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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagggatggatttatcccaatttttgttgtgataatacccaaatactaatgttatatttttattaacttttataaatcttttaaaaatgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCTTTGCTATCACTGTAGATTCAACATCATCAGTGACTATTCGGGAGAGGGA

Basic information

species Glycine max
transcript GLYMA08G47890.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 8
------ttttagggatggatttatcccaatttttgttgtgataatacccaaatactaatgttatatttttattaacttttataaatcttttaaaaatgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCTTTGCTATCACTGTAGATTCAACATCATCAGTGACTATTCGGGAGAGGGA
      ||||   ||  || || ||| || |    |     |  |     | |  ||    |||||  |||     ||   ||||| | | || ||  || |  |||  |  | || || ||||||||||||||||| |||||||||||  | |||||||| ||||| || |||||||||||||| || || ||||||||||||||
gcttcattttgatga--gacttctcctaaatgccctctctgtcttgttggattcata----tatataattaactgtttcactaaatatatgaataacatttttcagGGGCCACGATTGGGAAACGATATGCAAGAACCGATGAACTTGGTATACCCTTTGCAATCACCGTTGATTCAACATCATCGGTTACAATTCGGGAGAGGGA
















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|193607974|gb|FK555683.1|FK555683
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|193625182|gb|FK575140.1|FK575140
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|213612194|gb|DB976827.1|DB976827
EST:     TTCCAAGTCATTGACTGCTGAACGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|209713316|gb|BW684403.1|BW684403
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|8669278|gb|BE190385.1|BE190385
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|207787824|gb|GD761118.1|GD761118
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAA
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAA
EST: gi|298197407|gb|HO044886.1|HO044886
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|208068474|gb|GD862320.1|GD862320
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|214009459|gb|DB990162.1|DB990162
EST:     CTACAAGTCATTGACTGCTGATGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|14205293|gb|BG838971.1|BG838971
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|7285216|gb|AW597703.1|AW597703
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAT                         GTACATCAATAGGAAAACCATATGCAAGAACAGATGAACTTGGGCGTGCC-
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGG-CGTGCCC
EST: gi|207785601|gb|GD757378.1|GD757378
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|15202109|gb|BI425227.1|BI425227
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|21602158|gb|BQ612489.1|BQ612489
EST:     GTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: GTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|209716962|gb|BW679636.1|BW679636
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|151412699|gb|EV282511.1|EV282511
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|208330371|gb|GE129348.1|GE129348
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|209710762|gb|BW671053.1|BW671053
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|298163415|gb|HO012148.1|HO012148
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|192297232|gb|FG992371.1|FG992371
EST:     TTCCAAGTCATTGACTGCTGCTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|192297248|gb|FG992372.1|FG992372
EST:     TTCCAAGTCATTGACTGCTGCTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|193456883|gb|FK424819.1|FK424819
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAG
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAG
EST: gi|151408886|gb|EV278694.1|EV278694
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
EST: gi|9983372|gb|BE657480.1|BE657480
EST:     TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAG                         GTACATTAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT
genomic: TTCCAAGTCATTGACTGCTGTTGGAATTTCACACAAGATTGACACTACAGgtatgtggat ... tgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactaatgttatatttttattaacttttataaatcttttaaaaatgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCTTTGCTATCACTGTAGATTCAACATCATCAGTGACTATTCGGGAGAGGGA
                  tattaac  putative branch site (score: 1)
     aatgttatatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttagggatggatttatcccaatttttgttgtgataatacccaaatactaatgttatatttttattaacttttataaatcttttaaaaatgttatatagGTACATCAATAGGAAAACGATATGCAAGAACAGATGAACTTGGCGTGCCCTTTGCTATCACTGTAGATTCAACATCATCAGTGACTATTCGGGAGAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - -gggatgg
- - - - - - - - atcccaa
- - - - - - - - - - - - - -tgttgtg
- - - - - - - - - - - - - - - - - - - -acccaaa