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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgactcctacctgtcacttccagatccttatgtctgatgttctccgatttgctaaatccaaagaataactttttttcctaccaaaattttctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCCATAACAGAGATGCAGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGA

Basic information

species Glycine max
transcript GLYMA04G06250.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgttgactcctacctgtcacttccagatccttatgtctgatgttctccgatttgctaaat-ccaaagaataactttttttcctaccaaaattttctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCCATAACAGAGATGCAGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGA
      ||  |   |||| | |  |    | ||  |||  | |     |     | || |  | || ||   | |||||||    | ||      | ||   | |||||||||||||||| || || ||| | ||||| || |||||||||||||| || ||||||||||| || ||||| || || || || || |||||||||||
-----gtgcttttcacctttaatattgttagccagatgattcaataaatagacctagcaaggtgcctaattctgactttttcatttgcctg---ctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 4
gtatgttgactcctacctgtcacttccagatccttatgtctgatgttctccgatttgctaaatccaaagaataactttttttcctaccaaaattttctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCCATAACAGAGATGCAGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGA
     |||  ||||  ||||  |    |  ||  | | | |     | |  ||  || | | || ||| | ||   | ||    || |     | | |     |||||||||||||||| || || ||| | || || ||||||||||||||||  || || |||||||| ||||||||||| ||||| |||||  | ||||||||
---gtttgtttcctgactgtgccagtaatgtcactttctatagc-ctgtatgaagtgttcactctaaatactactgtcttaaattatc----ctctgtacatgcagCTGATGCATACAAGCACACAGACTCAGAATTTCTGAAATCAGAAAATAATCAGAATAGAGATGCTGGATCAACTGCCTCCACCGCTATCCTTGTTGGTGA
















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|192313213|gb|FK003333.1|FK003333
EST:     TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
EST: gi|254334939|gb|GR844724.1|GR844724
EST:     ATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: ATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
EST: gi|11412749|gb|BF424760.1|BF424760
EST:     TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
EST: gi|14999246|gb|BI320277.1|BI320277
EST:     TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAAT
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAAT
EST: gi|27425490|gb|CA937010.1|CA937010
EST:     TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
EST: gi|192313214|gb|FK003334.1|FK003334
EST:     TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
EST: gi|11412737|gb|BF424748.1|BF424748
EST:     TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
EST: gi|209712192|gb|BW681398.1|BW681398
EST:     TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGA
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGA
EST: gi|209722645|gb|BW654652.1|BW654652
EST:     TAATTTGATCAGTCACCCAA--TTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
EST: gi|120491886|gb|EH220053.1|EH220053
EST:     CAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: CAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
EST: gi|213618457|gb|DB969399.1|DB969399
EST:     TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
EST: gi|193489522|gb|FK455847.1|FK455847
EST:     TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAA                         CTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC
genomic: TAATTTGATCAGTCACCCAAAATTCATTTCTGACACCAAATCAGCAATAAgtatgttgac ... ctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttgctaaatccaaagaataactttttttcctaccaaaattttctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCCATAACAGAGATGCAGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGA
                 gaataac  putative branch site (score: 2)
                                         ttttctttccac  putative PPT
              aaagaataactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgactcctacctgtcacttccagatccttatgtctgatgttctccgatttgctaaatccaaagaataactttttttcctaccaaaattttctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCCATAACAGAGATGCAGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG