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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctagattaagaagcttgtctttgtaatgtggcattggcattaatcaaacatcccatattctattattacctctgttctattgatattttggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG

Basic information

species Glycine max
transcript GLYMA12G31740.1
intron # 5
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 5
lower sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
tctagattaagaagcttgtctttgtaatgtggcattggcattaatcaaacatcccatattctattattacctctgttctattgatattttggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG
             |   ||   |  ||  |     | |   ||   | |  | |  | |  | |||  ||| |    || |   | |||  | |||  |||||| |||||||| ||||| ||||| ||||| ||  | ||||| ||||| || || |||||||||||||||||
-------------gtgagttacttaaagattttgataggtcta--tataggttctctctcttgtta--accac----ctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG

upper sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
tctagattaagaagcttgtctttgtaatgtggcattggcattaatcaaacatcccatattctattattacctctgtt----ctattgatattttggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG
  || |||    | ||| ||  | | |    | |||   ||          ||  ||||| | || ||  || ||||    |  |  || ||||   |||  |||||| |||||||| ||||| |||||||||||||| || ||||| ||||| || ||||| || || ||||| ||
--taaattttttatcttatcaatctgaaa--gtatttttatgtgatgggattcttatattattttgttgtctttgttgcttccttctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
















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:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|192306233|gb|FG996847.1|FG996847
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|192330326|gb|FK019876.1|FK019876
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|10233586|gb|BE802474.1|BE802474
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|151411977|gb|EV281788.1|EV281788
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|192328346|gb|FK020057.1|FK020057
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACAGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|13790864|gb|BG653455.1|BG653455
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|151407416|gb|EV277231.1|EV277231
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGCC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|51345064|gb|CO985797.1|CO985797
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|24205709|gb|BU964962.1|BU964962
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|13790863|gb|BG653454.1|BG653454
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|298179193|gb|HO027664.1|HO027664
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|298183536|gb|HO028749.1|HO028749
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACCCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|298183933|gb|HO029146.1|HO029146
EST:     GGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: GGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|209717530|gb|BW679664.1|BW679664
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
EST: gi|151408961|gb|EV278769.1|EV278769
EST:     TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAAT                         GCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC
genomic: TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCTAAATgtgagttaga ... ggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaacatcccatattctattattacctctgttctattgatattttggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG
                                 tattgat  putative branch site (score: 3)
                                                ttttc  putative PPT
          atattctattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctagattaagaagcttgtctttgtaatgtggcattggcattaatcaaacatcccatattctattattacctctgttctattgatattttggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG

- - - - - - -gcttgtc
- - - - - - - - - - - - - atgtggc
- - - - - - - - - - - - - - - - - - ggcatta
- - - - - - - - - - - - - - - - - - - - - - -caaacat