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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAACTGGGGTCTCAAGCTTCTGATCCACCCAAGGAGGAATACATACATGTTAGAGCTCGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagattttgtgagaacttatctgtaatgaaaatgaagtttttgtatgaagaattttaaattagattttcactgcag

Basic information

species Glycine max
transcript GLYMA01G09400.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G09400.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv01s0010g00740.t01 (Vitis vinifera), 5'ss of exon 3
CAAACTGGGGTCTCAAGCTTCTGATCCACCCAAGGAGGAATACATACATGTTAGAGCTCGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagattttgtgagaac----ttatctgtaatgaaaatgaagtttttgtatgaa----gaattttaaattag---attttcactgcag
 || | |||| | |||||||| |||||||| ||||| ||||| || ||||| ||||| ||  | ||||| ||||||||||||||||| |||||||| |||||||||||||    | |     |||  | | ||  ||   |   | ||||   |     | | || ||  | |   |  || |   |||
TAAGCAGGGGGCACAAGCTTCAGATCCACCAAAGGAAGAATATATTCATGTCAGAGCACGGAGAGGTCAGGCAACAAACAGCCATAGTCTTGCAGAAAGAgtaagatttttcatggatagttttagttttgatagaagcaattctattgtcctagtcttggagttaaagctggtggaccttgatgacag
















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|193362293|gb|FK324809.1|FK324809
EST:     GCCGGGGTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
genomic: GCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
EST: gi|208160240|gb|GD953496.1|GD953496
EST:     TCGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
genomic: TCGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
EST: gi|193467285|gb|FK433924.1|FK433924
EST:     GCCGGGGTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
genomic: GCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
EST: gi|208027231|gb|GD822633.1|GD822633
EST:     GTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGGGAGAATGAAGTTTCTTCAAGATCTTGTA
genomic: GTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
EST: gi|207712306|gb|GD693770.1|GD693770
EST:     GCCGGGGTCAAGCAACAAACAGCCATAGTCCTTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
genomic: GCCGGGGTCAAGCAACAAACAGCCATAG-CC-TTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
EST: gi|23734956|gb|BU765737.1|BU765737
EST:     TTAGAGCTCGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
genomic: TTAGAGCTCGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
EST: gi|207711906|gb|GD693720.1|GD693720
EST:     CGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
genomic: CGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
EST: gi|193490748|gb|FK457749.1|FK457749
EST:     TTAGAGCTCGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
genomic: TTAGAGCTCGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
EST: gi|193455612|gb|FK418777.1|FK418777
EST:     CGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
genomic: CGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
EST: gi|208182235|gb|GD980248.1|GD980248
EST:     GCCGGGTTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA
genomic: GCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAACTGGGGTCTCAAGCTTCTGATCCACCCAAGGAGGAATACATACATGTTAGAGCTCGCCGGGGTCAAGCAACAAACAGCCATAGCCTTGCAGAGAGAgtaagattttgtgagaacttatctgtaatgaaaatgaagtttttgtatgaagaattttaaattagattttcactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA