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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGCTGCTTGTCCTGCATGTGAGATGGCGGTTGTTTGGATGCAGAACCAGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagttgtcttaattttgctattcaagcgtcctgctgcacctcttgatttatagcctcatgatgatagattgatattgcag

Basic information

species Glycine max
transcript GLYMA17G01500.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01500.1 (Glycine max), 5'ss of exon 11
lower sequence: AT1G62290.1 (Arabidopsis thaliana), 5'ss of exon 10
TGGTGCTGCTTGTCCTGCATGTGAGATGGCGGTTGTTTGGATGCAGAACCAGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagttgtcttaattttgc----tattcaagcgtcctgctgcacctcttgatttatagcctcatgatgatagattgatattgcag
 |  || | ||||||||||||||| ||||||||||| ||||| |||| |||  |||| |  ||   ||| |||||   |||| | |  ||||| ||  ||||          |   || |||      | |  |||           |    ||   || |     ||  ||  || |||  ||      
AGACGCGGGTTGTCCTGCATGTGAAATGGCGGTTGTGTGGATACAGAGCCAATTGAGGCAGAACATGACTCAAGAGAGGATAGTGAACTACATTAATGAGgtagaaagacaataacaagtttatatcttgtggaagtaagtaatgatattgtttttgttctgataccaaaatcgtaaattcttag-----

upper sequence: GLYMA17G01500.1 (Glycine max), 5'ss of exon 11
lower sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 11
TGGTGCTGCTTGTCCTGCATGTGAGATGGCGGTTGTTTGGATGCAGAACCAGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagttgtcttaattttgctattcaagcgtcctgctgcacctcttgatttatagcctcatgatgatagattgatattgcag-------------
 | |||||| ||| |||||||||||||||| ||||| ||||| |||| |||| |||| | |||   ||| ||||| |  ||| | |  ||| ||||| |||| |   |   ||  | ||||    | |     ||    | | |  | ||| | |   |  |  |||| ||| || | || ||  |             
AGATGCTGCGTGTTCTGCATGTGAGATGGCTGTTGTGTGGATCCAGAGCCAGTTGAGGCAAAACATGACTCAAGAGCGCATATTGAACTACGTCAACGAGgtaaccaataagttgtcatttcaagacttt--tgtgaaacagtagttattgttgtcctgattactgattataaatcgctactgtgggttttcttaacag
















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|208174819|gb|GD972126.1|GD972126
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|207810012|gb|GD781526.1|GD781526
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|13790574|gb|BG653165.1|BG653165
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGAAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|208140744|gb|GD935198.1|GD935198
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|209717932|gb|BW666125.1|BW666125
EST:     AAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|26047831|gb|CA784491.1|CA784491
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|163920919|gb|EH039437.1|EH039437
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|37996199|gb|CF807788.1|CF807788
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|208307795|gb|GE104981.1|GE104981
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|208056986|gb|GD855127.1|GD855127
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|193333772|gb|FK298318.1|FK298318
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
EST: gi|17021150|gb|BM092184.1|BM092184
EST:     AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAG                         CTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG
genomic: AGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagt ... gatattgcagCTTTGCGATAAAATGCCTAGCCCGATGGGAGAATCAGCTGTTGACTGTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGCTGCTTGTCCTGCATGTGAGATGGCGGTTGTTTGGATGCAGAACCAGCTGAGCCGAAATCAGACACAAGATCAGATACTAAGTTACATCAACCAGgtgagtcagttgtcttaattttgctattcaagcgtcctgctgcacctcttgatttatagcctcatgatgatagattgatattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA