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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCATTTGTTGCAATTGGAGCTACAATGGTTGGTAGCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaagttaccgttgattaccgtttttcctatcttatatgttgtctttgtttctaagtgacgtttatttgtttaatttacag

Basic information

species Glycine max
transcript GLYMA08G19310.3
intron # 18
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 18
lower sequence: AT4G25970.1 (Arabidopsis thaliana), 5'ss of exon 19
GTGGCATTTGTTGCAATTGGAGCTACAATGGTTGGTAGCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaagttaccgttgattaccgtttttcctatcttatatgttgtctttgtttctaagtgacgtttat-------ttgtttaatttacag
|| ||||||||||| |||||||| |||||||||||||| || |  |||   | | || |||| ||| |||| ||||| || || |||||      | | |    |||  ||| ||||||  ||   |     |||| || ||||| |   |  | ||        || |    ||| |||
GTCGCATTTGTTGCGATTGGAGCAACAATGGTTGGTAGTATCAGCTTTGTTAGGCAAGAGGGAGACCATGTGAAGAAAGGGGACGAGgt------aatcaattctga--accttttttctaattgaaagatatgtcattctttcttatgcaattctaaactagcattctcctttttccag

upper sequence: GLYMA08G19310.2 (Glycine max), 5'ss of exon 18
lower sequence: Vv12s0055g00710.t01 (Vitis vinifera), 5'ss of exon 16
GTGGCATTTGTTGCAATTGGAGCTACAATGGTTGGTAGCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaagttaccgttgattaccgtt-tttcctatctt-------atatgttgt-ctttgtttctaagtgacgttta---tttgttta---atttacag
||||||||||||||||| || || || |||||||||||||| || || || || || ||||||||||||||  |||| ||||| ||||||    |        || ||  |  || |||   ||  |       || | || | || || |||||| | || ||     ||  |||    ||||||||
GTGGCATTTGTTGCAATCGGGGCAACGATGGTTGGTAGCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaattcatttttttatctcttttatttttcattgtggtgtccatgtattctgctatgcttctaattaacattctaccttcatttgctcatttacag
















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:     GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAG                         TTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
genomic: GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaag ... taatttacagTTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
EST: gi|192307706|gb|FK001650.1|FK001650
EST:     GCATTACTTTTACAAAGAAAAAAGGCGACTATGTTAAGAAGGGAGATGAG                         TTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
genomic: GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaag ... taatttacagTTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
EST: gi|51338331|gb|CO982197.1|CO982197
EST:     GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAG                         TTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
genomic: GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaag ... taatttacagTTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
EST: gi|151397882|gb|EV267755.1|EV267755
EST:     GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAG                         TTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
genomic: GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaag ... taatttacagTTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
EST: gi|7030330|gb|AW460113.1|AW460113
EST:     GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAG                         TTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
genomic: GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaag ... taatttacagTTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
EST: gi|10255364|gb|BE823130.1|BE823130
EST:     GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAG                         TTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG
genomic: GCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaag ... taatttacagTTTGGATATTTCTCATTCGGTGGAAGCACTGTAATTTGCGTTTTTGAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCATTTGTTGCAATTGGAGCTACAATGGTTGGTAGCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaagttaccgttgattaccgtttttcctatcttatatgttgtctttgtttctaagtgacgtttatttgtttaatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG