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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATATTGAAAGTTATACTTGAAAAAGAGGACTTGTCTTCTGATATTGATATGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatgagtgttcctttttaacccaatactttttttaaattaaggttatgggtgccttcatgcttgctcttttattgcag

Basic information

species Glycine max
transcript GLYMA06G17940.1
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17940.1 (Glycine max), 5'ss of exon 25
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 24
AATATTGAAAGTTATACTTGAAAAAGAGGACTTGTCTTCTGATATTGATATGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatg-----agtgttcctttttaacccaatacttttttt-----aaatta-aggttatgg----gtgccttcatgct---tgctcttttattgcag----
 |||||||| || ||||||  |||||| ||||||||  ||||| | ||||| ||||   |||| ||||||||  |||||||||| ||||  ||||||||||| |       |||  | | ||||||||   | || |  |      |||| | | || |||      |   | |||| |   |||||||||  |||      
GATATTGAAGGTGATACTTTCAAAAGAAGACTTGTCCCCTGATTTCGATATTGATGAGGTTGCTAGTATGACAAATGGATATTCTGGAAACGATCTTAAGgtaaaattcctagtaattccttttaaccttttgctatggtctgacgaaatgataagtaatgctcatatatatccatgttacatgctcttttggtgcgtgcag

upper sequence: GLYMA06G17940.1 (Glycine max), 5'ss of exon 25
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 24
AATATTGAAAGTTATACTTGAAAAAGAGGACTTGTCTTCTGATATTGATATGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgtta--tgagtgttcctttttaacccaatacttttttt------------------aaattaaggttatgggtgccttcat-gcttgctcttttattgcag----
 ||||| || |||||||||| |||||| ||||||||  ||||| | ||||| | ||  ||||| ||||||||| |||||||||| ||||||||||||||||| |  |    ||   |  |||| ||  |  | |  |                   ||   || || ||   |||    ||   || |||||||  |||      
TATATTAAAGGTTATACTTGCAAAAGAAGACTTGTCCCCTGATTTGGATATTGGTGAGATTGCTAGTATGACTAATGGATATTCTGGAAGTGATCTTAAGgtaaattcctagtaattccttaaacctttgttgtggtctgccaaaagtgatagagaaaggcaaagtaattaatgctcatattattttctcttttggtgctctcag

upper sequence: GLYMA06G17940.1 (Glycine max), 5'ss of exon 25
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 25
AATATTGAAAGTTATACTTGAAAAAGAGGACTTGTCTTCTGATATTGATATGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatgagtgttcctttttaacccaatactttt--tttaaattaag---gttatgggtgccttcatgcttgctcttttattgcag-------------
 ||  | ||||| ||||| | |||||||||||||||| ||||| ||||| |||||||| |||||||||||||||||||||||||||||||||| ||||||||| |   || | |  | |   |    | || |  ||  |||| |    |   || | | |||     ||   ||||  | ||               
GATTCTAAAAGTGATACTGGCAAAAGAGGACTTGTCTCCTGATGTTGATTTGGATGCAGTTGCAAGTATGACTGATGGATATTCCGGAAGTGACCTTAAGgttttctttgcttccctattttctggaatttatgattataattcaatatgcagtgtggggctttgctttttaactttagtcgcttctctgtgttgcag

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|8670294|gb|BE191401.1|BE191401
EST:     TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAG                         AATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAG
genomic: TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatgagtg ... tttattgcagAATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAG
EST: gi|15338257|gb|BI498913.1|BI498913
EST:     TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAG                         AATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAA
genomic: TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatgagtg ... tttattgcagAATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAG
EST: gi|151404219|gb|EV274029.1|EV274029
EST:     TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAG                         AATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAG
genomic: TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatgagtg ... tttattgcagAATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAG
EST: gi|27427279|gb|CA938799.1|CA938799
EST:     TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAG                         AATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAG
genomic: TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatgagtg ... tttattgcagAATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAG
EST: gi|192318122|gb|FK010946.1|FK010946
EST:     TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATTTTAAG                         AATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAG
genomic: TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatgagtg ... tttattgcagAATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAG
EST: gi|10237116|gb|BE806004.1|BE806004
EST:     TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAG                         AATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAG
genomic: TGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatgagtg ... tttattgcagAATTTGTGTGTAACTGCTGCACACCGTCCAATTAAAGAGATATTAGAAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATATTGAAAGTTATACTTGAAAAAGAGGACTTGTCTTCTGATATTGATATGGATGCAATTGCAAGTATGACTGATGGATATTCCGGAAGTGATCTTAAGgttatgagtgttcctttttaacccaatactttttttaaattaaggttatgggtgccttcatgcttgctcttttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA