb|EE026794.2|EE026794
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|149096589|gb|EE182348.2|EE182348
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|74241694|gb|DT649608.1|DT649608
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|116820064|gb|EC863249.1|EC863249
EST:     AGCTCAACAAGCAGCTG-CCTACCTCGTTGGCAACATC--TGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|60346168|gb|DN213141.1|DN213141
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|149062853|gb|EE157572.2|EE157572
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|149077127|gb|EE165787.2|EE165787
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|78179300|gb|DV549673.1|DV549673
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|211077790|gb|FL088743.1|FL088743
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
EST: gi|149100563|gb|EE186648.2|EE186648
EST:     AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAG                         ATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT
genomic: AAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCGTTGAGgttcattttc ... actattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA
                                  cctttttctcaact  CT-rich tract
                                            aactatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccatattatttggtctttgtcaggcagggtgtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA