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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatattttagaaactccatcgtgtaatgtatatttttttatcatgggacattacatagctgtattacgtgtaatagtttttggtctataatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCTAAGACTCTTTGCAGCCCCTTTGATCAGCCAGAACTCCCAGAAG

Basic information

species Glycine max
transcript GLYMA03G38340.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 11
ttgatattttagaaactccatcgtgtaatgtatatttttttatcatgggacattacatagctgtattacgtgtaatagtttttggtctataatgctt---tagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCTAAGACTCTTTGCAGCCCCTTTGATCAGCCAGAACTCCCAGAAG
    |       | | | | |    | |||| |   ||||     ||  |||     |   | | |    | || |  || ||  ||| |  ||  |   ||||| |||||    ||||| ||||| ||||||||||| ||||  ||||||||||| ||||||||    || |||||||||||||| ||   ||   
---gttaggagaatattacttgacctcatgttttaattttgggtttgaaacacaggtttattttttattttttatttattattcatctgttttgactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCTAAAACTCTTTGTGCTCCTTTTGATCAGCCAGACCTTGAAG---
















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|151404914|gb|EV274728.1|EV274728
EST:     AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAG                         GAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
genomic: AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAGgtatttttgt ... aatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
EST: gi|208035639|gb|GD837320.1|GD837320
EST:     TGTGACGAGGAG                         GAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
genomic: TGTGACGAGGAGgtatttttgt ... aatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
EST: gi|213587445|gb|DB979065.1|DB979065
EST:     AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAG                         GAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
genomic: AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAGgtatttttgt ... aatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
EST: gi|209724629|gb|BW677722.1|BW677722
EST:     AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAG                         GAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
genomic: AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAGgtatttttgt ... aatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
EST: gi|214006980|gb|DB988431.1|DB988431
EST:     AGCTGAT-AACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAG                         GAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
genomic: AGCT-TTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAGgtatttttgt ... aatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
EST: gi|208023799|gb|GD824689.1|GD824689
EST:     AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAG                         GAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGG
genomic: AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAGgtatttttgt ... aatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGG
EST: gi|15814951|gb|BI787226.1|BI787226
EST:     AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAG                         GAGGTGGAGGTTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGTT
genomic: AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAGgtatttttgt ... aatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
EST: gi|193469538|gb|FK435926.1|FK435926
EST:     TCTTTGCTCCTTGGTGTGACGAGGAG                         GAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
genomic: TCTTTGCTCCTTGGTGTGACGAGGAGgtatttttgt ... aatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
EST: gi|192304984|gb|FG996116.1|FG996116
EST:     AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAG                         GAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT
genomic: AAGCTTTGAACCAAAGAAAAATGATCTTTGCTCCTTGGTGTGACGAGGAGgtatttttgt ... aatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggacattacatagctgtattacgtgtaatagtttttggtctataatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCTAAGACTCTTTGCAGCCCCTTTGATCAGCCAGAACTCCCAGAAG
                           taatagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatattttagaaactccatcgtgtaatgtatatttttttatcatgggacattacatagctgtattacgtgtaatagtttttggtctataatgctttagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCTAAGACTCTTTGCAGCCCCTTTGATCAGCCAGAACTCCCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - -ctccatc
- - - - - - - - - - - - - - - - - - - - - tcatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - agctgta