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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgctcttattctaatttcgctaattcttagtgatataaataatttctgttgacaacaccacgtagtggaagagattgctcatgatacaaaactt...

Basic information

species Zea mays
transcript GRMZM2G000393_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000393_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g07905.2 (Oryza sativa), 5'ss of exon 4
---TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgctcttattctaatt-tcgctaattcttagtgatataaataatttctgttgacaacaccacgtagtggaagagatt--gctcatgatacaaaactt--------------------------------------------------------------------------------
   || ||||||||| |||   | ||||| || ||||||||||||||||| ||||| ||||| ||||||||||||  |||||||||||| |||||||| ||||||| |||| ||||  |||  |  |  | | ||    | |||| ||    |      ||| ||||    || |      || ||    |  |  |  || |  |                                                                                
AGTTCTGACAAGAAGAAGC---TCCTTGCTGTTATTGGAGTTTACACTGGTTTTGGTTCCCGGCTCAAGAGGAACACCTTCCGTGGCTCATGGATGCCGAGAGgttcgctgttcttgctcttttagtttccagtttacggcgataaaatgtgtgcgccctgataacatttggttggaatgcagcttcatttttttttctaatagctattgctgatgcaaactatgttacttataaggtttcaactacaggagtataattgttcttttacctcactgtaaatttcag
















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|148982630|gb|EE028428.2|EE028428
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|78093005|gb|DV521379.1|DV521379
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|6626361|gb|AW257893.1|AW257893
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GNGATGCTCTGAAGAAGCTTGAGGAAAAG
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAG
EST: gi|32834517|gb|CD974195.1|CD974195
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|149106895|gb|EE188795.2|EE188795
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|76920610|gb|DV168260.1|DV168260
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|31359008|gb|CD443365.1|CD443365
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|78022345|gb|DV490732.1|DV490732
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|31357853|gb|CD442210.1|CD442210
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|149096405|gb|EE182139.2|EE182139
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|22819731|gb|BU499821.1|BU499821
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|4621544|gb|AI612377.1|AI612377
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|211507519|gb|FL321825.1|FL321825
EST:     GGCTCCCGTCTCAAGAG-AACGTCTTCCCGTG-CTC-TGNATGCAAAGAG                         -TGATGCTCTGAA
genomic: GGCTCCCGTCTCAAGAGGAACGTCTTCC-GTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAA
EST: gi|21843330|gb|BQ703911.1|BQ703911
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|149005474|gb|EE040029.2|EE040029
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|50323553|gb|CO518679.1|CO518679
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|89250822|gb|DY622608.1|DY622608
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|94479524|gb|EB708482.1|EB708482
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|149064607|gb|EE286478.2|EE286478
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|71311661|gb|DR792235.1|DR792235
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|32839844|gb|CD979525.1|CD979525
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|148994442|gb|EE034088.2|EE034088
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|71435123|gb|DR816173.1|DR816173
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|71448461|gb|DR829511.1|DR829511
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCCTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|22521196|gb|BU080007.1|BU080007
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGCTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|78090931|gb|DV519305.1|DV519305
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAA-GGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|5525207|gb|AI861205.1|AI861205
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGT-A
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|211281812|gb|FL349985.1|FL349985
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|211340421|gb|FL351902.1|FL351902
EST:     GGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCCTGGATGC-AAGAG                         GTGATGCTCTGAAGAAGC
genomic: GGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCC-TGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGC
EST: gi|67038278|gb|CO464608.1|CO464608
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|32928809|gb|CF033621.1|CF033621
EST:     TGGCTCCCGTCTCAAGAGGAACGCCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|71436237|gb|DR817287.1|DR817287
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|71772160|gb|DR970097.1|DR970097
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|32839845|gb|CD979526.1|CD979526
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|148938471|gb|EC882790.2|EC882790
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|71426994|gb|DR808044.1|DR808044
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|149084753|gb|EE174248.2|EE174248
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgctcttattctaatttcgctaattcttagtgatataaataatttctgttgacaacaccacgtagtggaagagattgctcatgatacaaaactt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA