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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttttccatatagcttgagttcacaagtcttgtgcacctttattttattcaaagatgtttagttcagcaaaaattttaataccaataaactttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGATAAGCATTAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGC

Basic information

species Glycine max
transcript GLYMA08G19620.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19620.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0055g00390.t01 (Vitis vinifera), 3'ss of exon 3
gcttttccatatagcttgagttcacaagtct----tgtgcacctttattttattcaaagatgttt-agttcagcaaaaattttaataccaataaactttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGATAAGCATTAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGC
    |    ||||||     || |||  | |    |         ||||    || | | || || || |||  |  |||| |  |   |||    ||||  ||||||||||||| ||| |||||||||| || || || ||||| |||||||| ||||||||| ||||||| ||| | ||||||||||||| ||||||||||| 
----taggctatagcaaccattgacagatttacacttgatgaaaatattgggctccatggtgcttcagatcactattaattgtcttttgaattc-tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGT
















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|31307756|gb|CD392959.1|CD392959
EST:     TGGCTTTGATTGGACTCAGGAACTCCTAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|192322362|gb|FK014603.1|FK014603
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|192297847|gb|FG988331.1|FG988331
EST:     CGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|33387927|gb|CA851134.1|CA851134
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|58024842|gb|CX711583.1|CX711583
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|151407739|gb|EV277554.1|EV277554
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCCTCTCTGCTTATTCTACG
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTC-TCTCTGCTTATTCTACG
EST: gi|8403794|gb|BE059361.1|BE059361
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|16347790|gb|BI973385.1|BI973385
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|298184345|gb|HO029558.1|HO029558
EST:     TGGCTTTGATTGGGCTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|192294140|gb|FG986229.1|FG986229
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|192334804|gb|FK025953.1|FK025953
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTTTCTGCTTATTTTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|58020870|gb|CX707612.1|CX707612
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|58020675|gb|CX707417.1|CX707417
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|254347672|gb|GR853921.1|GR853921
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|192334803|gb|FK025952.1|FK025952
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|9564042|gb|BE473551.1|BE473551
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|58017178|gb|CX703920.1|CX703920
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|298180054|gb|HO025269.1|HO025269
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA
EST: gi|192295778|gb|FG992604.1|FG992604
EST:     TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAG                         AACTTTACACAAAGGAGATGTTTCAGCTGCTTCTTTCTGCTTATTTTACGA
genomic: TGGCTTTGATTGGACTCAGGAACTCCAAACCCTAGTTGCTGCATTTTCAGgcaagacttt ... ctttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcaaagatgtttagttcagcaaaaattttaataccaataaactttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGATAAGCATTAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGC
                             ttttaat  putative branch site (score: 3)
                                             ctttttcc  putative PPT
                        aaaaattttaatacca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttttccatatagcttgagttcacaagtcttgtgcacctttattttattcaaagatgtttagttcagcaaaaattttaataccaataaactttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGATAAGCATTAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - -gcttgag
- - - - - - - - - - - - - - - - -tgcacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaataaa