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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggataggcatcaatacaatttggttttccctttgtcttctattatgcgcttttggcttgcaattttaatgggatttcctgactatgagattttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACATCTGAAAATTTTAATGAGGTTGTCTTAGATGAAACCAAAGATGTCTTGGT

Basic information

species Glycine max
transcript GLYMA06G24520.1
intron # 5
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|193731335|gb|FK664867.1|FK664867
EST:     GGGCCACGTCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAG                         GAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT
genomic: GGGCCACG-CACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAGgtactgcttg ... tttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT
EST: gi|208316849|gb|GE115855.1|GE115855
EST:     AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAG                         GAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTAC
genomic: AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAGgtactgcttg ... tttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTAC
EST: gi|208142142|gb|GD934888.1|GD934888
EST:     AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAG                         GAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT
genomic: AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAGgtactgcttg ... tttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT
EST: gi|208270669|gb|GE066919.1|GE066919
EST:     AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAG                         GAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTAC
genomic: AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAGgtactgcttg ... tttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTAC
EST: gi|193515760|gb|FK474330.1|FK474330
EST:     AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAG                         GAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT
genomic: AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAGgtactgcttg ... tttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT
EST: gi|193488849|gb|FK453214.1|FK453214
EST:     AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAG                         GAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT
genomic: AGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAGgtactgcttg ... tttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT
EST: gi|207754217|gb|GD724753.1|GD724753
EST:     TTCACTTGCTGAGTTTGTAAATACGGAAGGAG                         GAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT
genomic: TTCACTTGCTGAGTTTGTAAATACGGAAGGAGgtactgcttg ... tttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgcttttggcttgcaattttaatgggatttcctgactatgagattttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACATCTGAAAATTTTAATGAGGTTGTCTTAGATGAAACCAAAGATGTCTTGGT
                              tcctgac  putative branch site (score: 2)
                                            ttttctcgc  putative PPT
               aattttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggataggcatcaatacaatttggttttccctttgtcttctattatgcgcttttggcttgcaattttaatgggatttcctgactatgagattttctcgcagGAACAAATGTGAAGATTGCTACAGCTCCTTCCAATGTAGTGGTGCTTACATCTGAAAATTTTAATGAGGTTGTCTTAGATGAAACCAAAGATGTCTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - caataca
- - - - - - - - - - - - - -ccctttg
- - - - - - - - - - - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgag