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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgtgtttttcctttttcataaattttatttatttgttggtttttgttagttatcaatattttttcacaaggcccataaaattggtaggtattgaactgaaaaagaatgttccctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTAAAGAACTAAGTCAGTTGTTAGAATCAGTTTACATGGAAAAT

Basic information

species Glycine max
transcript GLYMA17G01120.1
intron # 9
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|192331982|gb|FK024512.1|FK024512
EST:     TTTCCTAGAAATCATGGCATGCCCTTCAG                         GTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
genomic: TTTCCTAGAAATCATGGCATGCCCTTCAGgtaccgtgtt ... ctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
EST: gi|9902332|gb|BE611300.1|BE611300
EST:     AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAG                         GTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
genomic: AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAGgtaccgtgtt ... ctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
EST: gi|31310021|gb|CD395224.1|CD395224
EST:     AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAG                         GTTGCTTAAATGGGGGAGGTCAAATTAAACCAAGTTCAGGGCAATCTCCTA
genomic: AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAGgtaccgtgtt ... ctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
EST: gi|6482176|gb|AW201447.1|AW201447
EST:     AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAG                         GTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
genomic: AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAGgtaccgtgtt ... ctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
EST: gi|14992014|gb|BI317687.1|BI317687
EST:     AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAG                         GTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
genomic: AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAGgtaccgtgtt ... ctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
EST: gi|254341393|gb|GR855121.1|GR855121
EST:     AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAG                         GTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
genomic: AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAGgtaccgtgtt ... ctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
EST: gi|10709530|gb|BF009254.1|BF009254
EST:     AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAG                         GTTGCTTANATGGAG-AGGTCAAATTAAACCAAGTTCAGGGC
genomic: AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAGgtaccgtgtt ... ctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGC
EST: gi|19269650|gb|BM885906.1|BM885906
EST:     AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAG                         GTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA
genomic: AACTGGGAAATGTGATTATCATTTCCTAGAAATCATGGCATGCCCTTCAGgtaccgtgtt ... ctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggcccataaaattggtaggtattgaactgaaaaagaatgttccctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTAAAGAACTAAGTCAGTTGTTAGAATCAGTTTACATGGAAAAT
                                       tgttccctc  CT-rich tract
       ataaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccgtgtttttcctttttcataaattttatttatttgttggtttttgttagttatcaatattttttcacaaggcccataaaattggtaggtattgaactgaaaaagaatgttccctcaatgcagGTTGCTTAAATGGGGGAGGTCAAATCAAACCAAGTTCAGGGCAATCTCCTAAAGAACTAAGTCAGTTGTTAGAATCAGTTTACATGGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA