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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACATTTGAGCTGGATATCAGCATCACAAAGAAGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcctttcctttgtttagacctactcgaaagaaatatcattttattttgaatatcaacatcatgctgatgatttatatggtttgtttag

Basic information

species Glycine max
transcript GLYMA02G42680.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G42680.1 (Glycine max), 5'ss of exon 8
lower sequence: AT2G04400.1 (Arabidopsis thaliana), 5'ss of exon 8
AAACATTTGAGCTGGATATCAGCATCACAAAGAAGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggc----ctttcctttgtttagacctactcga--aagaaatatcattttattttgaatatcaacatcatgctgatgatttatatggtttgtttag
||||||||||  |||| ||||| |  |||||||||||||||||||||||||  || | |  |||||||||||||| ||| | |||| ||       |||||| || || |       ||    |   | |   || | || |||| |    ||  |||| |||    || |   ||  ||| ||
AAACATTTGAAGTGGACATCAGTAATACAAAGAAGCTTCTTGAAGGAGAGCATGGTAGACAAATCCGTGAGAGAGACATGATTgtaagtacttccactttccattcttcaactggtgtctgtcatttactggaatataatcttgagtcctgac--catgatga-atcttgttgtgtgggttaag

upper sequence: GLYMA02G42680.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv12s0057g01240.t01 (Vitis vinifera), 5'ss of exon 8
AAACATTTGAGCTGGATATCAGCATCACAAAGAAGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcctttcctttgtttagacctactcgaaagaa-----atatcattttattttgaatatca-acatcatgc-tgatg------atttatatggtttgtttag-------------------------
 |||||||||| | ||||| |||| |||||||||||||||||||||||| || ||  ||||||||||| | | ||  |||| |||  ||| | |||| ||| || | |   |  |   | |      | || ||||  || || ||   |  | || ||  ||| |      ||| || | |||   ||                           
CAACATTTGAGGTTGATATTAGCAACACAAAGAAGCTTCTTGAAGGAGAACGTGGTGAAATAATCCGTCAAAAAGATATAATTgtgagtgac-tttcttttattcataatcatccagtaaaccgtatacattatttgcttgtgcatgctatgcttcttgtgtgaaggaaagaattcatcttgttcccttcacttagttttaattccggatcttcag
















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|208026780|gb|GD822980.1|GD822980
EST:     TTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACT                         ATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTCAG
genomic: TTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcc ... gtttgtttagATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
EST: gi|209704987|gb|BW653277.1|BW653277
EST:     AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACT                         ATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
genomic: AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcc ... gtttgtttagATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
EST: gi|214007942|gb|DB986489.1|DB986489
EST:     AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACT                         ATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
genomic: AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcc ... gtttgtttagATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
EST: gi|214008127|gb|DB988500.1|DB988500
EST:     AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACT                         ATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
genomic: AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcc ... gtttgtttagATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
EST: gi|193446484|gb|FK415815.1|FK415815
EST:     GAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCTTAACT                         ATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
genomic: GAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcc ... gtttgtttagATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
EST: gi|209729118|gb|BW660015.1|BW660015
EST:     AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACT                         ATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
genomic: AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcc ... gtttgtttagATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
EST: gi|209717560|gb|BW671482.1|BW671482
EST:     AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACT                         ATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
genomic: AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcc ... gtttgtttagATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
EST: gi|209726201|gb|BW659566.1|BW659566
EST:     AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACT                         ATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG
genomic: AGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcc ... gtttgtttagATGGTTGGAGAATCTGGTCTGTTCACCCCTGATGATATTGCCTATGTTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACATTTGAGCTGGATATCAGCATCACAAAGAAGCTTCTTGAAGGAGAGCGAGGCAAAATAATCCGTGAGAGAGGCATAACTgtatgtggcctttcctttgtttagacctactcgaaagaaatatcattttattttgaatatcaacatcatgctgatgatttatatggtttgtttag

- - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG