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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttaattgttttctctttaattgatatgtaacagaactgatagctgagcataccaaagaagaacttgaaggagaaggggaagaaaaactcttgtgtcttgtacgttatgttcatttttatttaaagagctaaaacttgcaataccatgaacaaacttttttcagGATCAAATGCGTGCTCTTGATATAGTTCAGAATGATCCAGAACTCTCCAGTTTATCAATGATCCAGGCACCACTCGTAGATGTTGAGATAAGAGGTGTTC

Basic information

species Glycine max
transcript GLYMA10G35320.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35320.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 10
gtactttaattgttttctctttaattgatatgtaacagaactgatagctgagcataccaaagaagaacttgaaggagaaggggaagaaaaactcttgtgtct-tgtacgttatgttcatttttatttaaagagctaaaacttgcaataccatgaacaaacttttttcagGATCAAATGCGTGCTCTTGATATAGTTCAGAATGATCCAGAACTCTCCAGTTTATCAATGATCCAGGCACCACTCGTAGATGTTGAGATAAGAGGTGTTC
                                                         |  |  | ||||    | | |    ||      | |  | | | | | ||| || | |     || |  |||| |  |  || || |  ||       ||||    || |||||||| |||||||||||||| ||  |  || ||||||||||||||||||  ||  || | ||||||||||| || || ||||| ||||| ||||||||||
--------------------------------------------------------tcttaccataact----gaacaccttgagattctatttatctatttatttactttttatatggattgaagtaaacaattttaattttctctatt-----caaa----ttccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAACTTGACACTAATCCAGGCACCCCTAGTTGATGTGGAGATCAGAGGTGTTC
















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|9258515|gb|BE346662.1|BE346662
EST:     TTCTTTCACCGGCTACATCTGATTGCAAGTTTTGTGCTATGAAAAGAAAG                         GATCAAATGCGTGCTC
genomic: TTCTTCCACCGTCTACATCTGATTGCAAGTTTTGTGCTATGAAAAGAAAGgtactttaat ... cttttttcagGATCAAATGCGTGCTC
EST: gi|7796764|gb|AW782158.1|AW782158
EST:     TTCTTCCACCGTCTACATCTGATTGCAAGTTNTGTGCTATGAAAAGAAAG                         GATCAAATGCGTGCTCTTGATATAGTTCAGAATGATCCAGAACTCTCCAGT
genomic: TTCTTCCACCGTCTACATCTGATTGCAAGTTTTGTGCTATGAAAAGAAAGgtactttaat ... cttttttcagGATCAAATGCGTGCTCTTGATATAGTTCAGAATGATCCAGAACTCTCCAGT
EST: gi|9903231|gb|BE612199.1|BE612199
EST:     TTCTTCCACCGTCTACATCTGATTGCAAGTTTTGTGCTATGAAAAGAAAG                         GATCAAATGCGTGCTCTTGATATAGTTCAGAATGATCCAGAACTCTCCAGA
genomic: TTCTTCCACCGTCTACATCTGATTGCAAGTTTTGTGCTATGAAAAGAAAGgtactttaat ... cttttttcagGATCAAATGCGTGCTCTTGATATAGTTCAGAATGATCCAGAACTCTCCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttttatttaaagagctaaaacttgcaataccatgaacaaacttttttcagGATCAAATGCGTGCTCTTGATATAGTTCAGAATGATCCAGAACTCTCCAGTTTATCAATGATCCAGGCACCACTCGTAGATGTTGAGATAAGAGGTGTTC
                 agctaaa  putative branch site (score: 3)
                                             cttttttc  putative PPT
     ttttatttaaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttaattgttttctctttaattgatatgtaacagaactgatagctgagcataccaaagaagaacttgaaggagaaggggaagaaaaactcttgtgtcttgtacgttatgttcatttttatttaaagagctaaaacttgcaataccatgaacaaacttttttcagGATCAAATGCGTGCTCTTGATATAGTTCAGAATGATCCAGAACTCTCCAGTTTATCAATGATCCAGGCACCACTCGTAGATGTTGAGATAAGAGGTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG