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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtttgtaatgctattatgtctattgtctatcctgggctttttcatctctgttgaattttccattaaaattaaaatatcagcttgccttgctcgtctcttgaatatttttaccttgatgtcacaattggattttgcag

Basic information

species Glycine max
transcript GLYMA0169S00210.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0169S00210.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 3
GTAGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtt-tgtaatgctattatgtctattgtctatcctgggctttttcatctctgttgaattt-tccattaaaattaaaatatcagcttgccttgct-cgtctcttgaatatttttaccttgatgtcacaattggattttgcag
|| || ||||||||||||||||| || ||||| || ||||| ||||| ||| ||||||| ||| ||    || ||   ||   ||  || |   |||    |||    |  |||| | | |   ||||  |  |  | |||||     | |  | |                                        
GTTGCTCCTTATGAACGTCCTGCGCTTAGCAAAGCCTACCTATTTCCTGAGGgtaagttatgtgat----ttgtgcgcatgaact--ccagaaatttaaattctaacctacatttgtacttctgaatttgataagtaacttgctacattgcagcaccc--------------------------------------
















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|209729132|gb|BW660031.1|BW660031
EST:     AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGT                         CCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA
genomic: AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtttgt ... gattttgcagCCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA
EST: gi|193542303|gb|FK497521.1|FK497521
EST:     AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGT                         CCCCTGCTAGACTTCCTGGGTTCCATGT
genomic: AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtttgt ... gattttgcagCCCCTGCTAGACTTCCTGGGTTCCATGT
EST: gi|151396143|gb|EV266020.1|EV266020
EST:     AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGT                         CCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA
genomic: AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtttgt ... gattttgcagCCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA
EST: gi|192296978|gb|FG990294.1|FG990294
EST:     AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGT                         CCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA
genomic: AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtttgt ... gattttgcagCCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA
EST: gi|213607100|gb|DB965070.1|DB965070
EST:     AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGT                         CCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA
genomic: AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtttgt ... gattttgcagCCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA
EST: gi|193510516|gb|FK468022.1|FK468022
EST:     AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGT                         CCCCTGCTAGACTTCCTGGGTTCCATGT
genomic: AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtttgt ... gattttgcagCCCCTGCTAGACTTCCTGGGTTCCATGT
EST: gi|213605771|gb|DB968603.1|DB968603
EST:     AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGT                         CCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA
genomic: AGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtttgt ... gattttgcagCCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGGGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGCACCTTATGAACGTCCTGCTCTGAGCAAGGCTTACCTTTTTCCAGAGTgtaagtttgtaatgctattatgtctattgtctatcctgggctttttcatctctgttgaattttccattaaaattaaaatatcagcttgccttgctcgtctcttgaatatttttaccttgatgtcacaattggattttgcag

- - - - - - - - - - - - -  AGCAAG