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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGCTTCTGCTGAACGTGATGATGTTGCTGTATGTGCTGCAGATTGCCGTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttttctttcttacaattcaattgaatatggaaggcttctaatctaaaaaaaacagttttttaaaatattttataatcaaattttgaaatctgc...

Basic information

species Glycine max
transcript GLYMA08G19310.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19310.2 (Glycine max), 5'ss of exon 14
lower sequence: AT4G25970.1 (Arabidopsis thaliana), 5'ss of exon 15
AATTGCTTCTGCTGAACGTGATGATGTTGCTGTATGTGCTGCAGATTGCCGTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtat-----tttttttctttcttacaattcaattga------atatggaagg--------cttctaatctaaaaaaaacagttttt----taaaatattttataatcaa--------attttgaaatctgc----------------------
|||||| |     || |  |||||||||||||||| |||||| ||||| ||  | | ||||||| |||| ||||||||||| ||| | |||||||||||||||        | |    |  | ||||| || | |       ||||| || |        ||  |||   ||   |  | | |  |    |  || | | || ||            ||| | |||| | |                      
AATTGCGTGCATGGATCAGGATGATGTTGCTGTATCTGCTGCTGATTGTCGATTAATGGCATTTCAATCGGTTGATGATAGCACACGGTTCTGGATCAAGgtaaagcggcctctagagtattcacaatacactaggcaaggcatatgaaaagttgaataactcttaacacaattgatgctgctgataacctgcaacactgtacaactgttactcgctattctaaaattttcagactgttttcaatattgttag

upper sequence: GLYMA08G19310.2 (Glycine max), 5'ss of exon 14
lower sequence: AT5G57190.1 (Arabidopsis thaliana), 5'ss of exon 15
AATTGCTTCTGCTGAACGTGATGATGTTGCTGTATGTGCTGCAGATTGCCGTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttttctttcttacaattcaattgaatatggaaggcttctaatctaaaaaaaacagttttttaaa-atattttataatcaa-attttgaaatctgc---------------------------------
||||||||      | ||  ||||||||||||||||||| || ||||| ||  | | ||||||| | || || || |||||||| ||||||||||||||||||   |  || | |     |  | | |  |   |  |    |  || || | |  | | | || |  ||| | ||  | ||    | ||  || ||                                      
AATTGCTTGCATGAACCGCAATGATGTTGCTGTATGTGCCGCTGATTGTCGATTAATGGCATTTCAGTCGGTGGAAGATAGTACCAGATTCTGGATCAAGgtaaaatggtt-tctagagtagcttactatatacttaatcaatattattcaagattagagaattctcaaaacaaatgatgtagctgatataatgcaacacatccttatttttttgcattgattctgcaatgatag

upper sequence: GLYMA08G19310.2 (Glycine max), 5'ss of exon 14
lower sequence: Vv12s0055g00710.t01 (Vitis vinifera), 5'ss of exon 12
AATTGCTTCTGCTGAACGTGATGATGTTGCTGTATGTGCTGCAGATTGCCGTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttttctttcttacaattcaattgaatatggaaggcttctaatctaaaaaaaacagttttt-taaaatattttataat-caaattttgaaatctgc--
|||||| |     ||||||||||||||||||||||||||||||||| | ||||| |||||||||||||| ||||| |||  |  |||||| ||||| |||||||| | | ||  | | |  |||       || |  |  ||| |  ||||   | |    |||||  |   |  ||||  |||    ||   | ||  ||   
AATTGCCTGCATGGAACGTGATGATGTTGCTGTATGTGCTGCAGATAGTCGTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAGgtattatctgtcactttgaatatttgt---gatgta-agagctacacatcttttagaggttgttttggtctcagcttttgcaatgttgataaggtaaaatgaaa

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|58020769|gb|CX707511.1|CX707511
EST:     GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAG                         GGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
genomic: GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttt ... ttacttttagGGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
EST: gi|192307706|gb|FK001650.1|FK001650
EST:     GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAG                         GGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
genomic: GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttt ... ttacttttagGGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
EST: gi|51338331|gb|CO982197.1|CO982197
EST:     GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAG                         GGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
genomic: GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttt ... ttacttttagGGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
EST: gi|15286683|gb|BI470574.1|BI470574
EST:     GAATGGGCACATTTCTCATCTTACGATGTTGGTATTCGATCTGGATCAAGTGCATCCCATATTCTG          
genomic: GAATGGGCACATTTCTCATCTTACGATGTTGGTATTCGATCTGGATCAAGTGCATCCCATATTCTGgtataggata
EST: gi|151397882|gb|EV267755.1|EV267755
EST:     GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAG                         GGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
genomic: GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttt ... ttacttttagGGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
EST: gi|9439775|gb|BE440289.1|BE440289
EST:     GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAG                         GGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
genomic: GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttt ... ttacttttagGGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
EST: gi|193658135|gb|FK602568.1|FK602568
EST:     GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAG                         GGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
genomic: GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttt ... ttacttttagGGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
EST: gi|193424345|gb|FK386414.1|FK386414
EST:     GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAG                         GGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT
genomic: GTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttt ... ttacttttagGGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGCTTCTGCTGAACGTGATGATGTTGCTGTATGTGCTGCAGATTGCCGTCTTACGGCATTTAAATCAGTTGATGATAGTACAAGATTCTGGATCAAGgtattttttttctttcttacaattcaattgaatatggaaggcttctaatctaaaaaaaacagttttttaaaatattttataatcaaattttgaaatctgc

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