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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgttttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaaaatataagatgacggttgtaa...

Basic information

species Zea mays
transcript GRMZM2G392975_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g44630.2 (Oryza sativa), 5'ss of exon 3
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgttttccta-gtttgttcagctgttagggttctgcttgaattcac-atttgcatatctaaaatataagatgacggttgtaa
 ||||| ||||| || ||||| ||||||||||||||||| ||||||||||||||||| ||||| |||||||||||||| ||||||||||| ||||| || |||||||  ||||  | ||| |   |   |  | ||         |||   |  |  ||   | |  | ||    |     |  |  |  | |         
TGACGGTCTTGGTGCTGAGATTGTTGGCACCTTCATCCTGGTCTACACCGTCTTCTCAGCCACTGATGCCAAGAGGAATGCCAGGGACTCACATGTTCCTgtaagtatccttctcctttttgcagtgtgatatgtgaaagttcagtagtagttagtgtggtctaatgagttatgcactgtgataactaattcatcaccaa--

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctt--tcgttttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaaaatataagatgacggttgtaa-
 || |||||||| || ||||| |||||||| || || || || ||||| |||||||| ||||| ||||||||||| ||||| || ||||| || ||||| |||  || |  || || ||  ||  | | ||  || || || || ||| |     |  || |  ||  |||   || |||   || ||||    |  |  |  
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatctttattctctcttctcattcgtgcaact-ttaagccaaagtgtgtaaacaggtttat-tagctagg-tagaagagagagactaaact

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G06680.1 (Glycine max), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagta-ctcttcgtcctttcgttttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaa-aatataagatgacggttgtaa
 || || ||||| || ||||| |||||||| |||||||| || |||||||| ||||| ||||||||||||||  | | |||||| |||||||| |||||||||||   | || | | |     ||  | |   |||||    | |||      ||     || |  |     | || | | ||| |   ||    |||  | 
TGATGGTCTTGGTGCTGAGATTGTTGGCACTTTCATCCTTGTTTACACCGTTTTCTCCGCCACCGATGCCAAACGTAGCGCCAGAGACTCCCACGTCCCCgtaagcctccctcccttccgaaattccctttaattgtttt-ttattataaaattgaccccatgcttaaacagagatttcataatcttccatatatgttaaa-

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G35030.1 (Glycine max), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgt-tttcctagtttgt--tcagc-tgt---tagggttctgcttgaattcacatttgcat-atctaaaatataagatgacggttgtaa---------------------
 || || ||||| || ||||| |||||||| ||||| || ||||||||||| ||||| ||||||||||||||| | | ||| || ||||| || ||||| ||| || |    | || | || | | || || | | |  | | | ||     |      | ||| |||  | |  || || ||  |    |    ||||      | |                     
TGATGGACTTGGTGCTGAGATTGTTGGCACTTTCATTCTTGTCTACACCGTTTTCTCTGCCACCGATGCCAAGCGTAGCGCTAGAGACTCACACGTCCCTgtatgtgcatgccctcttctcttgtctcataatatataattaacatgcatgcaaaaaattacttaaatagatacatgtatgattcatggaactgaatga-atcaatgaatcaatgaatcaaatgatcag

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G42220.3 (Glycine max), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgttttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaaaatataag-atgacggttgtaa----------
 || || ||||| || ||||| |||||||| ||| |||| || |||||||| ||||| ||||||||||||||  | |||||||| ||||| || |||||||||||  | |  |   || |||     ||  |||  |    | ||   |||       || |   ||||   |     |||  |||   ||  ||||| |           
TGATGGTCTTGGTGCTGAGATTGTTGGCACTTTCGTCCTTGTTTACACCGTTTTCTCCGCCACCGATGCCAAACGTAACGCCAGAGACTCTCACGTCCCCgtaagccccccaccctctgtcgaaaatctc-tttaattgctttttttcgttaaaaaaaaaatactatttttgtggactaaacctaattgtgtgggttgaatatatgagtag

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G37730.1 (Glycine max), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaag---tactcttcgtcctttcgttttcctagtttg-------ttcagctgttagggttctgcttgaattcacatttgca------tatctaaaatataagatgacggttgtaa----------------
 || || ||||| || ||||| |||||||| ||  | || ||||||||||| ||||| ||||| ||||||||||| ||||| || ||||| || || || ||| |   |||||||     || |    | | |  |||       | ||    || || || |   ||| |  | |||   |      |||  |     | |  | | | | |||                 
TGATGGACTTGGAGCTGAGATTGTTGGCACTTTTGTTCTTGTCTACACCGTTTTCTCTGCCACTGATGCCAAGAGAAACGCTAGAGACTCACACGTTCCTgtatgctatactctttccttttccccactacaatattgcattcattccattaatttggcttataaatgagtatatattctgactttgttattaatgtggttaatttatgatggtatgatataataattgtag

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G01860.1 (Glycine max), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgtt-ttcctagtttgttcagctgttagggttc-----tgcttgaattcacatttgcatatctaa-------aatataagatgacg-gttgtaa---------
 || || ||||| || ||||| |||||||| ||  | || ||||||||||| ||||| ||||| ||||||||||| ||||| || ||||| || || || ||| ||| ||||   |  | |  | || ||  ||  |||  ||  |  ||||      ||  |  ||||  | ||   ||  |||       ||| || ||||    | | |||         
TGATGGACTTGGAGCTGAGATTGTTGGCACTTTTGTTCTTGTCTACACCGTTTTCTCTGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCTgtatgtattctttcccactacaatattgcttattcattccactaatttggtttataaatggctatattctgactt-tgtaattaatgtggttaatgtatgatgctatgatataataattgtag

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctt--tcgttttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaaaatataagatgacggttgtaa
 || |||||||| || ||||| ||||||||||| || || || |||||||||||||| ||||| ||||||||||| ||||| || ||||| || || || |||   | || || || ||  ||  | | ||  ||||| || || ||| |     |  || |  ||  |||           | |  |||| |      || 
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaact-ttaagccaaagtgtgtaaacaggtttattagctaggtagaagagataaactcacta-

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgt--tttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaaaatataagatgac--ggttgtaa
 || || ||||| || ||||| |||||||| ||  | || |||||||| || ||||| || || ||||||||||| || ||||| ||||| |||||||| ||||||| | | | || ||   |  | ||   || |||     | |  | | | || || |  |     |  | |    || |  |||   ||    ||| |  
CGATGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTTTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTCCCTgtaagtattttccctcattgtatcatctctctgtatgtatgcatatgtgtggtttgtttta--tagatctaactttgtcaataggtaaagcgattgagttct--

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgttttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaaaatataagatgacggttgtaa-----
 || |||||||| || ||||| |||||||||||| | || || ||||| |||||||| || || ||||||||||| |||||||| ||||| || ||||| ||| ||| |||   |  |||| |||  | | ||  |    |  |    |||     | |  | |  ||    |   |  ||| | |  |   | || |       
TGATGGCCTTGGTGCTGAGATTGTTGGCACCTTCGTTCTTGTTTACACTGTCTTCTCTGCTACTGATGCCAAGAGAAACGCCAGAGACTCTCACGTCCCTgtatgtattctc--ttatttc-tttctcaacttcatgagaccatccttgtttcatatta--tgattttactttccttggaatcttattttttgttttttctcatt

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv13s0067g00220.t01 (Vitis vinifera), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgttttcctagtttgttcagctgttagggtt--ctgcttgaattcacatttgcatatctaa--aatataagatgacggttgtaa----------------------------------
 || || ||||| || ||||| |||||||||||| |||| |||||||| |||||||| ||||| || |||||| | ||||| || |||||||| ||||| |||||  || | | ||  |  || || ||  ||| |    || | | | |   |  ||  |   | || ||    ||| |   |||  |  ||  |  ||||                                    
AGATGGGCTTGGTGCTGAGATTGTTGGCACCTTCGTCCTTGTCTACACTGTCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaag--ctatacatctctctgtctttctc-tttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaaag

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ18960 (Selaginella moellendorffii), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgttttcctagtttgttcagctgttagg--gttctgcttgaattcac---atttgcatatctaaaatataagatgacggttgtaa-------------------------------------------------------------------------------------------
 || || ||||| || ||||| ||||| |||||| | || |||||||| |||||||| ||||| ||||||||||| |  ||||| |||||||||||||| ||| ||  ||||| ||| | |       | |||  |||  || | | |  ||| |||||   |||     || | | | | |    |      |     |||                                                                                              
AGATGGTCTTGGAGCTGAGATTGTTGGTACCTTCGTTCTCGTCTACACGGTCTTCTCCGCCACTGATGCCAAGAGAAGTGCCAGAGACTCCCATGTCCCGgtacgt-ttcttcttccatccaaagctttggttgattcccctctcatgaagttttgcttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacag

upper sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ11572 (Selaginella moellendorffii), 5'ss of exon 2
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgttttcctagtttgttcagctgt----tagggttctgcttgaattcac---atttgcatatctaaaatataagatgacggttgtaa-------------------------------------------------------------------------------------------
 || || ||||| || ||||| ||||| |||||| | || ||||||||||||||||| ||||| ||||||||||| |  ||||| |||||||||||||| ||| ||  ||| | ||| | |       | |||  |||  |  |    |   ||| | |||   |||     || | | | | |    |      |     |||                                                                                              
AGATGGTCTTGGAGCTGAGATTGTTGGTACCTTCGTTCTCGTCTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAGTGCCAGAGACTCCCATGTCCCGgtacgt-ttctccttccatccaaagctttggttgattcccccctctcatgaagttttacttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacag

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|148936891|gb|EC881041.2|EC881041
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACT
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACT
EST: gi|76285262|gb|DV024830.1|DV024830
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCCACTTTGC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCC-ACCTTGC
EST: gi|149079702|gb|EE168703.2|EE168703
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACC
EST: gi|76923442|gb|DV169489.1|DV169489
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|148931929|gb|EC875151.2|EC875151
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCCATTGGGTTCGCGGTGTTCCTGGGTCCACCTTGC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGG-TCCACCTTGC
EST: gi|94472445|gb|EB701403.1|EB701403
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|211489110|gb|FL100837.1|FL100837
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGGGTTCGCGGTG
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGG--TTCGCGGTG
EST: gi|71330068|gb|DR801773.1|DR801773
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCCCTGCCAATTGGGTTCGCGG
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGG
EST: gi|149099303|gb|EE185339.2|EE185339
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|149111018|gb|EE294517.2|EE294517
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTC-ACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|31350056|gb|CD434413.1|CD434413
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|76012460|gb|DT939630.1|DT939630
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCCATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctttcgttttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaaaatataagatgacggttgtaa

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