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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctaatatttgttttatcttttggggtaatgctctttagaaagattatgtttttggcaaagagatgcagttaaacttattgccttcttgtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAACTTAAGATGCTTGGAAAG

Basic information

species Glycine max
transcript GLYMA19G36960.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36960.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g04840.t01 (Vitis vinifera), 3'ss of exon 2
tctctaatatttgttttatct-tttggggtaatgctctt-tagaaagattatgtttttggcaaagagatgcagttaaacttattgccttcttgtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAACTTAAGATGCTTGGAAAG
    | ||||||||  ||    |||  || | |||| |  | | |  | | |    || | |      ||   | ||| ||  |   |     | || |||||| ||||| |||||| ||||| |||| ||| ||||||||||||| || || |||||| ||||||| |||
-acattatatttgtcctagagatttatgggactgctttcgtggcatcactcttgcctttgtatgatcttggcatcaaattt-ctatttctgcatatgcacagGTATGGCCTATCCATATTGACATGAAATTTATGGAACCAGTTGGACGGGAGCTTAAGCTGCTTGGGAAG
















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|7326530|gb|AW620328.1|AW620328
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|254319115|gb|GR828843.1|GR828843
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|192316243|gb|FK010104.1|FK010104
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|193514223|gb|FK468327.1|FK468327
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACC
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACC
EST: gi|11412406|gb|BF424417.1|BF424417
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|192312511|gb|FK004997.1|FK004997
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|21595577|gb|BQ610535.1|BQ610535
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|192302219|gb|FG995843.1|FG995843
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|213613833|gb|DB960882.1|DB960882
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|192324752|gb|FK016523.1|FK016523
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|26056188|gb|CA799102.1|CA799102
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|192316244|gb|FK010105.1|FK010105
EST:     ATTGTTTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|192302218|gb|FG995842.1|FG995842
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|13563097|gb|BG551317.1|BG551317
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|13563263|gb|BG551483.1|BG551483
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|254319116|gb|GR828844.1|GR828844
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
EST: gi|37995427|gb|CF807016.1|CF807016
EST:     ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAG                         GTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA
genomic: ATTGTCTCGTACCTGGCCAGAAAATGCCCATCCAATTACTTGGCCTCCAGgtttcattct ... gtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgtttttggcaaagagatgcagttaaacttattgccttcttgtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAACTTAAGATGCTTGGAAAG
                                   ttgccttcttgttt  CT-rich tract
                          ttaaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctaatatttgttttatcttttggggtaatgctctttagaaagattatgtttttggcaaagagatgcagttaaacttattgccttcttgtttggacagGTCTGGCCAATCCATGTTGACCTGAAGTTTTTGGAACCAGTTGGGCGAGAACTTAAGATGCTTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG