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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagaatgtgttgttaacatttatctttagactatcgtaatagtttaatatcttgatttagctccacaagtgacattttgtcatcttgcatgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTAGAGATACCGGAAAATGTGGAATTTCTGGGTCAAAAGATTGACCTTACAC

Basic information

species Glycine max
transcript GLYMA15G11910.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G11910.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22240.1 (Arabidopsis thaliana), 3'ss of exon 2
aaagaatgtgttgttaacatttatctttagactatcgtaatagtttaatatcttgatttagctccacaagtgacattttgtcatcttgcatgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTAGAGATACCGGAAAATGTGGAATTTCTGGGTCAAAAGATTGACCTTACAC
       ||    | | |||| |||    ||| ||  |   |  | || |||||||   | |      ||| |  |||||  || |    | |  |  |||| ||||||||| ||||| ||||||| || || ||||| ||||| ||  | |||||||||||| |||| ||  |||| |||||||||||||| ||||  |
-------gtaaattgaccattcatc----gaccatgatctgatatcaacatcttga---aacgttttcagtaatgttttgg-atttcatttttcttgcagATTAAGTTTGAGCAAGGCGTAATTGGGACGCCTCAGCTAACGGATTCTATTGAGATACCGGAATATGTAGAGGTTCTTGGTCAAAAGATTGATCTTAACC
















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|213610785|gb|DB974862.1|DB974862
EST:     CAATTAGTACTAATGCCAAATTTGATGAACGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|26058908|gb|CA801822.1|CA801822
EST:     CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|22524432|gb|BU083243.1|BU083243
EST:     CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|120496467|gb|EH224634.1|EH224634
EST:     CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGGAAG-CATAATTGGCACTCCACAGCTTACGGACTCATT
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGG-AAGGCATAATTGGCACTCCACAGCTTACGGACTCATT
EST: gi|213591964|gb|DB975198.1|DB975198
EST:     CAATTAGTACTAATGCCAGCCTGGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|214009389|gb|DB988614.1|DB988614
EST:     AGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTCCGAGGAAGGCATAATCAAAACTCCACAGCTTACGGACTCATTA
genomic: AGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|6725960|gb|AW310359.1|AW310359
EST:     CAATTAGGACTAATGCAAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|120491729|gb|EH219896.1|EH219896
EST:     CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|209702829|gb|BW660694.1|BW660694
EST:     CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|16343484|gb|BI969079.1|BI969079
EST:     CAATTAGTACTAATGCAAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|8402091|gb|BE057725.1|BE057725
EST:     CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|20812112|gb|BQ296590.1|BQ296590
EST:     ACTAATGCCAAATTTGATGTTGGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: ACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|213608713|gb|DB974410.1|DB974410
EST:     AACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: AACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
EST: gi|15203227|gb|BI425995.1|BI425995
EST:     CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAG                         ATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA
genomic: CAATTAGTACTAATGCCAAATTTGATGTTCGAAGTCCAAAACGTGTGCAGgtttgtttgt ... tgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatatcttgatttagctccacaagtgacattttgtcatcttgcatgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTAGAGATACCGGAAAATGTGGAATTTCTGGGTCAAAAGATTGACCTTACAC
     tcttgat  putative branch site (score: 4)
       ttgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagaatgtgttgttaacatttatctttagactatcgtaatagtttaatatcttgatttagctccacaagtgacattttgtcatcttgcatgttgtttagATAAAGTTTGAGGAAGGCATAATTGGCACTCCACAGCTTACGGACTCATTAGAGATACCGGAAAATGTGGAATTTCTGGGTCAAAAGATTGACCTTACAC

- -gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttgca