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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattttagaggcagtaaagaattcatactctcttgcattagtctcccgatttgacttgtttctgtttttttatttatttatttgctatttgtttggtagGTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAACTTATGATTTTCTGTATTTACCGATTGATTTCAAG

Basic information

species Glycine max
transcript GLYMA08G01040.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 10
aaattttagaggcagtaaa-gaattcatactctcttgcattagtctcccgatttgacttgtttctgtttttttatttatt--tatttgctatttgtttggta--------gGTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAACTTATGATTTTCTGTATTTACCGATTGATTTCAAG
              ||||  |||||||   | |||  |  |  |  || | |||      ||     ||  | |||| ||  ||||||   ||  | |||||        |||||||||| |||||||| || ||||| || || ||| | ||||||||||| ||||||||||| ||||| || ||||| ||||||
--------------gtaagtgaattcaccttttctccctattattccctgttttataacattatatgttgctcatttgttcctatttgtctttgttctggtaatggtttagGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG

upper sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 10
----------------------------------------aaattttagaggcagtaaagaattcatactctc--ttgcattagtctcccgatttgacttgtttctgtttttttatttatttatttgcta--tttgtt-tggt--agGTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAACTTATGATTTTCTGTATTTACCGATTGATTTCAAG
                                         |  ||  |   |  |  | | ||  |    |   ||  |   || | | | ||| |  | |  || | ||||| ||| ||| |||  ||  | || | ||||  ||||| ||||| |||||||||||  |||| || |||||||| |||||||||||||||||||| || ||||| || ||||| ||||||
gtacgtgaactcagtgtctctcttttatttttcttgtctatatcttctgcaactatttatagtttgtgtctttagttaaagatgtattctgttttcatctttgactctcttttttttttttttttttttaattctgctatggtttagGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG

upper sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 11
----aaattttagaggcagtaaagaat-tcatactctcttgcattagtctcccgatttgacttgtttctgtttttttatttatttatttgctatttgtttggtagGTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAACTTATGATTTTCTGTATTTACCGATTGATTTCAAG
     | || ||   |  ||     |   |||| |  ||   |||  | |  |    |   || ||||||  |||| ||||  |    || || |||     ||||||||||||||| ||||||||||||||||| || || ||   |  |||||||||||||||| | ||||| || ||||| ||||| 
cattcatttctatttgtggttttacacaccataattgctcagattcctgttgcatcctctgttatttctgccttttgatttgatataatggtaattg-----tagGTATACTTCAAAAATGCTTCTTGCTGCAATTGATGAACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA

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|16106132|gb|BI893872.1|BI893872
EST:     CGTGGGGAAGACAGCCGAACTATACTTATGATAAAAAATATTCCCAACAA                         GTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAAC
genomic: CGTGGGGAAGACAGCCGAACTACACTTATGATAAAAAATATTCCCAACAAgtatgttaat ... tgtttggtagGTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgatttgacttgtttctgtttttttatttatttatttgctatttgtttggtagGTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAACTTATGATTTTCTGTATTTACCGATTGATTTCAAG
    atttgac  putative branch site (score: 4)
                                           tttgttt  putative PPT
              tttctgtttttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattttagaggcagtaaagaattcatactctcttgcattagtctcccgatttgacttgtttctgtttttttatttatttatttgctatttgtttggtagGTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAACTTATGATTTTCTGTATTTACCGATTGATTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - gtaaagaa
- - - - - - - - - - - - catactc
- - - - - - - - - - - - - - - - - tgcatta
- - - - - - - - - - - - - - - - - - - - -gtctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctatt