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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatattcttctattgtctgcttacaaaattagtgagaacta...

Basic information

species Glycine max
transcript GLYMA17G01360.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01360.1 (Glycine max), 5'ss of exon 12
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatattcttctattgtctgcttacaaaattagtgagaacta
|||| ||||| |||||||||||||| ||||||||||| ||||||||| | | || | | | ||| | | || || || | | | | | ||| | ||
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtg-accctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagc-tctgcag---------------

upper sequence: GLYMA17G01360.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 14
GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatatatatatatatatatatatatatatatatatatatatatatatatatatata-ttcttctattgtctgcttacaa-aattagtgaga-acta---------------------------------------------------------------------------------
|||| ||||| ||||||||||||||||||||||| || ||||| |||| | | ||| | ||| || | | | | | | || | ||| | || | | |||| | | | | || || |||| | |||
GTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATGgta-agaagtatttctatgcatgcttgtcattttgtctccatttgtattaactcgtagaattgcttctagtcctagaaacatgcagcaaatagtcatttgctattaccccatattcatttgtttcacttgtgaatggttgtcgccccaaccaaatatgactaagcatacattttgaaatttcag
















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|193610338|gb|FK566168.1|FK566168
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|208025739|gb|GD826615.1|GD826615
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|254333171|gb|GR850421.1|GR850421
EST:     GGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|254317929|gb|GR832097.1|GR832097
EST:     GTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|58019435|gb|CX706177.1|CX706177
EST:     GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|7924124|gb|AW830150.1|AW830150
EST:     GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|254317928|gb|GR832096.1|GR832096
EST:     GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|207764437|gb|GD735802.1|GD735802
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|57574880|gb|CX547855.1|CX547855
EST:     GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|254330862|gb|GR842127.1|GR842127
EST:     GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
EST: gi|5342423|gb|AI794707.1|AI794707
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAA
EST: gi|193426110|gb|FK390397.1|FK390397
EST:     GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA
genomic: GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatat ... gaatcttcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGAGGGATGAGTGGGCCCTAAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatattcttctattgtctgcttacaaaattagtgagaacta

- - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - TTGAAG