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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaaaatttgtctataatccataatttaacttcattgtgaccattaatggatgtacccttccatttatttctttttctcaagtaactattattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG

Basic information

species Glycine max
transcript GLYMA14G00760.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G00760.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------gttaaaatttgtctataatccataat--ttaacttcattgtgaccat-taatgg----atgtacccttccatttatttctttttctcaagtaactat-tattt---tgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG
                                              || ||||  |  || | ||    | |   ||  ||  |  |  | ||  |   |    |||||  |        ||    || |||| | ||||  | ||| |   ||||||||||    || || ||||||||||||||  |  | || ||||||||||| |||||||||||||||||| ||               
gtaagtgtcatctttactaaactaccattctttgtggattttaaaagtcaaaacatcactttcatatgcattcgctatttttttatttgctatgcagcagcaacatgtaatcgcatgacaatagtattctctctactaacggtatatgtgcgtgcagGAAAAGACTAATGTTCATGGTGGAGCTGTATCTTTAGGACATCCTCTTGGGTGCAGTGGTGCTCGCATTTTG---------------

upper sequence: GLYMA14G00760.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 12
------gttaaaatttgtctata-atccataatttaacttcat---tgtgaccattaatggatgtacc--cttccatttatttctttttct-caagtaacta-----ttattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG
        | |||| ||| | |   |   |   |      |||   |||   | | |    ||        ||| ||   |  ||| || | |||||| |||     ||   |||||||||||||| || || |||||||| |||||  |  |||| |||||||| ||||||||||| || || ||  |||| ||||||||||||
gtgagttcttaaatctgtgtgtgtgtgtgtgtgtgtgtcacatgcatgtactcctcaccttattgtttaatttctatcggtaccttgttttacaagtacctaccccatttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG
















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|10848225|gb|BF070769.1|BF070769
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|192329989|gb|FK021575.1|FK021575
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|17021784|gb|BM092818.1|BM092818
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|15812294|gb|BI784569.1|BI784569
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|31472565|gb|CD414593.1|CD414593
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|151406879|gb|EV276694.1|EV276694
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|298184901|gb|HO030114.1|HO030114
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|192313001|gb|FK003653.1|FK003653
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|31472065|gb|CD414093.1|CD414093
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|192328380|gb|FK020091.1|FK020091
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGGTGGAGCTGTTGCACTGGGTCATCCTCTTGG
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGG-TGGAGCTGTTGCACTGGGTCATCCTCTTGG
EST: gi|15203843|gb|BI426611.1|BI426611
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|209708680|gb|BW678861.1|BW678861
EST:     GTTGTGGCTCTTGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACTTACACGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|10256517|gb|BE824283.1|BE824283
EST:     GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
EST: gi|37994372|gb|CF806118.1|CF806118
EST:     GTTGTGGCTCTCGCAAATCAGAA-CTTCTTGGACTTAACTCG                         GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT
genomic: GTTGTGGCTCTCGCAAATCAGAAACTTCTTGGACTTAACTCGgttagttttt ... tattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatggatgtacccttccatttatttctttttctcaagtaactattattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG
                                   aagtaac  putative branch site (score: 2)
                                            ttatttt  putative PPT
                  atttatttctttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaaatttgtctataatccataatttaacttcattgtgaccattaatggatgtacccttccatttatttctttttctcaagtaactattattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG

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