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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCCCTCTATAGAAGGGCCCAAGCATATATGCAGTTAACTGACTTGGATTTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctcagaataaattactctttttgacctttatgtatttgagatttactgaatcagttgctttaattttgggcaatttatcttttattttgccttgcaatgtaattgttctctatgcttgaaccag

Basic information

species Glycine max
transcript GLYMA08G46090.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46090.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv00s0958g00020.t01 (Vitis vinifera), 5'ss of exon 7
AAGCCCTCTATAGAAGGGCCCAAGCATATATGCAGTTAACTGACTTGGATTTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctcagaataaattactctttttgacctttatgtatttgagatttactgaatc--agttgctttaattttgg----gcaatttatctttt------attttgccttgcaatgtaattgttctctatgcttgaaccag-----------------------------
| || || || || ||||| ||||| ||||| ||  |  | ||  | |||||||| ||  |||| ||||||||||||||||| ||||||||| | |||||||||  | | | |        ||   | |||  |  |  | |     |||| |   |||  |  |  | |||||           ||| |  || |      || |    |   || ||| | | || | |     |||  |                              
AGGCACTTTACAGGAGGGCTCAAGCGTATATTCATCTGGCAGATCTTGATTTGGCCGAGTTTGATATTAAGAAAGCTCTTGAAATTGACCCTGATAACAGgtatcagattatatcttgcctcttgatctgatttcca-atgtgacgaatttgcatgatctaaaataatataattacaatacaatgattgaaattgtcacaacatgtccattaataaggtagtagatcccaactgaggaaagaattataactattaatgtttgtttaaaacag

upper sequence: GLYMA08G46090.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 5'ss of exon 11
AAGCCCTCTATAGAAGGGCCCAAGCATATATGCAGTTAACTGACTTGGATTTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctcagaataaattactctttttgacctttatgtatttgagatttactgaatc--agttgctttaattttgg----gcaatttatctttt------attttgccttgcaatgtaattgttctctatgcttgaaccag-----------------------------
| || || || || ||||| ||||| ||||| ||  |  | ||  | |||||||| ||  |||| ||||||||||||||||| ||||||||| | |||||||||  | | | |        ||   | |||  |  |  | |     | || |   |||  |  |  | |||||           ||| |  || |      || |    |   || ||| | | || | |     |||  |                              
AGGCACTTTACAGGAGGGCTCAAGCGTATATTCATCTGGCAGATCTTGATTTGGCCGAGTTTGATATTAAGAAAGCTCTTGAAATTGACCCTGATAACAGgtatcagattatatcttgcctcttgatctgatttcca-atgtgacgaacttgcatgatctaaaataatataattacaatacaatgattgaaattgtcacaacatgtccattaataaggtagtagatcccaactgaggaaagaattataactattaatgtttgtttaaaacag
















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|9259263|gb|BE347471.1|BE347471
EST:     TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAG                         GGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
genomic: TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctc ... cttgaaccagGGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
EST: gi|209724188|gb|BW659722.1|BW659722
EST:     TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAG                         GGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
genomic: TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctc ... cttgaaccagGGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
EST: gi|208330473|gb|GE131298.1|GE131298
EST:     TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAG                         GGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
genomic: TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctc ... cttgaaccagGGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
EST: gi|193566710|gb|FK526015.1|FK526015
EST:     TTGGCTGAACTTGACATTAAGAAAGCTCTTGTGATTGACCCTAACAACAG                         GGATGTCAAATTGGAGTACAGGACTTTGAAAGGAAAAGGTGAAAGCGAATA
genomic: TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctc ... cttgaaccagGGATGTCAAATTGGAGTACAGGACTTTGAA-GGAAAAGGTGAAAGCGAATA
EST: gi|58019857|gb|CX706599.1|CX706599
EST:     TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAG                         GGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
genomic: TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctc ... cttgaaccagGGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
EST: gi|213610535|gb|DB978562.1|DB978562
EST:     TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAG                         GGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
genomic: TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctc ... cttgaaccagGGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
EST: gi|193333493|gb|FK300447.1|FK300447
EST:     TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAG                         GGATGTCAAATTGGAGTACAGGACTTTGAGGGAAAAGGTGAAAGCGAATAA
genomic: TTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctc ... cttgaaccagGGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
EST: gi|208328160|gb|GE129598.1|GE129598
EST:     AAGAAAGCTCTTGAGATTGACCCTAACAACAG                         GGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA
genomic: AAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctc ... cttgaaccagGGATGTCAAATTGGAGTACAGGACTTTGAAGGAAAAGGTGAAAGCGAATAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCCCTCTATAGAAGGGCCCAAGCATATATGCAGTTAACTGACTTGGATTTGGCTGAACTTGACATTAAGAAAGCTCTTGAGATTGACCCTAACAACAGgtatatgctcagaataaattactctttttgacctttatgtatttgagatttactgaatcagttgctttaattttgggcaatttatcttttattttgccttgcaatgtaattgttctctatgcttgaaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA