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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactgatgtcatatatttatatattgtttgtgcttgcatgcgtatctctgaagtagctcatttgatttcttttttctattttttcctttaacttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG

Basic information

species Glycine max
transcript GLYMA20G31840.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g01580.t01 (Vitis vinifera), 3'ss of exon 2
cactgatgtcatatatttatatattgtttgtgcttgcatgcgtatctctgaagtagct-catttgatttcttttt--tctattttttcctttaactt-ttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG
      |   | || ||||| ||   | || | |    |   ||| |       | || ||||||  | |  |       || |    ||| ||||   | ||||||| |||||||||||||| |||||| |||||||| |  | |||||||| ||||| ||||||||||| | |||||  |||| ||||
----tgtactagatgtttatttaacttctgagatgttgtttctatgtgctcttcaccttcatttggatgcactgaagctaatatcagtcttaaactcactgcagGTTTACATGTTGTGGTTACAATGTTTTCTGGCTATTTGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG
















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|298187634|gb|HO034783.1|HO034783
EST:     TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTG                         GTTTACATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
genomic: TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTGgtaatttctt ... acttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
EST: gi|192327525|gb|FK018201.1|FK018201
EST:     TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTG                         GTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
genomic: TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTGgtaatttctt ... acttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
EST: gi|13787967|gb|BG650559.1|BG650559
EST:     TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTG                         GTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
genomic: TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTGgtaatttctt ... acttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
EST: gi|298184735|gb|HO029948.1|HO029948
EST:     TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTG                         GTTTACATGTTGTGGTTACCATGTTTACTGGCTGTCTTCTCGGATATGCAG
genomic: TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTGgtaatttctt ... acttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
EST: gi|16996305|gb|BM085677.1|BM085677
EST:     TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTG                         GTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
genomic: TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTGgtaatttctt ... acttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
EST: gi|298193968|gb|HO040616.1|HO040616
EST:     TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTG                         GTTTACATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
genomic: TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTGgtaatttctt ... acttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
EST: gi|192329380|gb|FK021834.1|FK021834
EST:     TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTG                         GTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG
genomic: TAAGGATGTTCCGGAACCGTTCTCTTCTTACAAGGATCAATTAGGCTTTGgtaatttctt ... acttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgaagtagctcatttgatttcttttttctattttttcctttaacttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG
                                        ctttaac  putative branch site (score: 3)
               tttgatttcttttttc  CT-rich tract
            tcatttgatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactgatgtcatatatttatatattgtttgtgcttgcatgcgtatctctgaagtagctcatttgatttcttttttctattttttcctttaacttttccagGTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA