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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagatactgcaaagaacaataacttatggatgatttaactgtgttagcagtgctttggttagatatagactgatttctttccatcaactcttgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTATCCTGATTCTCTTGGATTTGACGTGATTGATGAATGGGGAAGGATGCTCC

Basic information

species Glycine max
transcript GLYMA05G30770.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30770.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G26380.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatagatactgcaaagaacaataacttatggatgatttaactgtgttagcagtgctttggttagatatagactgatttctttccatcaactcttgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTATCCTGATTCTCTTGGATTTGACGTGATTGATGAATGGGGAAGGATGCTCC
     |  | ||  |    |  || | | | ||  || |||  || |  |   |   ||| ||   | |       ||  |||  ||          ||| ||| |||||||||||||| |||||||| ||||||||    || ||||||   ||||||||||| ||||| ||||||||||||||||||||  |||  |
-----gtaattgtgagtttctttatcctttaga--atgtaaaagtttaggtttttaattgcttgtgtttgtgtgtgttgatttggat--------acagTATGTTGTGGTGGATTACCTTTGGTATAGAAAGAAAGTTGAAGGAGCTTATGTGGATTCTCTTGGGTTTGATGTGATTGATGAATGGGGAAGATTGCATC
















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|5666743|gb|AI930779.1|AI930779
EST:     AAATAGTTTCTCAACGTCTCAAGGCTCATGGATATCAG                         TTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTAT
genomic: AAATAGTTTCTCAACGTCTCAAGGCTCATGGATATCAGgtatagatac ... actcttgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTAT
EST: gi|213593299|gb|DB973548.1|DB973548
EST:     TACAAAGTGCTGAAATAGTTTCTCAACGTCTCAAGGCTCATGGATATCAG                         TTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTAT
genomic: TACAAAGTGCTGAAATAGTTTCTCAACGTCTCAAGGCTCATGGATATCAGgtatagatac ... actcttgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTAT
EST: gi|151393893|gb|EV263764.1|EV263764
EST:     TACAAAGTGCTGAAATAGTTTCTCAACGTCTCAAGGCTCATGGATATCAG                         TTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTAT
genomic: TACAAAGTGCTGAAATAGTTTCTCAACGTCTCAAGGCTCATGGATATCAGgtatagatac ... actcttgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTAT
EST: gi|213599299|gb|DB960039.1|DB960039
EST:     TACAAAGTGCTGAAATAGTTTCTCAACGTCTCAAGGCTCATGGATATCAG                         TTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTAT
genomic: TACAAAGTGCTGAAATAGTTTCTCAACGTCTCAAGGCTCATGGATATCAGgtatagatac ... actcttgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttagcagtgctttggttagatatagactgatttctttccatcaactcttgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTATCCTGATTCTCTTGGATTTGACGTGATTGATGAATGGGGAAGGATGCTCC
                          gactgat  putative branch site (score: 3)
                                              ctcttgt  putative PPT
                 ttagatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagatactgcaaagaacaataacttatggatgatttaactgtgttagcagtgctttggttagatatagactgatttctttccatcaactcttgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTATCCTGATTCTCTTGGATTTGACGTGATTGATGAATGGGGAAGGATGCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG