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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttcatctgattggtgttctattcttggtgctacatggcatggtgatgtttgaacaaggatgtgttgaatagtgacccgttgcttgttatttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCCGGCGATGAG

Basic information

species Glycine max
transcript GLYMA02G31080.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 1
tgttcatctgattggtgttctattcttggtgctacatggcatggtgatgtttgaacaaggatgtgttgaatagtgacccgttgcttgt-tatttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCCGGCGATGAG
 |||      ||| ||    ||    | |   | | | |     |  |   ||   |      |   |   |  || |   ||  ||  | ||| |   ||||||||||||| ||   ||||||||||| ||| || |||| ||| || ||  | ||||| ||||||||||| ||||||||||| |||   |  ||||||
-gtttgatcaatttgtaccgtagctgttgcaattcttagttgttttcttggtggttagtagaattcagtgaaacgaactaatgaatgcgtctttgttgaagGTTCTTGGTGTTGAAGCAACAGCATCTCCACAAGAGATAAGGAAAGCGTATCATAAGTTAGCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAG

upper sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 1
----tgttcatctgattggtgttctattcttggtgctacatggcatggtgatgtttgaacaaggatgtgttgaatagtgacccgttgcttgttatttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCCGGCGATGAG
    | | | |||  ||||| | ||  | |   |  |   |   |   | |  ||| ||   |     |    ||  |||    |  | |  | | |||   |||||||||||||||| || || |||||||| |||||||| ||||| || ||||| |||||||||||| |||| ||||||||||| || || || ||||||
ccattctccctcttcttggtttactgatgtactttttttttattacaataaaatttcaagtggagcaag--agatgctgaataataacct--tgtgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG
















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|193668456|gb|FK609362.1|FK609362
EST:     TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTATCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
genomic: TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAGgtactttaca ... tttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
EST: gi|208165652|gb|GD959440.1|GD959440
EST:     TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAG                         GTTCTTGGTGTGGAGAAAATAGCATCTCAACAGGAAATAAAGAAGGCATAC
genomic: TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAGgtactttaca ... tttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
EST: gi|208273634|gb|GE069254.1|GE069254
EST:     CCCTTTCGATCAAAACGAACACACTCTCTACCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
genomic: CCCTTTCGATCAAAACGAACACACTCTCTACCAGgtactttaca ... tttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
EST: gi|208191153|gb|GD989169.1|GD989169
EST:     TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
genomic: TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAGgtactttaca ... tttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
EST: gi|208261794|gb|GE059561.1|GE059561
EST:     TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAG
genomic: TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAGgtactttaca ... tttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAG
EST: gi|208275938|gb|GE074288.1|GE074288
EST:     TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
genomic: TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAGgtactttaca ... tttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
EST: gi|208097573|gb|GD891320.1|GD891320
EST:     TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
genomic: TCGAATCTGACACCAACCCTTTCGATCAAAACGAACACACTCTCTACCAGgtactttaca ... tttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtttgaacaaggatgtgttgaatagtgacccgttgcttgttatttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCCGGCGATGAG
                                      cttgttatttctctt  CT-rich tract
                                       ttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttcatctgattggtgttctattcttggtgctacatggcatggtgatgtttgaacaaggatgtgttgaatagtgacccgttgcttgttatttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCCGGCGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - attggtg
- - - - - - - - - - - - - tggtgct
- - - - - - - - - - - - - - - - - - - gcatggt
- - - - - - - - - - - - - - - - - - - - - - - atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgttgc