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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAGgtaaggattggtctgtcatataccatgactattttttcccccttcagttgattgaagaagacaattttagaacatgtatttcaatactatctgccttttcttgatgattttttgtcacattatatgcag

Basic information

species Glycine max
transcript GLYMA03G37450.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G37450.1 (Glycine max), 5'ss of exon 19
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 5'ss of exon 17
AGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAGgtaaggattggtctgtcatataccatgactattttttcccccttcagttgattgaagaagacaattttagaacatgtatttcaatactatctgccttttcttgatgattttttgtcacattatatgcag
||||||||||||||| ||||||||||||||||||||||| || ||||| ||  ||||||| ||||| || |||||||||||||| |||||||  || ||||| |||  ||  ||| | |  |  |       ||| | ||  || ||||||  ||           || ||| ||   ||||| |   |                                        
AGAAGAGTTTGTTGGTAACATGAGTTCTAGGGAATTTGTTGATACTATCACCCGAGATCTTCTGGGAAGCCGTGTCTTTGTGTTTACACCAAAAGGCGAGgtgagg--tg--ctgacttggaggaca-----tttcttccatttgagttgagcgattgg-------tttgaatatagttttcattggcag---------------------------------------

upper sequence: GLYMA03G37450.1 (Glycine max), 5'ss of exon 19
lower sequence: GRMZM2G353147_T01 (Zea mays), 5'ss of exon 16
AGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAGgtaagg-attggtctgtcatatacca-tgactattttttcccccttcagttgattgaagaagacaattttagaacatgtatttcaatactatctgccttttcttgatgattttttgtcacattatatgcag
||||||||||||||| || |||||||||||||||||||| || ||||| ||  ||||||| || || || |||||||||||||| || || |  || ||||| ||| | ||  ||   | |||  | | |  |   |   |   ||  |  | |  ||  |  |  ||     |||||||                                                   
AGAAGAGTTTGTTGGTAATATGAGTTCTAGGGAATTTGTTGATACTATCACCCGAGATCTTCTAGGAAGCCGTGTCTTTGTGTTTACTCCTAAAGGCGAGgtgaggcaatgaactcagagatattagttaacagcatagactattttggaggctctaaataagctgtt-----acatgtag--------------------------------------------------

upper sequence: GLYMA03G37450.1 (Glycine max), 5'ss of exon 19
lower sequence: AT4G02260.3 (Arabidopsis thaliana), 5'ss of exon 17
AGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAGgtaaggattggtctgtcatataccatgactattttttcccccttcagttgattgaagaagacaattttagaacatgtatttcaata--ctatctgccttttcttgatgattttttgtcacattatatgcag
||| |||||||| || |||||||| ||||| |||||||| || || ||||| || |||||  | || |||||||| ||||| |||||||| |  |||||||||||||     ||   |||   ||   |   |||  ||  | ||      ||  |        |||| ||  |  |  ||   |   |||| |||                                   
AGAGGAGTTTGTGGGTAACATGAGCTCTAGAGAATTTGTGGATACCATTACGAGGGATCTTTTAGGTAGTCGTGTGTTTGTATTCACACCTAAAGGAGAGgtaagga-----ctactatacctcaaagcctctttaaccatcatctaacatttttat------gtttttgattaaatgctttggtgttctatttgcag---------------------------------

upper sequence: GLYMA03G37450.1 (Glycine max), 5'ss of exon 19
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 5'ss of exon 17
AGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAGgtaaggattggtctgtcatataccatgactattttttcccccttcagttgattgaagaagacaattttagaacatgtatttcaatactatctgccttttcttgatgattttttgtcacattatatgcag
||| |||||||| || |||||||  || ||||||||||| |||||| | || | ||||||| | || |||||||||||||| || || || |||||||||||||  ||  |  |  | | || |||    |           || || || |   ||        |||     ||   | || || ||||   |                                   
AGAGGAGTTTGTCGGAAACATGACCTCCAGGGAATTTGTAGACACTGTCACTAAAGATCTGTTAGGAAGTCGTGTCTTTGTATTTACGCCTAGGGGAGAGgtaaccatgtggataacttttaacatatgaaaa---------ttaagatgctcagag--------ttttatttatccttctccatgctattcacag---------------------------------

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|151406442|gb|EV276257.1|EV276257
EST:     CAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAG                         ATTAAGAATCTTCCTCAGGGTGCTACTGTCATTGACTACGCTTATATGATA
genomic: CAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAGgtaaggattg ... ttatatgcagATTAAGAATCTTCCTCAGGGTGCTACTGTCATTGACTACGCTTATATGATA
EST: gi|120496652|gb|EH224819.1|EH224819
EST:     CAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAG                         ATTAAGAATCTTCCTCAGGGTGCTACTGTCATTGACTACGCTTATATGATA
genomic: CAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAGgtaaggattg ... ttatatgcagATTAAGAATCTTCCTCAGGGTGCTACTGTCATTGACTACGCTTATATGATA
EST: gi|151402145|gb|EV271958.1|EV271958
EST:     CAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAG                         ATTAAGAATCTTCCTCAGGGTGCTACTGTCATTGACTACGCTTATATGATA
genomic: CAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAGgtaaggattg ... ttatatgcagATTAAGAATCTTCCTCAGGGTGCTACTGTCATTGACTACGCTTATATGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCAGTCGTGTCTTTGTGTTCACACCAAGGGGAGAGgtaaggattggtctgtcatataccatgactattttttcccccttcagttgattgaagaagacaattttagaacatgtatttcaatactatctgccttttcttgatgattttttgtcacattatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC