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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccacaaacatggagttaaccacaaaaatttatgcatccaagtgatgaatagagatcatatattcgtccctaactcccaacatgcttattttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCGAGCACCAAGAAAATCCTAATAATGGGAGGCACCAGGTTTATTGGTGTGT

Basic information

species Glycine max
transcript GLYMA19G41540.2
intron # 1
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|209712446|gb|BW671298.1|BW671298
EST:     CTTCCTCTCTTTCTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|209706965|gb|BW661524.1|BW661524
EST:     CTTCCTCTCTTTCTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|8670400|gb|BE191507.1|BE191507
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|209702885|gb|BW655995.1|BW655995
EST:     CTTCCTCTCTTTCTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|27426223|gb|CA937743.1|CA937743
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|213595578|gb|DB962434.1|DB962434
EST:     CTTCCTCTCTTTCTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|120530586|gb|EH258719.1|EH258719
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|5753286|gb|AI960573.1|AI960573
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|16348529|gb|BI974124.1|BI974124
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|213617672|gb|DB959340.1|DB959340
EST:     CTTCCTCTCTTTCTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|7284172|gb|AW596769.1|AW596769
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|7686625|gb|AW757282.1|AW757282
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|120533740|gb|EH261873.1|EH261873
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|209707067|gb|BW653204.1|BW653204
EST:     CTTCCTCTCTTTCTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|209719660|gb|BW669219.1|BW669219
EST:     CTTCCTCTCTTTCTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|15286291|gb|BI470182.1|BI470182
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|15287371|gb|BI471262.1|BI471262
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|20449765|gb|BQ253889.1|BQ253889
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|22523298|gb|BU082109.1|BU082109
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|20497984|gb|BQ272914.1|BQ272914
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|120533746|gb|EH261879.1|EH261879
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|17519820|gb|BM188862.1|BM188862
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
EST: gi|120533723|gb|EH261856.1|EH261856
EST:     CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAG                         TTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG
genomic: CTTCCTCTCTTTTTGACTTCAGTGGAACCAGACTTCAAACTCAACTTCAGgtcctcatat ... ttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatagagatcatatattcgtccctaactcccaacatgcttattttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCGAGCACCAAGAAAATCCTAATAATGGGAGGCACCAGGTTTATTGGTGTGT
                      ccctaac  putative branch site (score: 2)
                                       cttatttt  putative PPT
         atcatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccacaaacatggagttaaccacaaaaatttatgcatccaagtgatgaatagagatcatatattcgtccctaactcccaacatgcttattttgggtacagTTCAAGAGAAAACTATGCCATCCAAAAGGGTCTTTCTACGTCTCGGCATCGAGCACCAAGAAAATCCTAATAATGGGAGGCACCAGGTTTATTGGTGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
-ccacaaa
- cacaaac
- - - - - - - - - - - - - - - - -gcatcca
- - - - - - - - - - - - - - - - - - - - agtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgct