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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatctcttttccagataatgtatttgtatttttatatcctgcatgaatatcaggctatttgcaggttcagtaattgtgctttttctgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGACTACCCTGAAAAGCCCCCGAGCGTCCGGTTTCATTCACGGATCAATATGA

Basic information

species Glycine max
transcript GLYMA19G38450.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G36060.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------------ttatctctt-ttccagataatgtatttgtatttttatatcctgcatgaa--tatcaggctatttgcaggttcagtaattgtgctttttctgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGACTACCCTGAAAAGCCCCCGAGCGTCCGGTTTCATTCACGGATCAATATGA
                    |  || |||  |    || ||     | | | | |   || || |||    |   | | ||||   | ||    | ||    ||  |  | || ||    |||||||||||||| ||  | |||||||| |||||||| || ||||| ||||| |||||||| || || ||||  || ||||| ||||| || ||||| ||||
gttatatctctgtttttttttcttcacttgctatgaatgataggactttgtgtcttcttcttgaatggtgttggaatgatattgtgatgtgatttgatctgactggtaattttgtttgtgcagACTGTACATGAGGGTCGGATTTATCAGTTGAAGCTCTTCTGTGACAAAGATTACCCTGAGAAACCTCCGACTGTTCGGTTCCATTCGCGTATCAACATGA

upper sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G36060.3 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------ttatctctt-ttccagataatgtatttgtatttttatatcctgcatgaa--tatcaggctatttgcaggttcagtaattgtgctttttctgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGACTACCCTGAAAAGCCCCCGAGCGTCCGGTTTCATTCACGGATCAATATGA
                       |  || |||  |    || ||     | | | | |   || || |||    |   | | ||||   | ||    | ||    ||  |  | || ||    |||||||||||||| ||  | |||||||| |||||||| || ||||| ||||| |||||||| || || ||||  || ||||| ||||| || ||||| ||||
gtagttatatctctgtttttttttcttcacttgctatgaatgataggactttgtgtcttcttcttgaatggtgttggaatgatattgtgatgtgatttgatctgactggtaattttgtttgtgcagACTGTACATGAGGGTCGGATTTATCAGTTGAAGCTCTTCTGTGACAAAGATTACCCTGAGAAACCTCCGACTGTTCGGTTCCATTCGCGTATCAACATGA

upper sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 2
ttatctcttttccagataatgtatttgtatttttatatcctgcatgaatatcaggctatttgcaggttcagtaattgt--gctttttctgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGACTACCCTGAAAAGCCCCCGAGCGTCCGGTTTCATTCACGGATCAATATGA
     | | |    ||||   ||||     |  | |||| || ||    |      ||  | ||| ||   |  |  |   || |||   ||  | |  ||| |||||||||||||  | ||||||||| ||||||| |||||||||||||| || || || ||||| || || || ||||| |||||||| ||||| ||||
aagattttgtgtttgatagcttattcca--tcgtgtatcatgtattctcacatctatacatacagattttatgttcattaactattttaattactttttcagTCTGTACATGAAGGTCGCATTTATCAACTGAAGCTTTTTTGTGATAAAGATTATCCGGAGAAGCCTCCTAGTGTACGGTTCCATTCACGCATCAACATGA

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|10232200|gb|BE801079.1|BE801079
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|120532072|gb|EH260205.1|EH260205
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|298194351|gb|HO040999.1|HO040999
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|298191697|gb|HO035779.1|HO035779
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACTTGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|7684987|gb|AW755635.1|AW755635
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|23726374|gb|BU761179.1|BU761179
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|7042450|gb|AW472344.1|AW472344
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|9819465|gb|BE554978.1|BE554978
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|298175656|gb|HO015175.1|HO015175
EST:     ATGGCATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|298179361|gb|HO027832.1|HO027832
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|6071041|gb|AW100428.1|AW100428
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATGAT                         ACTGTGCATGAAGGGAAGAATGTATCAATTGAAGCTGTTTTGTGATAAAGA
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGG-AAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGA
EST: gi|12774302|gb|BG239229.1|BG239229
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|8826260|gb|BE209990.1|BE209990
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|13478519|gb|BG507961.1|BG507961
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|23063958|gb|BU578731.1|BU578731
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|10231884|gb|BE800772.1|BE800772
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|13481901|gb|BG511244.1|BG511244
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|298170303|gb|HO018927.1|HO018927
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|9900251|gb|BE609219.1|BE609219
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|27427102|gb|CA938622.1|CA938622
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|298172821|gb|HO019805.1|HO019805
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|16348942|gb|BI974537.1|BI974537
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|8826180|gb|BE209840.1|BE209840
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
EST: gi|13311453|gb|BG405104.1|BG405104
EST:     ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC
genomic: ATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatatcaggctatttgcaggttcagtaattgtgctttttctgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGACTACCCTGAAAAGCCCCCGAGCGTCCGGTTTCATTCACGGATCAATATGA
                             ttgtgctttttctgtt  CT-rich tract
                                           tttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatctcttttccagataatgtatttgtatttttatatcctgcatgaatatcaggctatttgcaggttcagtaattgtgctttttctgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGCTGTTTTGTGATAAAGACTACCCTGAAAAGCCCCCGAGCGTCCGGTTTCATTCACGGATCAATATGA

- - - - - - - - - - - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaggt