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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaaatgtgatcttactaacacttttacacatttgctaactttagaggagccaaattccctactcatatttacagtaattcattttcaattgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG

Basic information

species Glycine max
transcript GLYMA01G03260.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 2
lower sequence: AT1G70580.4 (Arabidopsis thaliana), 3'ss of exon 2
agtaaatgtgatcttactaacacttttacacatttgctaactttagaggagccaaattccctactcatatttacagtaattcattttcaattgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG
      |   | |||  | |  | ||| ||   ||   | ||| |   |      |             | |   ||     |  ||  |   ||  |||||||| || || |||||||| ||||| ||||| || ||||||||||| ||||  || |||||||||
-----gtaacaactttgttatgcgtttgca--gttatgagcttcattagctgttgagatatgggaagcgtctttggtttcctaactttcacaatta-cagATTATTTTCACAAATGTTGGAAACCCTCATGCTTTAGGACAGAAACCTCTGACTTTTCCTCGTCAG
















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|120529201|gb|EH257335.1|EH257335
EST:     GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|14205452|gb|BG839130.1|BG839130
EST:     GAGGHGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|15285990|gb|BI469890.1|BI469890
EST:     CTTCCGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: CTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|7283746|gb|AW596349.1|AW596349
EST:     GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|21887563|gb|BQ740776.1|BQ740776
EST:     ATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: ATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|23052838|gb|BU577329.1|BU577329
EST:     TGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: TGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|13481869|gb|BG511212.1|BG511212
EST:     CTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: CTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|298167407|gb|HO012670.1|HO012670
EST:     GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|120491572|gb|EH219739.1|EH219739
EST:     GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|14205590|gb|BG839268.1|BG839268
EST:     GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|15285988|gb|BI469879.1|BI469879
EST:     AAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: AAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|10847451|gb|BF070138.1|BF070138
EST:     GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
EST: gi|213588415|gb|DB959735.1|DB959735
EST:     GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAG                         ATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG
genomic: GAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgtaggtttta ... ttgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggagccaaattccctactcatatttacagtaattcattttcaattgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG
                     atatttacagtaattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaaatgtgatcttactaacacttttacacatttgctaactttagaggagccaaattccctactcatatttacagtaattcattttcaattgttggcagATTATATTTACTAATGTTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - ctaacac
- - - - - - - - - - - - - - - - - tgctaac