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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGTTTACTACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAGgtaaccttttagtttgccttgaaaaaatcatcctttaagagtatgaaagggagatattaagtagattttcttcaccttagtagaaagtgattgtgtttaa...

Basic information

species Glycine max
transcript GLYMA11G12120.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12120.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G058910_T01 (Zea mays), 5'ss of exon 11
ATTTCTT-TTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGTTTACTACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAGgta-accttttagtttgccttgaaaaaatcatcctttaagagtatgaaagggagatattaagtagattttcttcaccttagtagaaagtgattgtgtttaa-
 |||||| |||||||| ||||||||||||||||| |||||||| || ||  |||| ||  | || ||| | |||||| |||||||||||||  ||   |||||   ||   |||| |   ||| |     | ||  |||  | |  ||   | || | |    || | ||     ||||   | | |  ||  |  |||||  
-TTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGCTTGTTACTTGCAACACTCTATCTTATAATCCGGGAGAAGAAACTAGCTTCACAGgtttgcccactagtcttggttgcattttgcttcacttatcattg-gatctgtagttctgtgctacaattctaaaacctgttttggagttggat-cgtttagc

upper sequence: GLYMA11G12120.1 (Glycine max), 5'ss of exon 11
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 11
ATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGTTTACTACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAGgtaaccttttagtttgccttgaaaaaatcatcctttaagagtatgaaagggagatattaagtagattttcttcaccttagtagaaagtgattgtgtttaa--------------
 || ||||| ||||| |||||||||||||||||||||||||||||  | || || ||  || | || || ||| | |  || ||||||||| | || |||||||     || |   ||    ||      ||  ||| |||| | ||   | || |||    | || |   ||| |  || ||||  || || |  || |              
CTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGCATTCTGCTTGCAACTATGTACTTGATATTGAAAGAAAAGAAACTTGCCAGCCAGgtaa-----taatactcc----aactgatgtcacttacgagtgttaacacgcgagattg---aaatctgtctcatc--agcagaacttgcttataatttagctgtttgttttac

upper sequence: GLYMA11G12120.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 5'ss of exon 11
ATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGTTTACTACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAGgtaaccttttagtttgccttgaaaaaatcatcctttaagagtatgaaagggagatattaagtagattttct--tcaccttagtagaaagtgattgtgtttaa-
||||||||||||||| ||||||||||||||||| |||||| |||| ||  |||| ||  |  | | ||| ||||||||||| |||||||| || | ||||||||||     |  ||  ||     |||    | |||| | |    |      ||    |  |  |  |    |||| |   | | |  | | | | | |   
ATTTCTTTTTGCTGTCATGTTTGGTGATTGGGGACATGGATTATGCTTGTTACTCGCTACATTGTTTTTTATAATCAGGGAAAAGAAACTCTCCAATCAGgtaaccagc--gcatgagttagttgaatttcacattaaca-ttcagattttcaatgcagaacaactccttgaatcacatctattgcagctaaatatatctcta

upper sequence: GLYMA11G12120.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S107_75V6.1 (Physcomitrella patens), 5'ss of exon 10
ATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGTTTACTACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAGgtaaccttttag---tttgccttgaaaaaatcatcctttaagagtatgaaagggagatattaagtagattt-tcttcaccttagtag--aaagtgattgtgtttaa---------
 || || || ||||| ||||||||||| ||||| |||||||| |||||||| |||| |||||| ||| |  || | |  ||||||||||||   ||  ||||||  ||| |     || |  ||     ||  || ||||||  | | ||   ||  |       || ||| |||  |  || || |  ||| | |   ||||  |         
TTTCCTATTCGCTGTTATGTTTGGTGACTGGGGACATGGAATCTGTTTACTTCTGGGGGCTCTTTATCTTGTATTAAATGAGAAGAAACTTGGGAGCAAGgtaatttttgaaagactttctctgcgctcatggtcatttaagcatctcaagttgaccttcagttgaggtttgtctcaagttttgtggtgaaactaaacctgttggactgctgcag

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|208179178|gb|GD974525.1|GD974525
EST:     TACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAG                         AAGCTTGATGACATCACGGAGATGACTTTTGGAGGTCGTTATGTTATTTTG
genomic: TACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAGgtaacctttt ... tgaaaaacagAAGCTTGATGACATCACGGAGATGACTTTTGGAGGTCGTTATGTTATTTTG
EST: gi|193540033|gb|FK499017.1|FK499017
EST:     TACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTGGTCAG                         AAGCTTGATGACATCACGGAGATGACTTTTGGAGGTCGTTATGTTATTTTG
genomic: TACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAGgtaacctttt ... tgaaaaacagAAGCTTGATGACATCACGGAGATGACTTTTGGAGGTCGTTATGTTATTTTG
EST: gi|208231872|gb|GE032717.1|GE032717
EST:     TACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAG                         AAGCTTGATGACATCACGGAGATGACTTTTGGAGGTCGTTATGTTATTTTG
genomic: TACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAGgtaacctttt ... tgaaaaacagAAGCTTGATGACATCACGGAGATGACTTTTGGAGGTCGTTATGTTATTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGTTTACTACTGGCGGCTCTATATTTCATAATCAGGGAGAAGAAACTTTCTAGTCAGgtaaccttttagtttgccttgaaaaaatcatcctttaagagtatgaaagggagatattaagtagattttcttcaccttagtagaaagtgattgtgtttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaaaaa