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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgagatctgagatctctatttcgtacaacgattatttcagatttgtgcgttctactatttcgtggtttttgattctatttatttttctacgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGGCAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGT

Basic information

species Glycine max
transcript GLYMA04G01840.8
intron # 2
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|208329120|gb|GE128416.1|GE128416
EST:     ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAAGGAAACCCG
genomic: ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTA-GGAAACCCG
EST: gi|193340893|gb|FK307170.1|FK307170
EST:     ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|208240700|gb|GE037248.1|GE037248
EST:     ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCA
genomic: ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCA
EST: gi|193546645|gb|FK503648.1|FK503648
EST:     AGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAG                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: AGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|193434275|gb|FK399321.1|FK399321
EST:     ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|193592416|gb|FK545634.1|FK545634
EST:     ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|208119912|gb|GD919763.1|GD919763
EST:     GAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATCCCAA                         ACTTGCTGTGAATAAGAAGGG
genomic: GAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGG
EST: gi|193629203|gb|FK578151.1|FK578151
EST:     ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|193621980|gb|FK569216.1|FK569216
EST:     AGCCGATGCCAA                         ACTTGCTGTGAATAANAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: AGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|207832519|gb|GD802663.1|GD802663
EST:     AGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: AGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|207785780|gb|GD757879.1|GD757879
EST:     ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAAAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|207690945|gb|GD671567.1|GD671567
EST:     ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|193535155|gb|FK491699.1|FK491699
EST:     TCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: TCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|208196615|gb|GD994910.1|GD994910
EST:     TGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: TGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|208205358|gb|GE004089.1|GE004089
EST:     AGGAGAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: AGGA-AAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|207763040|gb|GD731171.1|GD731171
EST:     AAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: AAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|193455897|gb|FK417018.1|FK417018
EST:     TGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
genomic: TGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG
EST: gi|10233700|gb|BE802588.1|BE802588
EST:     ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAA                         ACTTGCTGTGAATAAGAAGGGCGCCGCCACCAATACTAGGAAACCCGCCGG
genomic: ATCATGAAAGGAGGAAAGTCCAAGACCGAATCTAAGAGAGCCGATGCCAAgtaagtttca ... cgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcgttctactatttcgtggtttttgattctatttatttttctacgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGGCAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGT
                      ttttgat  putative branch site (score: 4)
                                     tttttctac  putative PPT
                     tttttgattctattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgagatctgagatctctatttcgtacaacgattatttcagatttgtgcgttctactatttcgtggtttttgattctatttatttttctacgaatctcagACTTGCTGTGAATAAGAAGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGGCAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG