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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaactattttttaaccaaatcgcatggggatagtgtaataaatttgaactcggataattggattgctatcaatattgggtatgatccacatga...

Basic information

species Glycine max
transcript GLYMA12G30540.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30540.1 (Glycine max), 5'ss of exon 19
lower sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 11
GTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaactattttttaaccaaatcgcatggggatagtgtaataaatttgaactcggataattggattgctatcaatattggg----tatgatccacatga-
||  || | ||||| || ||||||||||| || || ||||||||||| || || |||||||| |||||||||||| || |  | ||    |   |    | ||       | || ||  | || |   |   |  ||   || | | |  ||| |||     ||| |    | |   
GTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgtta--ccatcaagttctctgtgcacagtttctgaatgaaaacatttcggcattaaaacat---atagttgtgtatactggagctctataacttccttttt

upper sequence: GLYMA12G30540.1 (Glycine max), 5'ss of exon 19
lower sequence: AT5G22750.1 (Arabidopsis thaliana), 5'ss of exon 18
GTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaactattttttaaccaaatcgcatggggatagtgta-ataaatttgaactcggataattggattgctatcaatattgggtatgatccacatga
||  |||| ||||| |||||||||||||| || || ||||| |||||||| || || |||||||||||||||||| |  | |    |   || | |      ||      ||| |  |||   || |   |   ||||  | |       |||||       ||     |   
GTACTGTTGATGTCTCTAAAAGCTGGTGGCGTTGGGATAAATCTAACAGCTGCGTCCAATGCTTTTGTCATGgtatggaatatctatagatatctatgaaagatcatatcagtttctataggatttagaccatgtaat-agctcatccaaaatatgaaaatcgagtagtagtt
















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|193321928|gb|FK287436.1|FK287436
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|193333255|gb|FK298789.1|FK298789
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|193508871|gb|FK465467.1|FK465467
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|207838025|gb|GD810359.1|GD810359
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|193599772|gb|FK551567.1|FK551567
EST:     AGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: AGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|193429943|gb|FK395017.1|FK395017
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|207694182|gb|GD674277.1|GD674277
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|193356432|gb|FK320905.1|FK320905
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|193443396|gb|FK409170.1|FK409170
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|208307393|gb|GE107071.1|GE107071
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaactattttttaaccaaatcgcatggggatagtgtaataaatttgaactcggataattggattgctatcaatattgggtatgatccacatga

- - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - GGTGGA
- - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - GCAGCT