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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGGGGTGGAAGGATAAGAATCAAGTTGAGGATGATTCACCAATATTTAGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgtttccagtttccattactttattactttcttttctgctatgctgtcttgatgtgtcaaatttaagaatagagaaaatctgtcttgtctttctctatggtattcatgggtgaagtgttttttttttccttttctttttctatag

Basic information

species Glycine max
transcript GLYMA08G28320.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G28320.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0005g04550.t01 (Vitis vinifera), 5'ss of exon 1
TTTTGGGGTGGAAGGATAAGAATCAAGTTGAGGATGATTCACCAATATTTAGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgtttccagtttccattactttattactttcttttctgctatgctgtcttgatgtgtcaaatttaagaatagagaaaatctgtcttgtctttctctatggtattcatgggtgaagtgttttttttttccttttctttttctatag
           |  || |  ||  || ||||   |  ||| || || ||  | |||||||||||| | ||||||||||||||| | |||||||  |||||||       | || | |    |   || | |  |||   ||  |    |                                                                                                     
ACCCCACCCCAACTGAAACTAAAGAAATTGAATCTTCTTCTCCCATTTTCCGCAACAAAGAGAAGGTGTTGGTCACTTGCTCTCGCCGCATCAGCTACAGgt------cttcactatttcctctcttctcagcttcccctcccccccccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn--------------------------------------------
















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|13181521|gb|BG352861.1|BG352861
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|27808906|gb|CB063328.1|CB063328
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|208325012|gb|GE118330.1|GE118330
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|7283962|gb|AW596563.1|AW596563
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|151409158|gb|EV278966.1|EV278966
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|17021807|gb|BM092841.1|BM092841
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|298197751|gb|HO039290.1|HO039290
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|151399665|gb|EV269536.1|EV269536
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|213619549|gb|DB957250.1|DB957250
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACAGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|17154077|gb|BM144010.1|BM144010
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|15815223|gb|BI787498.1|BI787498
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
EST: gi|7458614|gb|AW666064.1|AW666064
EST:     AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAG                         GTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA
genomic: AGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgttt ... ttttctatagGTACCGGCATTTGATGTTGAATTTGGTCACACTTTTGCCTCATTGTAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGGGGTGGAAGGATAAGAATCAAGTTGAGGATGATTCACCAATATTTAGGAACAAAGAGAAGCTATTGGTCACTTGCTCTAGGCGCATCAATTACAGgtgattgtttccagtttccattactttattactttcttttctgctatgctgtcttgatgtgtcaaatttaagaatagagaaaatctgtcttgtctttctctatggtattcatgggtgaagtgttttttttttccttttctttttctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC