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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcctaggccttatataacatggctcacttttgtaatagttaaatgatgttgtattcctgaatgatatagtgatggttttctgtgaatgggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGTAATTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC

Basic information

species Glycine max
transcript GLYMA06G19250.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G19250.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv17s0000g08560.t01 (Vitis vinifera), 3'ss of exon 7
tcttcctaggccttatataacatggctcacttttgtaatagttaaatgatgttgtattcctga-atgatatagtgatggttttctgtgaatgggcc--tgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGTAATTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC
  ||| |  |    |  | ||         | |||   |  ||  || ||     | | | || |  || | |  |   | ||  |  | |||     ||||||| || ||||||||||||||||||||||| || |||||||||||||||||||||||||| |||||||| ||||||||||| |  |||||  |||||||||
--ttctttagtgagagttgactcctaaatttgttgctgtctttgtattattcatcaattccgacaaaatttggcta-aatatttagaaattggattgatgcagGTCTCTTATATGATATTGCAAAGGGTATCCCCAGTTACCCACTCTGTGGGTAATTGTGTTAAGCGGGTGGTGGTCATTGTTACTTCTGTTCTCTTCTTCC

upper sequence: GLYMA06G19250.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 7
tcttcctaggccttatataacatggctcacttttgtaatagttaaatgatgttgtattcctgaatgatatagtgatggttttctgtgaatgggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGTAATTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC
                                                   |||   |  || | | | ||| | ||  ||||||      |   ||||||| || || |||||||||||||||||||| || ||||| ||||| || || || ||||| ||||| ||  | || ||||| |  || |||||||||||  
-------------------------------------------------gtttgctctgatgcaagtt-tagcgttg--tttctgaaggacgatttgcagGTGTCCTACATGATATTGCAAAGGGTATCGCCGGTTACGCACTCCGTTGGAAACTGTGTCAAGCGCGTGATTGTGATTGTAACTTCAGTCATCTTCTTTA
















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|120496570|gb|EH224737.1|EH224737
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|10253112|gb|BE820878.1|BE820878
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|11687638|gb|BF595314.1|BF595314
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|22522844|gb|BU081655.1|BU081655
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|261497053|gb|GT185228.1|GT185228
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTTTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|11687750|gb|BF595426.1|BF595426
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|13789795|gb|BG652386.1|BG652386
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|51337755|gb|CO981621.1|CO981621
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|254322816|gb|GR839837.1|GR839837
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|8404251|gb|BE059885.1|BE059885
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|6725472|gb|AW309871.1|AW309871
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
EST: gi|208032805|gb|GD830464.1|GD830464
EST:     TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAA                         GTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT
genomic: TTTACATCAGATCTCTTCTTGCTGCTCTCTGTTTCCATGCGTATCAACAAgtgagttttt ... gggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatgttgtattcctgaatgatatagtgatggttttctgtgaatgggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGTAATTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC
                 aatgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttcctaggccttatataacatggctcacttttgtaatagttaaatgatgttgtattcctgaatgatatagtgatggttttctgtgaatgggcctgcagGTTTCGTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCTGTGGGTAATTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC