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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgatatcttcctttttacggaaacatctttttgcaacatggttcctttctctctttttttcatgagaaataacattttggatgttgtgattttgttttctcttttcagATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTAGGAAATGCTTTGAACCAAGGAACTGCCAAGG

Basic information

species Glycine max
transcript GLYMA02G36440.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G36440.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 4
gcatgatatcttcctttttacggaaacatctttttgcaacatggttcctttctctct-ttttttcatgagaaataacattttggatgttgtgattttgttttctcttttcagATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTAGGAAATGCTTTGAACCAAGGAACTGCCAAGG
                         |||   || |  || |||    |     |||    |||||  |    |  |  ||    ||| ||| || |  | || | |   ||| | ||||| ||||| ||  | ||| || | ||||||||||| ||||| || |||||||| || |||||||||||||| | ||
-----------------------gtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
















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|58023146|gb|CX709887.1|CX709887
EST:     TTTCTGACCTTAGAAATAGCCTAATTGTTGTGAATGCTGCTTCAGAAGAG                         ATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTA
genomic: TTTCTGACCTTAGAAATAGCCTAAGTGTTGTGAATGCTGCTTCAGAAGAGgcatgatatc ... ctcttttcagATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTA
EST: gi|7587962|gb|AW703768.1|AW703768
EST:     TTTCTGACCTTAGAAATAGCCTGAGTGTTGTGAATTCTGCTTCAGAAGAG                         ATCAGGAATTCTGTCAAATTA
genomic: TTTCTGACCTTAGAAATAGCCTAAGTGTTGTGAATGCTGCTTCAGAAGAGgcatgatatc ... ctcttttcagATCAGGAATTCTGTCAAATTA
EST: gi|57574575|gb|CX547550.1|CX547550
EST:     TTTCTGACCTTAGAAATAGCCTAATTGTTGTGAATGCTGCTTCAGAAGAG                         ATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTA
genomic: TTTCTGACCTTAGAAATAGCCTAAGTGTTGTGAATGCTGCTTCAGAAGAGgcatgatatc ... ctcttttcagATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTA
EST: gi|10236909|gb|BE805797.1|BE805797
EST:     TTTCTGACCTTAGAAATAGCCTAAGTGTTGTGAATGCTGCTTCAGAAGAG                         ATCAGGAATTCTGTCAAATTAAAG
genomic: TTTCTGACCTTAGAAATAGCCTAAGTGTTGTGAATGCTGCTTCAGAAGAGgcatgatatc ... ctcttttcagATCAGGAATTCTGTCAAATTAAAG
EST: gi|17020797|gb|BM091831.1|BM091831
EST:     TTTCTGACCTTAGAAATAGCCTAAGTGTTGTGAATGCTGCTTCAGAAGAG                         ATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTA
genomic: TTTCTGACCTTAGAAATAGCCTAAGTGTTGTGAATGCTGCTTCAGAAGAGgcatgatatc ... ctcttttcagATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcatgagaaataacattttggatgttgtgattttgttttctcttttcagATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTAGGAAATGCTTTGAACCAAGGAACTGCCAAGG
             aaataac  putative branch site (score: 2)
                                    ttttgttttctctttt  putative PPT
           agaaataacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgatatcttcctttttacggaaacatctttttgcaacatggttcctttctctctttttttcatgagaaataacattttggatgttgtgattttgttttctcttttcagATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTAGGAAATGCTTTGAACCAAGGAACTGCCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA