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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagatttggcatttaaactgtaatcctaaataattgctgaagaccattgattgtaggggaaaaaagtgttattccttatctaaactctacattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTCTATAAAAAATTCACTTCACTTTGGGATGAGCACAAAGACGGTGCTGGTG

Basic information

species Glycine max
transcript GLYMA20G26580.1
intron # 4
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|6228208|gb|AW156807.1|AW156807
EST:     AAATGATCGAAAA                         TCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
genomic: AAATGATCGAAAAgtaggtcccc ... cattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
EST: gi|151395006|gb|EV264877.1|EV264877
EST:     TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAA                         TCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
genomic: TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccc ... cattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
EST: gi|9987542|gb|BE661650.1|BE661650
EST:     TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAA                         TCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
genomic: TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccc ... cattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
EST: gi|254322009|gb|GR837423.1|GR837423
EST:     TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAA                         TCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
genomic: TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccc ... cattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
EST: gi|24205958|gb|BU965211.1|BU965211
EST:     TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAA                         TCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
genomic: TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccc ... cattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
EST: gi|151395015|gb|EV264886.1|EV264886
EST:     TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAA                         TCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
genomic: TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccc ... cattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
EST: gi|10232185|gb|BE801081.1|BE801081
EST:     TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAA                         TCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
genomic: TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccc ... cattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
EST: gi|254332676|gb|GR844046.1|GR844046
EST:     TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAA                         TCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC
genomic: TGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccc ... cattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgattgtaggggaaaaaagtgttattccttatctaaactctacattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTCTATAAAAAATTCACTTCACTTTGGGATGAGCACAAAGACGGTGCTGGTG
                                 atctaaa  putative branch site (score: 3)
               aaaaaagtgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagatttggcatttaaactgtaatcctaaataattgctgaagaccattgattgtaggggaaaaaagtgttattccttatctaaactctacattatgcagTCCTATAAGGAGTGGATTCTTAAGACGATTGAAGACAGTTGGAATCTTTTCTATAAAAAATTCACTTCACTTTGGGATGAGCACAAAGACGGTGCTGGTG

- - - - ggcattt
- - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtagggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaag