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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacctatttgacttggaaaaaaaaaatcagctgcaacataatttccattatgtatttaactgagttgcacagttctgaaatcattttttgttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCTTCGTTTGGGGTTGCTCTTGCAAATGGATCTGACAAGACAAAAGCAGCGG

Basic information

species Zea mays
transcript GRMZM5G836674_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836674_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g53720.2 (Oryza sativa), 3'ss of exon 11
caacctatttgacttggaaaaaaaaaatcagctgcaacataatttccattatgtatttaactg--agttgcacagttctgaaatcattttttg-ttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCTTCGTTTGGGGTTGCTCTTGCAAATGGATCTGACAAGACAAAAGCAGCGG
      |||| |  |||| |  | |  || | |    ||| |   |||||        | |||  |       |  |   |  | |||||||  || |||||||||||||| || || || |||||||||||||| |||||| | || ||||| || || || ||||| ||||||||||| ||||| || || ||||||| ||
--gtagatttaaaatggatattagacctctgatcttccatcaaa-ccattgaaagcccacctgcaatccttctaacttcaactttatttttttcttttgcaagGTAATGGCTATCGGGGATGGAGAAAATGACATAGAAATGCTACAGCTAGCATCATTGGGTGTTGCGCTTGCAAATGGGTCTGAGAAAACCAAAGCAGTGG

upper sequence: GRMZM5G836674_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT2G25870.1 (Arabidopsis thaliana), 3'ss of exon 11
----caaccta------tttgacttgg--aaaaaaaaaatcagctgcaacataatttccattatgtatttaactgagttgcacagttctgaaatcatttt---ttgttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCTTCGTTTGGGGTTGCTCTTGCAAATGGATCTGACAAGACAAAAGCAGCGG
     || |||      ||||||   |    ||| ||| |||  |    ||||| |       |  |   ||   | |   | ||||    || ||       || |  |   || ||||||| ||||| || |||||||||||||| || ||| ||||||| || ||||| || ||||||||    || ||  | || || ||||| || | ||
gtaataatctagcatcttttgacggcgttgtaaagaaactcaagta-ggcataagtatagaagtcaaacaaa--aaataagatagttgatgaagcaacccggattttcttatcagATAATGGCGATTGGAGATGGAGAAAATGACATAGAGATGCTGCAACTGGCCTCGTTGGGAGTTGCTCTGAGCAACGGTGCAGAAAAAACAAAGGCGGTGG

upper sequence: GRMZM5G836674_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv04s0008g00450.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------------------caacctatttgacttggaaaaaaaaaatcagctgcaacataatttccattatgtatttaactgagttgcacagttctgaaatcattttttgttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCTTCGTTTGGGGTTGCTCTTGCAAATGGATCTGACAAGACAAAAGCAGCGG
                                                  || | | || |    |||||  ||  |||  |  |||  ||  | |||| ||   | |  ||  |  |       | | |    ||| | ||  |||||||||| |||||||| ||||||||||||||||||||| |  || |||||||  | ||  |||||||    ||||| || || ||||||||||| | ||
gtacagaccagcaaattttagatctctattttctgttttttttttttggtctttgttacctcatcaaaaaggat--gctaaagaata--ttgaaatatg-atgatattatgtaaccaaacctctgattgacacattgct-tgttagGTAATGGCTATTGGTGATGGAGAAAATGACATTGAAATGCTTGAATTAGCTTCTCTAGGCATTGCTCTCAGTAATGGTTCGGAGAAGACAAAAGCTGTGG

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|211210967|gb|FL454934.1|FL454934
EST:     GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAG                         GTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
genomic: GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAGgtagaattaa ... gttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
EST: gi|211172338|gb|FL126915.1|FL126915
EST:     GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAG                         GTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
genomic: GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAGgtagaattaa ... gttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
EST: gi|37380377|gb|CF626997.1|CF626997
EST:     GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAG                         GTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
genomic: GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAGgtagaattaa ... gttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
EST: gi|211172339|gb|FL126916.1|FL126916
EST:     GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAG                         GTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
genomic: GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAGgtagaattaa ... gttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
EST: gi|211210968|gb|FL454935.1|FL454935
EST:     GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAG                         GTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
genomic: GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAGgtagaattaa ... gttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
EST: gi|211190907|gb|FL449388.1|FL449388
EST:     GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAG                         GTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
genomic: GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAGgtagaattaa ... gttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
EST: gi|211391895|gb|FL468022.1|FL468022
EST:     GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAG                         GTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
genomic: GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAGgtagaattaa ... gttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
EST: gi|32912236|gb|CF017048.1|CF017048
EST:     GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAG                         GTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
genomic: GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAGgtagaattaa ... gttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
EST: gi|149033217|gb|EE155000.2|EE155000
EST:     GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAG                         GTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT
genomic: GCAATGGTGTGAAGGTTCTGTTGAACCACCTTTCCATTAGTCCAGATGAGgtagaattaa ... gttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattatgtatttaactgagttgcacagttctgaaatcattttttgttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCTTCGTTTGGGGTTGCTCTTGCAAATGGATCTGACAAGACAAAAGCAGCGG
         atttaac  putative branch site (score: 3)
                                       ttttttgtt  putative PPT
                                 aaatcattttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacctatttgacttggaaaaaaaaaatcagctgcaacataatttccattatgtatttaactgagttgcacagttctgaaatcattttttgttgtgcaagGTAATGGCAATTGGTGACGGAGAAAATGACATTGAAATGTTGCAACTAGCTTCGTTTGGGGTTGCTCTTGCAAATGGATCTGACAAGACAAAAGCAGCGG

- - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - cagctgc
- - - - - - - - - - - - - - - - - -aacataa
- - - - - - - - - - - - - - - - - - - - - - - - -tatgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgaa