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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttttttgggggtggggtatatcttgtgtgtgtttctgttttaggtcgtcacctttgatgcgctaacaaggattagtggattacttttttgtttgcagGCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTATAATGCGTTCAAAGCCATTCAGGAGTCTCCTAATTGGCAGACACTTAGTG

Basic information

species Glycine max
transcript GLYMA01G02480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 2
gttttttttgggggtggggtat-atcttgtgtg-tgtttctg--ttttaggtcgtcacctttgatgcgctaacaaggattagtggattactttttt--gtttgcagGCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTATAATGCGTTCAAAGCCATTCAGGAGTCTCCTAATTGGCAGACACTTAGTG
      |||     |||  |   ||   || || ||| | ||  || ||     |    |||       ||       ||| |   ||  ||||||    |||||| |||| || || || ||| |||||||  |||| ||||||||||| ||||||||||| || ||||| ||||| || |||||| | ||||| ||||| ||||
------tttaacaatggcctcccattaagtatgatgtctatgaattgtacactctttattttctccatttatttctacttaattcttttttttttttaaattgcagCCAGACAAGGTCAAATTTGAGCTTAGGTTGGGGCAAAGCAAACCCATTTATAATGCATTTAAAGCTATTCAAGAATCTCCTGAGTGGCAAACACTGAGTG
















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|209717152|gb|BW657615.1|BW657615
EST:     AGGCTGTTAAGGATAGTTCGGAGCTACGTTCTGCTATTGAAGATGTGCAG                         GCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTAT
genomic: AGGCTGTTAAGGATAGTTCGGAGCTACGTTCTGCTATTGAAGATGTGCAGgtattgtttt ... ttgtttgcagGCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTAT
EST: gi|192297389|gb|FG990681.1|FG990681
EST:     AGGCTGTTAAGGATAGTTCGGAGCTACGTTCTGCTATTGAAGATGTGCAG                         GCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTAT
genomic: AGGCTGTTAAGGATAGTTCGGAGCTACGTTCTGCTATTGAAGATGTGCAGgtattgtttt ... ttgtttgcagGCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTAT
EST: gi|7147129|gb|AW509051.1|AW509051
EST:     GGCTGTTAACGATAGTTCGGAGCTACCGT-CTGCTATTGAAGATGTGCAA                         GCAGAAAAAGTTAAGCTTCAACCTAGACTG
genomic: GGCTGTTAAGGATAGTTCGGAGCTAC-GTTCTGCTATTGAAGATGTGCAGgtattgtttt ... ttgtttgcagGCAGAAAAAGTTAAGTTTCAGCTTAGACTG
EST: gi|209701313|gb|BW655908.1|BW655908
EST:     AGGCTGTTAAGGATAGTTCGGAGCTACGTTCTGCTATTGAAGATGTGCAG                         GCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTAT
genomic: AGGCTGTTAAGGATAGTTCGGAGCTACGTTCTGCTATTGAAGATGTGCAGgtattgtttt ... ttgtttgcagGCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcgtcacctttgatgcgctaacaaggattagtggattacttttttgtttgcagGCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTATAATGCGTTCAAAGCCATTCAGGAGTCTCCTAATTGGCAGACACTTAGTG
                 cgctaac  putative branch site (score: 2)
                                     ttacttttttgttt  putative PPT
                                    attacttttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttttgggggtggggtatatcttgtgtgtgtttctgttttaggtcgtcacctttgatgcgctaacaaggattagtggattacttttttgtttgcagGCAGAAAAAGTTAAGTTTCAGCTTAGACTGGGTCAAAGCAAACCTATTTATAATGCGTTCAAAGCCATTCAGGAGTCTCCTAATTGGCAGACACTTAGTG

- - - - - -gggtggg
- - - - - - - - - - - - - -gtgtgtg
- - - - - - - - - - - - - - - - - -ttctgtt