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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtttgggggggggggtgtattattgatactttctattttattataactatcgctttttgtacattaatcaatgtttcctctgcatctatactatagAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTGCTGAATACCGAGCTCAACTAGAGGCTGAGTTTCAAAAGAAAGTGTCAGA

Basic information

species Glycine max
transcript GLYMA13G20310.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20310.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g01910.t01 (Vitis vinifera), 3'ss of exon 1
ttttgtttgggggggggggtgtattattgatactttctattttattataactatcgctttttgtacattaatcaatgtttcctctgcatctatactat-agAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTGCTGAATACCGAGCTCAACTAGAGGCTGAGTTTCAAAAGAAAGTGTCAGA
     |    |     |  | | || ||   |||   | |   ||| ||    | | |||    |  ||  |   |  |  || ||  | | | |  | || |||| |||||||  | ||||| ||||| |||||||||||||||||||||||||  |||||||| ||  | ||   |||||| || |||||| || | ||
aagcataaatgctattgtttttgttcttacaactcaatgtaacatt-tagaactggttttccaaattttgtttcctaatcactttggttttttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTGCTGCTTACCGAGCCCAGGTTGAACTTGAGTTCCAGAAGAAATTGGCTGA
















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|151403808|gb|EV273618.1|EV273618
EST:     GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCNNNNNNNN                         NNNNNTTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG
genomic: GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCAAAAAATGgtattttttc ... tatactatagAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG
EST: gi|192325493|gb|FK017219.1|FK017219
EST:     GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCNNNNNNNN                         NNNNNTTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG
genomic: GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCAAAAAATGgtattttttc ... tatactatagAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG
EST: gi|192300654|gb|FG989641.1|FG989641
EST:     GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCNNNNNNNN                         NNNNNTTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG
genomic: GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCAAAAAATGgtattttttc ... tatactatagAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG
EST: gi|48575259|gb|CO036314.1|CO036314
EST:     GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCANAAAATG                         AAAAATTGGCTAGGTCGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG
genomic: GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCAAAAAATGgtattttttc ... tatactatagAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG
EST: gi|120528947|gb|EH257081.1|EH257081
EST:     GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCNNNNNNNN                         NNNNNTTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG
genomic: GTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGCTGCAAAAAATGgtattttttc ... tatactatagAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataactatcgctttttgtacattaatcaatgtttcctctgcatctatactatagAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTGCTGAATACCGAGCTCAACTAGAGGCTGAGTTTCAAAAGAAAGTGTCAGA
                                tttcctctgcatct  CT-rich tract
            tttttgtacattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtttgggggggggggtgtattattgatactttctattttattataactatcgctttttgtacattaatcaatgtttcctctgcatctatactatagAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTGCTGAATACCGAGCTCAACTAGAGGCTGAGTTTCAAAAGAAAGTGTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA