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 5'  3'   		2  
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 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaataaaaaaccctaatttcctctcttttcggttttgtggattgtagtttgagtaattttctgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCTGTTTGTCATTCGCAAGCAGAAGAGAGATAGCCCCGACAAAGTTACACCT

Basic information

species Glycine max
transcript GLYMA08G21290.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21290.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S31_183V6.2 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------------------------------------gtgagtaaataaaaaaccctaatttcctctcttttcggttttgtggattgtagtttgagtaattttctgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCTGTTTGTCATTCGCAAGCAGAAGAGAGATAGCCCCGACAAAGTTACACCT
                                                                                                                      || | || |||| ||     | ||| |  | ||  || | ||| |||   || |    | || |  | |  | |||||| |  || || | |||||| ||  |   ||| | |  |||||||||||| ||||| ||||||||||||||| | ||| | || || |||||  |  | 
gtacgtgacttgctttccgacttccattgtgcttgttcgagtgcggatgacgtttatgatatcgggattcaagttcactactgcttttattgggaggtcacagaactcgtttaattcctgcgaaactaaagaatatatacttcattccatt--gggtctgttgata--agatatcattatctaatttgttgcagGAAGAAAACAGGTATGGAGTACATATTACACGAGGCTCAGGAGCCGCACCTCTTTGTGATTCGCAAGCAGAAGCGTGATGGTCCTGAAAAAGTATCTGCA
















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|12774777|gb|BG239725.1|BG239725
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|7042352|gb|AW472246.1|AW472246
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|298175338|gb|HO015997.1|HO015997
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|298177612|gb|HO027279.1|HO027279
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|298167187|gb|HO010626.1|HO010626
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|24136066|gb|BU926576.1|BU926576
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|192307836|gb|FG999315.1|FG999315
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|192329244|gb|FK020163.1|FK020163
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|298188965|gb|HO035658.1|HO035658
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|26045900|gb|CA783324.1|CA783324
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|192334789|gb|FK025280.1|FK025280
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|151411678|gb|EV281489.1|EV281489
EST:     GAGCAGCTCCGCATGCGCCCCGTTCACCCCCTCGACATCTTTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|298198662|gb|HO042025.1|HO042025
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|298187896|gb|HO031853.1|HO031853
EST:     GAGCAGCTCCGCATGCGCTCCGTTCGCCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|298167682|gb|HO012945.1|HO012945
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCC-TCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|192330592|gb|FK022261.1|FK022261
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|19346977|gb|BM891857.1|BM891857
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
EST: gi|298171957|gb|HO021549.1|HO021549
EST:     GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTC                         GAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT
genomic: GAGCAGCTCCGCATGCGCTCCGTTCACCCCCTCGACATCTCTCAACTCTCgtgagtaaat ... tgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctctcttttcggttttgtggattgtagtttgagtaattttctgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCTGTTTGTCATTCGCAAGCAGAAGAGAGATAGCCCCGACAAAGTTACACCT
                                        ttttctgtt  CT-rich tract
                                   agtaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaaataaaaaaccctaatttcctctcttttcggttttgtggattgtagtttgagtaattttctgttgttcagGAAAATGACGGGGACGGAGTATATGCTCAGCGAAGTTATGGAGCCGCACCTGTTTGTCATTCGCAAGCAGAAGAGAGATAGCCCCGACAAAGTTACACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA