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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttagagtttttacagctgctctatattgttttgataatgatacatgagttttcaattcacttgatatacatttgcttgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCCACTGTAGGCATTCACCCAAGTGCAGCTGAGGAATTTGTTACCATGAGGA

Basic information

species Glycine max
transcript GLYMA02G16010.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G16010.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 8
gtttttagagtttttacagctgctctatattgttttgataatgatacatgagttttcaattcacttgatatacatttgcttgata--cccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCCACTGTAGGCATTCACCCAAGTGCAGCTGAGGAATTTGTTACCATGAGGA
           |||  |  ||  || |  ||| ||   | ||  |   |   | | ||||| | | | | ||   ||     | |  ||||||| |||||||||||| | | |||| ||||||| ||||| ||||||||||||||||| || || ||||| | |||||| |||||  |||| || |||||||
----------gtttgccttctaatcca--ttgcttgacttatttttgttagatctgcaattaattggttgtattcttatggcaaaaccccagGGCTTTGCAGTTGCTGTGAGAGCTGGCTTGACAAAGGCAGACTTTGATGCCACTGTGGGAATCCACCCTACTGCAGCAGAGGAGCTTGTCACAATGAGGA
















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|27424963|gb|CA936483.1|CA936483
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|192311298|gb|FK003769.1|FK003769
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|31467102|gb|CD409130.1|CD409130
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|10237572|gb|BE806460.1|BE806460
EST:     AAGTTCTAGGTTTGCATATGTGTGNAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGAACCAAG-CTGACTTTGATGC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGA-CCAAGGCTGACTTTGATGC
EST: gi|37995085|gb|CF806674.1|CF806674
EST:     ATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: ATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|254346696|gb|GR856418.1|GR856418
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|192314162|gb|FK011534.1|FK011534
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|214007958|gb|DB987846.1|DB987846
EST:     GAAATTGTGCAG                         GGGTTTGCAGTTTTTCATAAAGCTCGCTTGACCAAGGCTGACTTTGATG-C
genomic: GAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|192311299|gb|FK003770.1|FK003770
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|7925628|gb|AW831654.1|AW831654
EST:     GAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: GAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|14258668|gb|BG881576.1|BG881576
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|254344596|gb|GR855467.1|GR855467
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|12773202|gb|BG238129.1|BG238129
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|10238450|gb|BE807338.1|BE807338
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|16997020|gb|BM086392.1|BM086392
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|7924612|gb|AW830638.1|AW830638
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGANATTGTGCAG                         GGGTTTGCAGTTGCTCTTA
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTA
EST: gi|193526955|gb|FK483305.1|FK483305
EST:     AAGTTCTAGGTTTGCATATGTGTGGGGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|6134950|gb|AW133343.1|AW133343
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|8283020|gb|BE020581.1|BE020581
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGACGATGCTCCTGAAATTGTGCAN                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|254323696|gb|GR836035.1|GR836035
EST:     AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCT-CTGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: AAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
EST: gi|21995150|gb|BQ786678.1|BQ786678
EST:     TGAAATTGTGCAG                         GGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC
genomic: TGAAATTGTGCAGgtttttagag ... tgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgataatgatacatgagttttcaattcacttgatatacatttgcttgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCCACTGTAGGCATTCACCCAAGTGCAGCTGAGGAATTTGTTACCATGAGGA
                                       tttgctt  CT-rich tract
                                atatacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttagagtttttacagctgctctatattgttttgataatgatacatgagttttcaattcacttgatatacatttgcttgatacccagGGGTTTGCAGTTGCTCTTAAAGCTCGCTTGACCAAGGCTGACTTTGATGCCACTGTAGGCATTCACCCAAGTGCAGCTGAGGAATTTGTTACCATGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA