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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttttttttttctcgaatgggtgttctttcttttcaattgggcattgttttctttttttttcttatggatgttctttgttttcaactgtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGCGATTGCTAGGAAGGGGATTGGGAAGGATCATGCTAAATGGTCACCTGCT

Basic information

species Glycine max
transcript GLYMA20G02360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G15430.1 (Arabidopsis thaliana), 3'ss of exon 1
tttgttttttttttctcgaatgggtgttctttcttttcaattgggcattgttttctttttttttct-tatggat---gttctttgttttcaactgtgtatt-cagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGCGATTGCTAGGAAGGGGATTGGGAAGGATCATGCTAAATGGTCACCTGCT
    |   |      | | |||  | |||||  |  |  ||||     |||||  || |  |   | | ||| |      || ||||||    |  |  || ||| || ||||||||||||||  || | || ||||||||| ||||||| |||||||| || ||||| ||||||||||| |||||||| |||||||| ||||| 
----tcgatggccctttgcatgactcttcttgttcgt-gattgtttgatgtttaattatggtggttgtgtgggttaaagactctgtttttggtttcgggtttcagGGGAATTATCATTGTGAAACTGCGTCGGGGACAAGAGTTGAAGCTTAGAGCGATAGCGAGGAAAGGGATTGGGAAAGATCATGCGAAATGGTCTCCTGCA

upper sequence: GLYMA20G02360.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 1
-tttgttttttttttctcgaatgggtgttctttcttttcaattgggcatt--gttttctttttttttcttatggatgttctt-tgtt--ttcaactgtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGCGATTGCTAGGAAGGGGATTGGGAAGGATCATGCTAAATGGTCACCTGCT
 | | | | | ||||   |  |  | ||| |    ||||  | |||  ||  | ||| |    ||||   |||| |||  |  || |  ||    | |||  | || || ||||| ||||||||| || | || || ||||| |||| ||||||||| ||||| || ||||||||||||||||| || || ||||||||||| || 
gtatttatatatttttaagttttagggttttagagtttct-tagggttttagggtttttgaaattttgcaatggctgtgttaatgatggtttctttttgtgattagGGGAATTATAATTGTGAAGCTGCGGCGAGGGCAAGAACTGAGGCTGAGAGCTATTGCCAGAAAGGGGATTGGGAAGGACCACGCCAAATGGTCACCGGCG
















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|208102102|gb|GD899083.1|GD899083
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTGAGGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
EST: gi|193649683|gb|FK596246.1|FK596246
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTGAAG
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAG
EST: gi|193541602|gb|FK498360.1|FK498360
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
EST: gi|208055814|gb|GD849811.1|GD849811
EST:     CTCCCCAGACAACAACAG                         AGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
genomic: CTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
EST: gi|254315327|gb|GR825136.1|GR825136
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACA-CA-CAG                         AGGGATTATCATTGTGAAGT
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAGT
EST: gi|13790386|gb|BG652977.1|BG652977
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
EST: gi|193418971|gb|FK382257.1|FK382257
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTGAAGTTGAG
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAGTTGAG
EST: gi|120531834|gb|EH259967.1|EH259967
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGC
EST: gi|193640338|gb|FK589335.1|FK589335
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTG
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTG
EST: gi|193687337|gb|FK633938.1|FK633938
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTG
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTG
EST: gi|193539708|gb|FK495192.1|FK495192
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTGAAG
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTGAAG
EST: gi|193560566|gb|FK517241.1|FK517241
EST:     CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAG                         AGGGATTATCATTGTG
genomic: CCCGTTGATTTCTCTGACCCCTCTGCCACTGACTCCCCAGACAACAACAGgtgcgtttct ... gtgtattcagAGGGATTATCATTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgttttctttttttttcttatggatgttctttgttttcaactgtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGCGATTGCTAGGAAGGGGATTGGGAAGGATCATGCTAAATGGTCACCTGCT
     ttttctttttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttttttttttctcgaatgggtgttctttcttttcaattgggcattgttttctttttttttcttatggatgttctttgttttcaactgtgtattcagAGGGATTATCATTGTGAAGTTGAGACGCGGACAAGAGCTGAAGCTGAGAGCGATTGCTAGGAAGGGGATTGGGAAGGATCATGCTAAATGGTCACCTGCT

- - - - - - - - - - -gggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgtt