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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCAAAGGTGAAGGATTCGTTCTTAGGAAACGTTCTGATGAAAGTGCTGAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGGgtactattttcttacctctcttttcctttagtttaattttgagtttaatgatcatgcactgctttgcattgtcattcaatcacaaatcaccgtagaaatg...

Basic information

species Glycine max
transcript GLYMA12G08390.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08390.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv06s0061g00330.t01 (Vitis vinifera), 5'ss of exon 3
AATGCAAAGGTGAAGGATTCGTTCTTAGGAAACGTTCTGATGAAAGTGCTGAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGGgtactatt-ttcttacctctcttttcct--ttagtttaattttgagtt----taatgatcatgcactgctttgcattgtcattcaatcacaaatcaccgta--gaaatg-
||||||| ||||||||||| || |||| |||||  || || | ||||||||||||||||||| ||   || ||||||||||| || |||| ||| |||||||||  || | |||||||   | |  ||     || ||| |||| | |    ||||| ||      ||   | ||||    ||| |  |    || | | |  | ||   
AATGCAATGGTGAAGGATTTGTGCTTAAGAAACTGTCAGAGGCAAGTGCTGAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGGgtacatttgtccttaccttagtgtctctaccctgtataaatttgggctgcattaatgttctaaatttgggctccattaatgttctaa-atttgtcgctgcattgtaacag
















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|4405528|gb|AI507677.1|AI507677
EST:     GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGG                         GCTTTCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCC
genomic: GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGGgtactatttt ... cttgtaccagGCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCC
EST: gi|22522921|gb|BU081732.1|BU081732
EST:     GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGG                         GCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG
genomic: GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGGgtactatttt ... cttgtaccagGCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG
EST: gi|7795276|gb|AW780673.1|AW780673
EST:     GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGG                         GCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG
genomic: GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGGgtactatttt ... cttgtaccagGCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG
EST: gi|23725468|gb|BU760689.1|BU760689
EST:     GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGG                         GCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG
genomic: GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGGgtactatttt ... cttgtaccagGCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG
EST: gi|192300610|gb|FG991532.1|FG991532
EST:     GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGG                         GCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG
genomic: GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGGgtactatttt ... cttgtaccagGCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG
EST: gi|213589752|gb|DB957601.1|DB957601
EST:     GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGG                         GCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG
genomic: GAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGGgtactatttt ... cttgtaccagGCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGCAAAGGTGAAGGATTCGTTCTTAGGAAACGTTCTGATGAAAGTGCTGAGAAGGCAAGAGTGCAAGCTAAGAATATGGCCACCCGATTCACGGCAGGgtactattttcttacctctcttttcctttagtttaattttgagtttaatgatcatgcactgctttgcattgtcattcaatcacaaatcaccgtagaaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT