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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcttgtatgatctatctcaatctagtagagaaaaggaattatattcttcttgcttcaatttttgggtgtatttatttatcccttttatacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGACCTATGCTGATGACTGCCTTGTTGAGAGAGTTACTCAG

Basic information

species Glycine max
transcript GLYMA12G31740.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 5
atttcttgtatgatctatctcaatctagtagagaaaaggaattatattcttcttgcttcaatttttgggtgtatttatttatcccttttatacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGACCTATGCTGATGACTGCCTTGTTGAGAGAGTTACTCAG
          | |    | |  |  |  |   ||| | |  || | |  || | | ||   ||  ||| |   |   |   |  || | |||  |   |||||||| || |||||||  || || ||| |||  ||||  || |||||||| |||||||||||||| || ||||| ||||||||||||
---------gtaaatcttttagacttttt---gaacaaggcttttctgtttatggttttgtttcgtggattcgtaattggtttactataatatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGACATATGCTGATGACTGTCTCGTTGACAGAGTTACTCAG

upper sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G26530.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------atttcttgtatgatctatctcaatctagtaga----gaaaaggaattat--attcttcttgcttcaatttttgggtgtatttatttatcccttttatacataac-agGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGACCTATGCTGATGACTGCCTTGTTGAGAGAGTTACTCAG
                                   | || ||||      |  | || ||  | ||     || | || || |  | |    |||  ||| ||||   |  | || ||   |  ||||||||  |    |||||||| || ||||| |||||||| ||| |||  |||   |  |||||||| |||||||||||||| ||||| || ||||||||||||
gtgtcatggctgagctggagaagttaggtcagaagtatcgtgtagctctgaggtaaagctttttgacttcaaagaagagtttttcagtagaattgtatcatttttgtcgattcttaataagttacttttatatttggttagGATTGCAAAAGATCCACGATTTGAAAGACTACCTTGTGTACTCAAAGGGACATATGCTGATGACTGTCTTGTGGACAGAGTTACTCAG

upper sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 5
atttcttgtatgatctatctcaatctagtagagaaaaggaattatattc--ttcttgcttcaatttttgggtgtatttatttatcccttt-tatacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGACCTATGCTGATGACTGCCTTGTTGAGAGAGTTACTCAG
      || ||  |   || ||||  |  | |   |   | | |||| |  || |  | | || |     |   |  | | | |   | |   | | |  ||||||||| ||||||||||| ||||| ||| |||| ||||||||||| || || ||||||||||||||  ||||||| ||||||||||||
---agatgaatatttattcccaattgaagaaattgagacattgatatccagttttaccataaaatagaaagataagatgtctcttgatctactttcttggcagGATTGCAAAGGATCCTCGGTTTGAAAGATTACTCTGTACTCATAAGGGAACTTATGCTGATGACTGTATTGTTGATAGAGTTACTCAG

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|192330947|gb|FK021660.1|FK021660
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|192306233|gb|FG996847.1|FG996847
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|192330326|gb|FK019876.1|FK019876
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|21676190|gb|BQ628541.1|BQ628541
EST:     AAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: AAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|10233586|gb|BE802474.1|BE802474
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATGTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|151411977|gb|EV281788.1|EV281788
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|192328346|gb|FK020057.1|FK020057
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|13790864|gb|BG653455.1|BG653455
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAA                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAA
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAA
EST: gi|151407416|gb|EV277231.1|EV277231
EST:     GTGATGGCAGAACTCGAGAAATTAGGCCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|51345064|gb|CO985797.1|CO985797
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|24205709|gb|BU964962.1|BU964962
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|13790863|gb|BG653454.1|BG653454
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|298179193|gb|HO027664.1|HO027664
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|298183536|gb|HO028749.1|HO028749
EST:     GTGATGGCAGAACCCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAA
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAA
EST: gi|298183933|gb|HO029146.1|HO029146
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|209717530|gb|BW679664.1|BW679664
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
EST: gi|151408961|gb|EV278769.1|EV278769
EST:     GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG                         GATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC
genomic: GTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAGgtagatgtca ... tacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttcttgcttcaatttttgggtgtatttatttatcccttttatacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGACCTATGCTGATGACTGCCTTGTTGAGAGAGTTACTCAG
                                tttatcccttttat  CT-rich tract
                          tatttatttatccctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcttgtatgatctatctcaatctagtagagaaaaggaattatattcttcttgcttcaatttttgggtgtatttatttatcccttttatacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGACCTATGCTGATGACTGCCTTGTTGAGAGAGTTACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - tgtatga
- - - - - - - - - - - - - - - - -aaaaggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgggtg