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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtaataaatctttacaccgttagtgcatatattatttattcataattacatactactaagtcctaagttattgaatgaccaatgtatgtaatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTGCACAGTATGGGGTTCAGATTGAGACTGCTGTGAGGGATAGGTTGGCAGC

Basic information

species Glycine max
transcript GLYMA04G40030.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40030.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g02870.t01 (Vitis vinifera), 3'ss of exon 3
atgtaataaatctttacaccgttagtgcatatattatttattcataattac-atactactaagtcctaagttattgaatgaccaatgtatgtaat--gtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTGCACAGTATGGGGTTCAGATTGAGACTGCTGTGAGGGATAGGTTGGCAGC
   ||    |  ||  |         | |  |  | |  || || |||  | |  ||  | | |  |   | || ||   |||  | | | |  |   | ||||||| |  ||||||||| | ||| ||||||||||||| |||||||||||| ||||||| ||||| ||| | |||| ||| || |||||  | ||||||||
---taggcgactttccctagaaataagtaactgatgtgaatgcaaaatctcgacccttttgacttatgcatgatagaggaacccttttttatggttaatgcagCTCCTGGAGAGAAGTTTTTGAGAATTGTGGTGATCAAGGAGATCAAGGGTTCACAGTACGGGGTGCAGCTAGAGAGTGCAGTCAGGGACCGATTGGCAGC
















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|15815653|gb|BI787928.1|BI787928
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|254342752|gb|GR858914.1|GR858914
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|192302413|gb|FG997353.1|FG997353
EST:     GCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTTTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: GCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|298179554|gb|HO028025.1|HO028025
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|192305625|gb|FG994335.1|FG994335
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGCGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|58020389|gb|CX707131.1|CX707131
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|151404578|gb|EV274392.1|EV274392
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|26268875|gb|CA819938.1|CA819938
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|151393172|gb|EV263047.1|EV263047
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|9901324|gb|BE610292.1|BE610292
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|298168598|gb|HO009528.1|HO009528
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|192327228|gb|FK019535.1|FK019535
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|254320382|gb|GR826399.1|GR826399
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|254320381|gb|GR826398.1|GR826398
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|7588785|gb|AW704573.1|AW704573
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|58017161|gb|CX703903.1|CX703903
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|192302412|gb|FG997352.1|FG997352
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|9899641|gb|BE608609.1|BE608609
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|151394357|gb|EV264228.1|EV264228
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|21285634|gb|BQ473505.1|BQ473505
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|192305626|gb|FG994336.1|FG994336
EST:     AAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGCGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: AAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
EST: gi|254342751|gb|GR858913.1|GR858913
EST:     TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTG                         CTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG
genomic: TGCAAAGGAGCTGGAAGAGAACGATGAGTTCTTCAATGCTCTCATTTCTGgtaattatga ... taatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacatactactaagtcctaagttattgaatgaccaatgtatgtaatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTGCACAGTATGGGGTTCAGATTGAGACTGCTGTGAGGGATAGGTTGGCAGC
                    taagttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtaataaatctttacaccgttagtgcatatattatttattcataattacatactactaagtcctaagttattgaatgaccaatgtatgtaatgtacagCTCCGGTGGAGAAGTTTATTAGACTTGTGGTGATCAAAGAGATCAAGGGTGCACAGTATGGGGTTCAGATTGAGACTGCTGTGAGGGATAGGTTGGCAGC

- - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - tacatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaatgt