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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggaaatgctcctgacacctgtggagttcattgcctttttattggatcctgttataagttgtgaagaccttcttgatgataaatttcatttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTACTGAACAGCTGGCAAAGGATATTCTAGAGAACAATAAGGATTTGCAGTT

Basic information

species Glycine max
transcript GLYMA04G03080.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g13280.t01 (Vitis vinifera), 3'ss of exon 2
tgggaaatgctcctgacacctgtggagttcattgcctttttattggatcctgttataagttgtga-agaccttcttgatgataaatttcatttgtctct---agGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTACTGAACAGCTGGCAAAGGATATTCTAGAGAACAATAAGGATTTGCAGTT
       |  |  |   |  | |    ||  ||      ||     || |  ||    || |||   ||  ||  |  |  |   |||| ||| | | |   |||||| ||||| |||||  | ||||| |||||||| ||||| ||||| || || |||||||||||| | ||| | |||||||| |||||||||||||| ||
----ttttattattattatttttatgtttacttctggacttggactattcgattgattgtggtgctggaattttctttttttctttttcttttttttttctcagGAATATTTCATTTTGCTTTGGAGGGCAATGCACTAAAGGCCATTGAACTGACAGAACAGCTGGCAGATGATTTACTAGAGAAAAATAAGGATTTGCATTT
















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|192298544|gb|FG989220.1|FG989220
EST:     GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAA                         GAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
genomic: GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAAgtaggtttgt ... ttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
EST: gi|19054068|gb|BM732735.1|BM732735
EST:     GGGAGCAAAGCAGCCGACAGATTATTTGGAGGGCATGGATAAAAGGAAAA                         GAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
genomic: GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAAgtaggtttgt ... ttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
EST: gi|9566116|gb|BE475554.1|BE475554
EST:     GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAA                         GAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
genomic: GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAAgtaggtttgt ... ttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
EST: gi|298168072|gb|HO013335.1|HO013335
EST:     GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAA                         GAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGGGCTTA
genomic: GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAAgtaggtttgt ... ttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
EST: gi|209723413|gb|BW679947.1|BW679947
EST:     GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAA                         GAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
genomic: GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAAgtaggtttgt ... ttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
EST: gi|207730605|gb|GD707492.1|GD707492
EST:     GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAA                         GAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
genomic: GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAAgtaggtttgt ... ttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
EST: gi|254325123|gb|GR834548.1|GR834548
EST:     GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAA                         GAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA
genomic: GGGAGCAAAGCAGCCGACAGATTATTTGGAGGACATGGATAAAAGGAAAAgtaggtttgt ... ttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcctgttataagttgtgaagaccttcttgatgataaatttcatttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTACTGAACAGCTGGCAAAGGATATTCTAGAGAACAATAAGGATTTGCAGTT
                          tcttgat  putative branch site (score: 4)
                                       tttcatttgtctct  putative PPT
                               atgataaatttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggaaatgctcctgacacctgtggagttcattgcctttttattggatcctgttataagttgtgaagaccttcttgatgataaatttcatttgtctctagGAATTTTTCACTTTGCACTAGAGGGAAATGCACTCAAGGCTATTGAGCTTACTGAACAGCTGGCAAAGGATATTCTAGAGAACAATAAGGATTTGCAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG