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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgctgtatatcgctgtggctagtgatcgtgaaacgcgtgttttgagtgtcgtttttgtgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGGAATGTTGTTCTCGAAAGCAAGTACGGCTCGCCGAAAATCGTTA

Basic information

species Glycine max
transcript GLYMA15G40110.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------gtacgtgctgtatatc---gctgtggctagtgatcgtgaaacgcgtgttttgagtgtcgtttttgtgttttgcagAGC-GGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGGAATGTTGTTCTCGAAAGCAAGTACGGCTCGCCGAAAATCGTTA
                           |     ||  ||  |    | |  ||||  | |      ||   |  | ||  |     ||||||||| | |   || ||||| ||||||||||| ||||| ||||| || || ||||| ||||| ||| | ||||||||||| || |||||||| || || ||   ||| ||||
gtaagtatcttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggttt----acattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
------------gtacgtgctgtatatcgctgtggctagtgatcgtgaaacgcgtgttttgagtgtcgtttttgtgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGGAATGTTGTTCTCGAAAGCAAGTACGGCTCGCCGAAAATCGTTA
            | |     | | |   |   ||  |||   ||||   |    || |||  |  |   |  | |||| |  |||  ||||| |||||||||||||| || ||||| ||||| ||||| || || || || ||||||||||| || |||||||| || || || | ||| ||||
gtgagaattaatgaattgattttctggagtaatgattaggattcgttttatttttggtttctg-attactcgtttgttat-tagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ16507 (Selaginella moellendorffii), 3'ss of exon 1
----gtacgtgctgtatatcgctgtggctagtgatcgtgaaacg-cgtgttttgagtgtcgtttttgtgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGGAATGTTGTTCTCGAAAGCAAGTACGGCTCGCCGAAAATCGTTA
    | |       | | || ||  |  | |   | |   |  | || |||||   | |||  ||| ||     |||   || |||||||||||||||||||| ||||| || ||  | |||||||| ||||||||||| || ||||| || ||||| || || || || ||  | |
gtttgcagaaaagctttctctctcggattggcattgggccattggcgagtttttcttatcgggtttttgcgaaacagGCTGGAGTGAACAAGCTCGCGGATCTTGTTGGAGTGACTTTGGGTCCCAAAGGAAGGAATGTCGTCCTCGAGAGTAAGTATGGTTCTCCAAAGATTATCA

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 1
----gtacgtgctgtatatcgctgtggctagtgatcgtgaaacg-cgtgttttgagtgtcgtttttgtgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGGAATGTTGTTCTCGAAAGCAAGTACGGCTCGCCGAAAATCGTTA
    | |       |   || ||  |  | |   | |   |  | || |||||   | |||  ||| ||     |||   || |||||||||||||||||||| ||||| || ||  | |||||||| ||||||||||| || ||||| |||||||| || || || || ||  | |
gtttgcagaaaagcttcctctctcggattggcattgggccattggcgagtttttcttatcgactttttgcgaaacagGCTGGAGTGAACAAGCTCGCGGATCTTGTTGGAGTGACTTTGGGTCCCAAAGGAAGGAATGTCGTCCTCGAGAGCAAGTATGGTTCTCCAAAGATTATCA

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|10846882|gb|BF069733.1|BF069733
EST:     CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAGGAAGCTCCAG                         AGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG
genomic: CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAGGAAGCTCCAGgtacgtgctg ... tgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG
EST: gi|22541364|gb|BU091207.1|BU091207
EST:     CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAGGAAGCTCCAG                         AGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG
genomic: CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAGGAAGCTCCAGgtacgtgctg ... tgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG
EST: gi|4292240|gb|AI437734.1|AI437734
EST:     CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAGGAAGCTCCAG                         AGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG
genomic: CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAGGAAGCTCCAGgtacgtgctg ... tgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG
EST: gi|7926195|gb|AW832221.1|AW832221
EST:     CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAGGAAGCTCCAG                         AGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG
genomic: CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAGGAAGCTCCAGgtacgtgctg ... tgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG
EST: gi|213599108|gb|DB962215.1|DB962215
EST:     CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAAGAAGCTCCAG                         AGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG
genomic: CCAAGGAGTTGCACTTCAACAAAGACGGCACCGCAATTAGGAAGCTCCAGgtacgtgctg ... tgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtggctagtgatcgtgaaacgcgtgttttgagtgtcgtttttgtgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGGAATGTTGTTCTCGAAAGCAAGTACGGCTCGCCGAAAATCGTTA
                                       tttttgt  CT-rich tract
                                       tttttgt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgctgtatatcgctgtggctagtgatcgtgaaacgcgtgttttgagtgtcgtttttgtgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGGAATGTTGTTCTCGAAAGCAAGTACGGCTCGCCGAAAATCGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG