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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaagttactctgatcttattgttaattataacttttacctgatagccaagttctttttgctcattgctactgctttcatgtttccattttagGGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATCTTGTCTCCAATGATCCAAATGTAATTGCTTGCAACATGGAAAAT

Basic information

species Glycine max
transcript GLYMA19G08930.1
intron # 4
splice site 3'
intron type U2

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|26057623|gb|CA800537.1|CA800537
EST:     GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTG                         GGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
genomic: GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTGgtgagaagtt ... tccattttagGGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
EST: gi|9820197|gb|BE555707.1|BE555707
EST:     TGGCTGNNNNNNNCAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTG                         GGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
genomic: TGGCTG-AAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTGgtgagaagtt ... tccattttagGGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
EST: gi|151406301|gb|EV276116.1|EV276116
EST:     GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTG                         GGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
genomic: GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTGgtgagaagtt ... tccattttagGGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
EST: gi|298197544|gb|HO045023.1|HO045023
EST:     GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTG                         GGGAAGCACTC
genomic: GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTGgtgagaagtt ... tccattttagGGGAAGCACTC
EST: gi|192327181|gb|FK015573.1|FK015573
EST:     GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTG                         GGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
genomic: GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTGgtgagaagtt ... tccattttagGGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
EST: gi|254349200|gb|GR859945.1|GR859945
EST:     GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTG                         GGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
genomic: GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTGgtgagaagtt ... tccattttagGGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
EST: gi|51343885|gb|CO984618.1|CO984618
EST:     GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTG                         GGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC
genomic: GTGGCTGAAAAAACAGAGCCTTTCTTTTGTTGTTGCCGATTTTGGTTGTGgtgagaagtt ... tccattttagGGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgatagccaagttctttttgctcattgctactgctttcatgtttccattttagGGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATCTTGTCTCCAATGATCCAAATGTAATTGCTTGCAACATGGAAAAT
 acctgat  putative branch site (score: 4)
                                           tttccatttt  putative PPT
             ttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaagttactctgatcttattgttaattataacttttacctgatagccaagttctttttgctcattgctactgctttcatgtttccattttagGGGAAGCACTCATTGCTAAAAGTGTGAAGAATGAAGTATTCTCTCTAGATCTTGTCTCCAATGATCCAAATGTAATTGCTTGCAACATGGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA