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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGCCGGGGACGAATCTATGTGATTTGCTCTGGGAACCCTAAGCACAAGCAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgtttttctttttcctggttttgaattgccatatggtgtggagaaattgtagaaccaacactaactattgtttttagggatatcgtattttaact...

Basic information

species Glycine max
transcript GLYMA17G12290.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12290.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv11s0016g05390.t01 (Vitis vinifera), 5'ss of exon 2
AGCGCCGGGGACGAATCTATGTGATTTGCTCTGGGAACCCTAAGCACAAGCAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgtttttctttttcctggttttgaattgccatatggtgtggagaaattgtagaaccaacactaactattgtttttagggatatcgtattttaact-
| || || || ||| | |||||  | ||| | |  || || ||||||||||||||||| |||||| ||||||||||   |||||||||   ||  ||| ||||||  ||||  |    |    | ||   ||  ||| | | || |      |||  | |       ||  |||    |||  | |   | ||| | |   
AACGTCGTGGGCGAGTATATGTACTATGCACAGCCAATCCCAAGCACAAGCAACGACAAGGCATGTCAACATTTGCCCATGAAGGCCCTCTTCCTCCAATgtatgcattttcttcaagctctatctttc-ttttcattttgagttgttcttgtgtgcaccatgggtgaagaatttaggttactgctgaggcattgtcaaaa
















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|208279256|gb|GE079245.1|GE079245
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|208178546|gb|GD977827.1|GD977827
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|193657812|gb|FK601475.1|FK601475
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|207817208|gb|GD788847.1|GD788847
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATGAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|19934906|gb|BQ079936.1|BQ079936
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|208132013|gb|GD928966.1|GD928966
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|208140946|gb|GD935260.1|GD935260
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|298191145|gb|HO038624.1|HO038624
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|17020758|gb|BM091792.1|BM091792
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|14125779|gb|BG790217.1|BG790217
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|208325897|gb|GE124549.1|GE124549
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|208113477|gb|GD912922.1|GD912922
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|9820852|gb|BE556362.1|BE556362
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|193714440|gb|FK655011.1|FK655011
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|208289613|gb|GE086760.1|GE086760
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|7640110|gb|AW734418.1|AW734418
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|208246649|gb|GE044317.1|GE044317
EST:     CATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|208134708|gb|GD927433.1|GD927433
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGAT-GGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|193361131|gb|FK323899.1|FK323899
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|193413627|gb|FK379990.1|FK379990
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|193346943|gb|FK310918.1|FK310918
EST:     CAACGACA-GGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
EST: gi|193313062|gb|FK279619.1|FK279619
EST:     CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGT                         GTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC
genomic: CAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgttt ... atcatttcagGTCCTCGGAAACAAGTAGCTGGAAGATGGGGATAAAGCCTGCTCAAATTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGCCGGGGACGAATCTATGTGATTTGCTCTGGGAACCCTAAGCACAAGCAACGACAGGGCATGGCAACATTTGCAAGTGAAGGCCCATCTCGACCAGTgtatgtgtttttctttttcctggttttgaattgccatatggtgtggagaaattgtagaaccaacactaactattgtttttagggatatcgtattttaact

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