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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGCAACCAAGTTGTGAAAATAGGGAAACAGATTAAATTTTCGCTGGTAAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAGgtaggttgacctccaaattatgtgctgttacctagttgtagtaaatcaatttatctattgagcatactccattaaattcaatgatcccacataaagagtctaaatcaaatactatttgattattttttag

Basic information

species Glycine max
transcript GLYMA03G22450.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 11
lower sequence: AT5G48460.1 (Arabidopsis thaliana), 5'ss of exon 10
AACTGCAACCAAGTTGTGAAAATAGGGAAACAGATTAAATTTTCGCTGGTAAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAGgtaggttgacctccaaattatgtgctgttacctagttgtagtaaatcaatttatctattgagcatactccattaaattcaatgatcccacataaagagtctaaatcaaatactatttgattattttttag
||||| || |||||||||||| ||||||| ||| | || || ||  |||| ||  ||||||||||||||||||| || ||||| || ||| | ||||||||||     |  ||  || | | |  |  |   |  || |     | ||| ||   || ||||     |   || ||  ||    | |||                                         
AACTGTAATCAAGTTGTGAAATTAGGGAAGCAGCTCAAGTTCTCTTTGGTTAACATTGCTGGAAATGACATTGTTCAAGGAAACAAGAAACTCATACTAGgtaaa--aatttctcaactctataattgtgtgtttttatgaatcaccaactttaataatgagt----tgttttgaaaccatc--ttccag----------------------------------------

upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv00s1365g00010.t01 (Vitis vinifera), 5'ss of exon 8
AACTGCAACCAAGTTGTGAAAATAGGGAAACAGATTAAATTTTCGCTGGTAAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAGgtaggttgacctccaaattatgtgctgttacctagttgtagtaaatcaatttatctat-tgagcatactccattaaattcaatgatcccacataaagagtctaaatcaaatactatttgattattttttag
||||||||||||||||| || || ||||||||  | || ||||| ||||| ||| ||||||||||||| ||||| |||||||| || ||||||||| | |||| ||||   || ||  | | |  | |  ||||  | |   | | ||| ||   ||  ||| || |     ||    |   |  ||                                            
AACTGCAACCAAGTTGTAAAGATTGGGAAACAATTAAAGTTTTCCCTGGTTAATATTGCTGGAAATGATATTGTACAGGGAAACAAGAAATTAATATTGGgtatgttg---tctaacatttct-ttttcccctatatattagataccaacttgattacctgaacaaaaaatgttggccttgctcttcag------------------------------------------
















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|193478136|gb|FK440681.1|FK440681
EST:     AAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAG                         CTTATCTGTGGCAATTGATGCGATACAATA
genomic: AAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAGgtaggttgac ... tattttttagCTTATCTGTGGCAATTGATGCGATACAATA
EST: gi|208068976|gb|GD864180.1|GD864180
EST:     AAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAG                         CTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT
genomic: AAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAGgtaggttgac ... tattttttagCTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT
EST: gi|9258812|gb|BE346959.1|BE346959
EST:     AAAAATTAATACTAG                         CTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT
genomic: AAAAATTAATACTAGgtaggttgac ... tattttttagCTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT
EST: gi|193611213|gb|FK561723.1|FK561723
EST:     TGACATTGTGCAGGGAAATAAAAAATTAATACTAG                         CTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT
genomic: TGACATTGTGCAGGGAAATAAAAAATTAATACTAGgtaggttgac ... tattttttagCTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT
EST: gi|208059512|gb|GD858326.1|GD858326
EST:     TGTTTGTCTTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAG                         CTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT
genomic: TG-TTG-C-TGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAGgtaggttgac ... tattttttagCTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT
EST: gi|193573679|gb|FK531013.1|FK531013
EST:     AAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAAT-CTAG                         CTTATCTGTGGCAATTGATGCGATACAATA
genomic: AAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAGgtaggttgac ... tattttttagCTTATCTGTGGCAATTGATGCGATACAATA
EST: gi|193438158|gb|FK402177.1|FK402177
EST:     CTGGAAATGACATTGTGTCAGGGAAATAAAAAATTAATACTAG                         CTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT
genomic: CTGGAAATGACATTGTG-CAGGGAAATAAAAAATTAATACTAGgtaggttgac ... tattttttagCTTATCTGTGGCAATTGATGCGATACAATATCCTACAACTTCTCAAGAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGCAACCAAGTTGTGAAAATAGGGAAACAGATTAAATTTTCGCTGGTAAATGTTGCTGGAAATGACATTGTGCAGGGAAATAAAAAATTAATACTAGgtaggttgacctccaaattatgtgctgttacctagttgtagtaaatcaatttatctattgagcatactccattaaattcaatgatcccacataaagagtctaaatcaaatactatttgattattttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA