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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagatatttatttctaaacatttaaagaatagtacacatttgaatcttgatttagattgctttatcaatgtccctgatttgcattaaactgatgttcagGATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGCCCCATCGCCAAGTCATACCGGGCAGTTAGTAATGTCCTTCCACTTGTTG

Basic information

species Glycine max
transcript GLYMA20G31850.2
intron # 3
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|10846082|gb|BF069071.1|BF069071
EST:     ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAG                         GATGGTTCAAAGCATGAGGCATGCAATGATTGGCTGCAAAACGGTAACTGC
genomic: ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAGgtatacatta ... tgatgttcagGATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
EST: gi|192299721|gb|FG993301.1|FG993301
EST:     ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAG                         GATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
genomic: ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAGgtatacatta ... tgatgttcagGATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
EST: gi|4395813|gb|AI494810.1|AI494810
EST:     ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAG                         GATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
genomic: ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAGgtatacatta ... tgatgttcagGATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
EST: gi|6502469|gb|AW203842.1|AW203842
EST:     ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAG                         GATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
genomic: ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAGgtatacatta ... tgatgttcagGATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
EST: gi|6483214|gb|AW202392.1|AW202392
EST:     ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAG                         GATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
genomic: ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAGgtatacatta ... tgatgttcagGATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
EST: gi|192300503|gb|FG988860.1|FG988860
EST:     ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAG                         GATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC
genomic: ACAACCAGAAAAGAAAATCCAAATCATCAAAAAATAATCCTTCTTCGCAGgtatacatta ... tgatgttcagGATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatttagattgctttatcaatgtccctgatttgcattaaactgatgttcagGATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGCCCCATCGCCAAGTCATACCGGGCAGTTAGTAATGTCCTTCCACTTGTTG
                                          aactgat  putative branch site (score: 3)
     atttagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagatatttatttctaaacatttaaagaatagtacacatttgaatcttgatttagattgctttatcaatgtccctgatttgcattaaactgatgttcagGATGGTTCAAAGCATGAGGCAGGCAATGATTGGCTGCAAAACGGTAACTGCCCCATCGCCAAGTCATACCGGGCAGTTAGTAATGTCCTTCCACTTGTTG

- - - - - - - ctaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatta