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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgcctgacatatgttgctccactattcctttacctcttgaaggggggttttcaaaatgcaatgttagtaagtgattacatttacatgtctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGA

Basic information

species Glycine max
transcript GLYMA12G03640.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 15
--------actgcctgacatatgttgctccactattcctttacctcttgaaggggggttttcaaaatgcaatgttagtaagtgattacatttacatgtctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAAT---GGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGA
        |||   | ||| || |      | |||  | |||    |  |   |   |||| |  || || | ||  ||     ||| | || ||| ||  |||||||| ||| || ||  |||  |   |  || | || || | |   || || || |||| ||| |||||||||||||| ||||| ||||| ||||| |||||||   
aatttttgactatttaacaaatatga----attat--cattaaggatcaacatgaacttttgactattca-tattcataga-atttatacttgcatatcatggtgcagCATTCTTCGAGCACAGTCAGCACAGCAGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACC---
















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|193449879|gb|FK413498.1|FK413498
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|9259017|gb|BE347164.1|BE347164
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|193345012|gb|FK311638.1|FK311638
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|208242403|gb|GE043319.1|GE043319
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|15815265|gb|BI787540.1|BI787540
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|21602284|gb|BQ612615.1|BQ612615
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|192314633|gb|FK008141.1|FK008141
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|192327460|gb|FK017817.1|FK017817
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAAT
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAAT
EST: gi|51335365|gb|CO979231.1|CO979231
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTTGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|12688675|gb|BG155011.1|BG155011
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|254331304|gb|GR845883.1|GR845883
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
EST: gi|192314634|gb|FK008142.1|FK008142
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggttttcaaaatgcaatgttagtaagtgattacatttacatgtctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGA
                              attacattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgcctgacatatgttgctccactattcctttacctcttgaaggggggttttcaaaatgcaatgttagtaagtgattacatttacatgtctgggtgcagCTTTCGTCAAGTGCAGCTAATGCTTCATCTAACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - cctgaca
- - - - - - - - tgctcca
- - - - - - - - - - - - - - - - - cctcttg
- - - - - - - - - - - - - - - - - - - - - agggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacatgt