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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGGCAACCTTTCTAGCTTTCCATCCTCAGGATAACAATATTATCGCTATAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctgtctgcctgtaaccagtttgtacttatgatttgagattttttatgttaatgcaaagttcctttgcag

Basic information

species Glycine max
transcript GLYMA08G22910.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22910.1 (Glycine max), 5'ss of exon 21
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 5'ss of exon 21
TGCGGCAACCTTTCTAGCTTTCCATCCTCAGGATAACAATATTATCGCTATAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgta----acagctgtc---tgcctgtaac-cagtttgtac-ttatgatttgagattttttatgttaatgcaaagttcctt-tgcag
||| ||||| ||||| |||||||||||||| |||||||||||||| ||||| || |||||||||||  | || || |||||||| ||||| || |||||||||    |||| |      |   ||| |  ||     ||  |||  |    ||| || |||| |  || | |  ||| |  |||||
TGCAGCAACATTTCTTGCTTTCCATCCTCAAGATAACAATATTATTGCTATCGGGATGGATGATTCTACAATCCAGATATATAACGTCCGCGTAGATGAGgtagagtacagttaatgggtagttgtcatacatcccatatgttaacaagcaagacttcttatttggataccattttcttgatgcag

upper sequence: GLYMA08G22910.1 (Glycine max), 5'ss of exon 21
lower sequence: EFJ17248 (Selaginella moellendorffii), 5'ss of exon 21
TGCGGCAACCTTTCTAGCTTTCCATCCTCAGGATAACAATATTATCGCTATAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctgtctgcctgtaac-cagtttgtacttatgatttgagattttttatgttaatgcaaagttcctttgcag
 || ||||| || || ||||| |||||||||||||| ||| |||| ||||| || ||||| |||||  |||| || ||||| || || ||||| |||||||||        |    ||   |   |||| |     ||||| |   ||  || |   | ||||    ||  || |||
AGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGCTATCCATATATACAACGTTCGTGTCGATGAGgtatggaaaaccgatttgcgtcatggtttat-----tgattagcatttcattgtaacattgca---ctcgctttcag
















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|19934774|gb|BQ079804.1|BQ079804
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctg ... tcctttgcagGTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
EST: gi|193510745|gb|FK466683.1|FK466683
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctg ... tcctttgcagGTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
EST: gi|14999140|gb|BI320223.1|BI320223
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctg ... tcctttgcagGTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
EST: gi|27427240|gb|CA938760.1|CA938760
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctg ... tcctttgcagGTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
EST: gi|15812260|gb|BI784535.1|BI784535
EST:     TTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: TTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctg ... tcctttgcagGTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
EST: gi|19054194|gb|BM732861.1|BM732861
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctg ... tcctttgcagGTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
EST: gi|10239010|gb|BE807898.1|BE807898
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctg ... tcctttgcagGTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
EST: gi|26048827|gb|CA785280.1|CA785280
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctg ... tcctttgcagGTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGGCAACCTTTCTAGCTTTCCATCCTCAGGATAACAATATTATCGCTATAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagctgtctgcctgtaaccagtttgtacttatgatttgagattttttatgttaatgcaaagttcctttgcag

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