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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgcattcatttggctcttccttaacacaaatagaaattctaattgaaagaaaaaaattgcctgcttgaaattaaacttgcataatatttgaggccttagatacatgctcaagtgctaggtttgcatttgtaatttagtagtgcttctaggcaatgaatggatgtggttacttgtttttcattttttagCTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGTAAAGATTATTACTGACATTAACATTGCTGTTGAATCCGGAGAATTTGAC

Basic information

species Glycine max
transcript GLYMA08G23440.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23440.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0018g01780.t01 (Vitis vinifera), 3'ss of exon 7
gtgatgcattcatttggctcttccttaacacaaatagaaattctaattgaaagaaaaaaattgcctgcttgaaattaaacttgcataatatttgaggccttagatacatgctcaagtgctaggtttgcatttgtaatttagtagtgcttctaggcaatgaatggat-gtgg-ttacttgtttttcattttttagCTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGTAAAGATTATTACTGACATTAACATTGCTGTTGAATCCGGAGAATTTGAC
                                                                                           ||||||    ||   ||          |||   |   | | ||  |   | | ||| | |   ||        || ||   ||| || || | | | ||  |||||||| |||||||| || || ||||| |||||||||||||| ||||| |||||||  || |||||||||||||| | ||||||||| ||||| ||||||
-----------------------------------------------------------------------------------------tgttgaggttgaagccccacat---gacactaccctcctaat-gttgtggggcaatgcct-tgatcagcaggcaaatagtaacttagttcttatccttgttgcagCTTGCTTTATGTGGAAACTGCAGATCGCCCTGGATTACTGGTGGATCTCGTAAAGAGCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGAC
















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|192298594|gb|FG988535.1|FG988535
EST:     GTAGACATAGCAACCCACATAAACATTTCTGATGATTGCCCAGATAGAAG                         CTTGCTGTATGTGGAGACAGCTG
genomic: GTAGACATAGCAACCCACATAAACATTTCTGATGATTGCCCAGATAGAAGgtgatgcatt ... cattttttagCTTGCTGTATGTGGAGACAGCTG
EST: gi|12496583|gb|BG047137.1|BG047137
EST:     CCACATAAACATTTCTGATGATTGCCCAGATAGAAG                         CTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT
genomic: CCACATAAACATTTCTGATGATTGCCCAGATAGAAGgtgatgcatt ... cattttttagCTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT
EST: gi|192326608|gb|FK017295.1|FK017295
EST:     GTAGACATAGCAACCCACATAAACATTTCTGATGATTGCCCAGATAGAAG                         CTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT
genomic: GTAGACATAGCAACCCACATAAACATTTCTGATGATTGCCCAGATAGAAGgtgatgcatt ... cattttttagCTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT
EST: gi|213595816|gb|DB981496.1|DB981496
EST:     GTAGACATAGCAACCCACATAAACATTACTGATGATTGCCCAGATAGAAG                         CTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT
genomic: GTAGACATAGCAACCCACATAAACATTTCTGATGATTGCCCAGATAGAAGgtgatgcatt ... cattttttagCTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT
EST: gi|151405909|gb|EV275724.1|EV275724
EST:     GTAGACATAGCAACCCACATAAACATTTCTGATGATTGCCCAGATAGAAG                         CTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT
genomic: GTAGACATAGCAACCCACATAAACATTTCTGATGATTGCCCAGATAGAAGgtgatgcatt ... cattttttagCTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT
EST: gi|7691333|gb|AW759392.1|AW759392
EST:     CCCACATAAACATTTCTGATGATTGCCCAGATAGAAG                         CTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT
genomic: CCCACATAAACATTTCTGATGATTGCCCAGATAGAAGgtgatgcatt ... cattttttagCTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtagtgcttctaggcaatgaatggatgtggttacttgtttttcattttttagCTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGTAAAGATTATTACTGACATTAACATTGCTGTTGAATCCGGAGAATTTGAC
                                    cttgtttttcattttt  CT-rich tract
                                 ttacttgtttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgcattcatttggctcttccttaacacaaatagaaattctaattgaaagaaaaaaattgcctgcttgaaattaaacttgcataatatttgaggccttagatacatgctcaagtgctaggtttgcatttgtaatttagtagtgcttctaggcaatgaatggatgtggttacttgtttttcattttttagCTTGCTGTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGTAAAGATTATTACTGACATTAACATTGCTGTTGAATCCGGAGAATTTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA