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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgaaaaaccctaataattcttgagatcgcactttgttatttcgacggattcatgtgaaagctgatctcttttctttttctttttttgtgatccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAACAAATTCGGAAGGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCA

Basic information

species Glycine max
transcript GLYMA10G30520.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30520.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G08780.1 (Arabidopsis thaliana), 3'ss of exon 1
gtattgaaaaaccctaataattcttgagatcgcactttgttatttcgacggattcatgtgaaagctgatctcttttctttttctttttttgtgatccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAACAAATTCGGAAGGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCA
| |||| | | | | | | ||||||| | | |||| ||| ||| || | | | | | ||| | | | | |||||||||| ||| || |||||||| |||||||||||||| || | ||| | | | || || | | || || || || || |
--gtaagaaaatcatctcgaataggagtaatttattttgttag--catcttcttcaattgat-gctaatggatggt----tgatgatgatgttgcagGGGAGTAAGAGTGGATCTGAGATGGAGGTGACATGGGAGGACCAGCAGAACATTAATATCTTCAGCCGTCTCAACAACAGAGTCCATGACCTCGATGACG------

upper sequence: GLYMA10G30520.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0081g00080.t01 (Vitis vinifera), 3'ss of exon 1
gtattgaaaaaccctaataattcttgagatcgcactttgttatttcgacggattcatgtgaaagctgatctcttttctttttctttttttgtgatccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAACAAATTCGGAAGGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCA
|||| | ||||||||| || | | | || ||| || | | ||| | || ||||| || | | || | | ||||||||||| || || || |||||||| || ||||||||||| |||||||||||||| | || || | ||||||||||| || ||||||||||
gtat-gtaaaaccctaccaaaaccctaatttt--tttcgttcttactatt--ttcttcataatactgataaggca-------------ttacaacatggaa-gAGTGGAGGATCTGAAACAGAGGTGACATGGGAGGATCAGCAGAACATTAACAAATTCGGAAGACTAAACAACAGATTTCACGAGCTCGAAGATGAGATCA

upper sequence: GLYMA10G30520.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S341_64V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------------------------------gtattgaaaaaccctaataattcttgagatcgcactttgttatttcgacggattcatgtgaaagctgatctcttttctttttctttttttgtgatccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAACAAATTCGGAAGGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCA
||| | | | || ||| ||||| | || || | || | || ||||| | | || || ||| | | |||||| ||| ||||||||||| |||||||||||||||||||| || || ||||| | | ||||| ||||| || |||||||| ||||| |
gtaagttgcgccttgtttaggtgttttaattccccattctgttttgaatttgtaggtcgccttgttcacttttttgttttaggatttccgtgcttttattctttacgatttggattctgttgcggttgttgcgatcgttgtggtgtagtttgtcgtttcgggtagatgattgatc------cagggtattggattatga--ctgatagGGGGATGGAGTAGAGACGGAAGTGACATGGGAAGACCAGCAGAATATTAATGCCTTCGGTCGTCTCAATAACAAGTTTCATGAACTTGAGGACGAGATTA

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|298165379|gb|HO011428.1|HO011428
EST:     TCGGATCGAAAACCCTAAATTGAATTCGAACACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|298183639|gb|HO028852.1|HO028852
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|208047066|gb|GD846067.1|GD846067
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGTAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|23063883|gb|BU578665.1|BU578665
EST:     CGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: CGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|8403847|gb|BE059481.1|BE059481
EST:     CCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: CCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|298194434|gb|HO041082.1|HO041082
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|298189349|gb|HO037752.1|HO037752
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGACACGGAAGTAACATGGGAAGACCAACAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|151408749|gb|EV278557.1|EV278557
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|193403208|gb|FK369434.1|FK369434
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|298181905|gb|HO026080.1|HO026080
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|208288067|gb|GE083926.1|GE083926
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAACACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCGGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|192325157|gb|FK019088.1|FK019088
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|207799518|gb|GD769693.1|GD769693
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|9985019|gb|BE659127.1|BE659127
EST:     GTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: GTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|298195641|gb|HO044032.1|HO044032
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|207718487|gb|GD700059.1|GD700059
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAA
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGA-GGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAA
EST: gi|192331578|gb|FK022767.1|FK022767
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|151396928|gb|EV266801.1|EV266801
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGACGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|207714274|gb|GD696383.1|GD696383
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|208063826|gb|GD861980.1|GD861980
EST:     CGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: CGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|192298490|gb|FG989196.1|FG989196
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|151411474|gb|EV281285.1|EV281285
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|192294153|gb|FG986242.1|FG986242
EST:     TCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|192323134|gb|FK016325.1|FK016325
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|298187726|gb|HO031683.1|HO031683
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|193402738|gb|FK366402.1|FK366402
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|208131225|gb|GD931112.1|GD931112
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|10847424|gb|BF070111.1|BF070111
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|192326352|gb|FK015884.1|FK015884
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|298182302|gb|HO026477.1|HO026477
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|193532194|gb|FK490152.1|FK490152
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGGAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|6952039|gb|AW424107.1|AW424107
EST:     AAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: AAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
EST: gi|192295132|gb|FG986851.1|FG986851
EST:     TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAG                         GGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC
genomic: TTGTCGGATCGAAAACCCTAAATTGAATTCGAATACACAACATGCAGCAGgtattgaaaa ... atccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggattcatgtgaaagctgatctcttttctttttctttttttgtgatccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAACAAATTCGGAAGGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCA
              agctgat  putative branch site (score: 4)
 tctcttttctttttct  CT-rich tract
 ttttctttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgaaaaaccctaataattcttgagatcgcactttgttatttcgacggattcatgtgaaagctgatctcttttctttttctttttttgtgatccgaaaagGGGGGAGGATCTGAGACGGAAGTAACATGGGAAGACCAGCAGAACATCAACAAATTCGGAAGGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA