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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaaaccggatgaccaagagaaaatacctttttacgcttttgattcctcatttttatctctctctcttttttaaattttcttattcatttgatcttcagGAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGAAGGAAGGGAACTATCAAATATGGTGCAGCGGATGCACAAGAACAG

Basic information

species Glycine max
transcript GLYMA04G39170.1
intron # 11
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|21601591|gb|BQ611922.1|BQ611922
EST:     GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAACCCAGACAG                         GAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGA
genomic: GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAACCCAGACAGgtaccgattt ... tgatcttcagGAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGA
EST: gi|207731193|gb|GD706610.1|GD706610
EST:     TTCTTAGGTCACCGCAAGACAATCAACCCAGACAG                         GAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGA
genomic: TTCTTAGGTCACCGCAAGACAATCAACCCAGACAGgtaccgattt ... tgatcttcagGAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGA
EST: gi|120494146|gb|EH222313.1|EH222313
EST:     GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAANCCAGACAG                         GAAAGGACTTGTTGGAATTTTT-ATATGCTGGAAACTGGAGAGCTAGAAGA
genomic: GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAACCCAGACAGgtaccgattt ... tgatcttcagGAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGA
EST: gi|12489962|gb|BG043483.1|BG043483
EST:     GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAACCCAGACAG                         GAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGA
genomic: GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAACCCAGACAGgtaccgattt ... tgatcttcagGAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGA
EST: gi|120494144|gb|EH222311.1|EH222311
EST:     GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAACCCAGACAG                         GAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGA
genomic: GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAACCCAGACAGgtaccgattt ... tgatcttcagGAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGA
EST: gi|298194946|gb|HO043418.1|HO043418
EST:     GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAACCCAGACAG                         GAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAA
genomic: GAGGGGCACCGCAGATTCTTAGGTCACCGCAAGACAATCAACCCAGACAGgtaccgattt ... tgatcttcagGAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcatttttatctctctctcttttttaaattttcttattcatttgatcttcagGAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGAAGGAAGGGAACTATCAAATATGGTGCAGCGGATGCACAAGAACAG
                                          atttgat  putative branch site (score: 5)
            tctctctctctttttt  CT-rich tract
                      ttttttaaattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaaaccggatgaccaagagaaaatacctttttacgcttttgattcctcatttttatctctctctcttttttaaattttcttattcatttgatcttcagGAAAGGACTTGTTGGAATTTTTTATATGCTGGAAACTGGAGAGCTAGAAGAAGGAAGGGAACTATCAAATATGGTGCAGCGGATGCACAAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
tgcaaac
- - - - - - - - - - gaaaatac
- - - - - - - - - - - - - - - - - - gcttttg