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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caactaaacatagctcattcctgtccggttccaaatttatacatcaaaagatttaacgatactgagatgttatagcttataacatttccttttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAGAGAAACTG

Basic information

species Glycine max
transcript GLYMA09G40990.1
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|213608125|gb|DB972593.1|DB972593
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|193365164|gb|FK331433.1|FK331433
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTT-CAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|208195566|gb|GD991243.1|GD991243
EST:     TCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATTGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: TCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAAT-GGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|213595971|gb|DB966274.1|DB966274
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGCTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|193719544|gb|FK652210.1|FK652210
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
EST: gi|208148837|gb|GD944993.1|GD944993
EST:     TTCAGGGGGGATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAAGTAACGAAAGAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|193522167|gb|FK482082.1|FK482082
EST:     TCAGGGGGAATCTTCTTGCTAATAGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
genomic: TCAGGGGGAATCTTCTTGCTAAT-GGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
EST: gi|208309100|gb|GE106742.1|GE106742
EST:     CAAGGGGGAAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
genomic: CA-GGGGGAA-TCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
EST: gi|193575393|gb|FK527606.1|FK527606
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAAACGAAAAA
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAA-CGAAAAA
EST: gi|209707241|gb|BW670572.1|BW670572
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|207770436|gb|GD744164.1|GD744164
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAAT
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAAT
EST: gi|193338311|gb|FK305114.1|FK305114
EST:     TTCAAGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAAT
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAAT
EST: gi|207797728|gb|GD771540.1|GD771540
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|207689956|gb|GD673525.1|GD673525
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|193629905|gb|FK576025.1|FK576025
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|208304429|gb|GE104356.1|GE104356
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|208076712|gb|GD875641.1|GD875641
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|208181405|gb|GD974658.1|GD974658
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|193557754|gb|FK513621.1|FK513621
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAAACGAAAAAA
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAA-CGAAAAAA
EST: gi|208153170|gb|GD948749.1|GD948749
EST:     TTCAGGGG-AATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
EST: gi|193629927|gb|FK573261.1|FK573261
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
EST: gi|193393685|gb|FK358921.1|FK358921
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAAACGAAAAAATGATCA
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAA-CGAAAAAATGATCA
EST: gi|213589246|gb|DB957778.1|DB957778
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGGACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAG
EST: gi|193312374|gb|FK276116.1|FK276116
EST:     TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGG                         ATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACG
genomic: TTCAGGGGGAATCTTCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGGgtatgtgtgt ... tttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagatttaacgatactgagatgttatagcttataacatttccttttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAGAGAAACTG
                               ttataac  putative branch site (score: 2)
                                     catttcctttt  CT-rich tract
                               ttataacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caactaaacatagctcattcctgtccggttccaaatttatacatcaaaagatttaacgatactgagatgttatagcttataacatttccttttggtgcagATGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAGAGAAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- -ctaaaca
- - - - - - - -cattcct
- - - - - - - - - - - - - - - ccaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatactg