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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatgtgatccttttctctgaaaatttcttggttatatttgtctcataaagaaacccagatagtgccaaattgtgtttacatgtcaaatagacct...

Basic information

species Glycine max
transcript GLYMA14G36280.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36280.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 12
AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaa-atgatgtgatccttttctctgaaaatttcttggttatatttgtctcataaagaaacccagatagtgccaaattgtgtttacatgtcaaatagacct
|| |||  || |||||||||||||||||| |||||||| ||||||||||||||||||||||| ||  | |  | |||||||| |  |     |      || ||    ||| |  | ||| || ||   ||     |       |  ||     |      || |  |  |   |    
AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCATTTAGTGTTGGTAAATCTCAAGAGCAAGgtaagacaaacatgtgggacgctttgggtgttt-tgagatattttagttctatctttcagtttctcttatgagtgctcaccaataaactttcagctgcttc

upper sequence: GLYMA14G36280.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 11
AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgta----aatgatgtgatcctt-ttctctgaaaatttcttggttat-atttgtctcataaagaaacccagatagtgc------caaattgtgtttacatgtcaaatagacct------------------------------------------------------------------------
||  || |   |||||| || ||||| || |||||||| |||||||||||||||||  |||||||  | |  || ||||||    ||   |||| | |   || | | |   |||  | | ||| |  | |  | | |   |  | || || |        |  ||| | |  |  ||  ||||||||                                                                          
AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaaagtgtgtttcacgttttgtcatttttttatagatattagctattgctttatacatactagctacttttttgtacgtattatctaaatgtgctaaatagacaaaacctacttgtttccagttctaatgccatgtctgaacaatattgtatttttaaaaaaaatttatgtatatag

upper sequence: GLYMA14G36280.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 12
AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaa----atgatgtgatccttttctctgaaaatttcttggttatatttgtctcataaagaaacccagatagtgccaaattgtgtttacatgtcaaatagacct
||| ||||||| |||||||| |||||||||||||| |||||||| ||||||||||| |||||||| || | |||||||||||    |  ||||      || || ||  |   | ||| || |    || | |   ||   | |   |   |  | ||| | |||  |    | |||||   
AGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAGgtaataggagaatgttccttcttgctttggcatcattttgcttctgcaagtttta---agtttctccccttcagaaatattatcttttaaccctatatagagg-

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|19269481|gb|BM885737.1|BM885737
EST:     TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG                         GGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAG
genomic: TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatg ... tgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAG
EST: gi|6915301|gb|AW396831.1|AW396831
EST:     TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG                         GGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
genomic: TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatg ... tgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
EST: gi|7796703|gb|AW782097.1|AW782097
EST:     TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG                         GGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
genomic: TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatg ... tgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
EST: gi|19348549|gb|BM893081.1|BM893081
EST:     TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG                         GGTATTGATGGTTCTAGGGTTGAGAAG
genomic: TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatg ... tgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAG
EST: gi|105631822|gb|DW246196.1|DW246196
EST:     TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG                         GGTATTGATGGTTCTAGGGTTGAGAAGGT
genomic: TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatg ... tgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAGGT
EST: gi|151409184|gb|EV278992.1|EV278992
EST:     TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG                         GGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
genomic: TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatg ... tgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
EST: gi|192315079|gb|FK010449.1|FK010449
EST:     TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG                         GGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
genomic: TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatg ... tgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
EST: gi|13240115|gb|BG359424.1|BG359424
EST:     TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG                         GGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
genomic: TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatg ... tgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
EST: gi|192298247|gb|FG992067.1|FG992067
EST:     TATCTGGTGGAACTGACAACCATTTAGTGTTGGCGAACTTAAGAAACAAG                         GGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT
genomic: TATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatg ... tgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAGgtaaatgatgtgatccttttctctgaaaatttcttggttatatttgtctcataaagaaacccagatagtgccaaattgtgtttacatgtcaaatagacct

- - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA