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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGATTGGTGAAGCATTGAGGGCCAAATTGGATCCTTTGGGTAGGCTGGTGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaattctctttgttctgccatattatgttacatgtcctgacaccaaagaaatcagagtttagattgtgtataaggctataatacttctttgatg...

Basic information

species Glycine max
transcript GLYMA09G08150.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g26880.3 (Oryza sativa), 5'ss of exon 3
ACAGATTGGTGAAGCATTGAGGGCCAAATTGGATCCTTTGGGTAGGCTGGTGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtat-cgcaatt-ctctttgttctgccatattatgttacatg--tcctgacaccaaagaaatcaga--gtttagattgtgtataaggctataatacttctttgatg
    |||||||| |||||||| || ||  |  |||   |||| ||||| ||||| ||||||||||| |||||||| || ||||| ||||| || |||||||||     |||| |     ||||| |||      | | |||   |  |  |||  | || |  | |        ||  ||| |      | |||| |||  |||| 
----ATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaata-ttcagtgat-

upper sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g26880.1 (Oryza sativa), 5'ss of exon 3
ACAGATTGGTGAAGCATTGAGGGCCAAATTGGATCCTTTGGGTAGGCTGGTGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtat-cgcaattctcttt-gttctgccatattatgttacat--gtcctgacaccaaagaaatcaga--gtttagattgtgtataaggctataatacttctttgatg
 || |||||||| |||||||| || ||  |  |||   |||| ||||| ||||| ||||||||||| |||||||| || ||||| ||||| || |||||||||     ||||  |    ||||| |||      | | |||   |  |  |||  | || |  | |        ||  ||| |      | |||| |         
GCAAATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcag------
















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|14258546|gb|BG881454.1|BG881454
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|208083788|gb|GD881736.1|GD881736
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|254327078|gb|GR836687.1|GR836687
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|208034630|gb|GD836794.1|GD836794
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATGTGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|193521194|gb|FK480305.1|FK480305
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|208076069|gb|GD875124.1|GD875124
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|254341577|gb|GR852714.1|GR852714
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|151408630|gb|EV278438.1|EV278438
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|6668020|gb|AW279471.1|AW279471
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|16347961|gb|BI973556.1|BI973556
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAA                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|254331835|gb|GR846145.1|GR846145
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|27427065|gb|CA938585.1|CA938585
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaat ... tccattacagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGATTGGTGAAGCATTGAGGGCCAAATTGGATCCTTTGGGTAGGCTGGTGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcgcaattctctttgttctgccatattatgttacatgtcctgacaccaaagaaatcagagtttagattgtgtataaggctataatacttctttgatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaagaaa