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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgcctaaaaacataatgcaattttagctaccttctttcttattaataccagtgtggtcctgtttcgatgtaagtaattccttgttttgctcctcgcagTGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCAAATTTTTTTTTCTGAGGGTAACAAATGTGGGCCCCCTGTTTTACTCTGA

Basic information

species Zea mays
transcript GRMZM2G000645_T01
intron # 24
splice site 3'
intron type U2

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|60349772|gb|DN216745.1|DN216745
EST:     TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACG                         TGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
genomic: TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACGgtgattcact ... ctcctcgcagTGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
EST: gi|9730934|gb|BE509686.1|BE509686
EST:     TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACG                         TGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
genomic: TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACGgtgattcact ... ctcctcgcagTGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
EST: gi|60346615|gb|DN213588.1|DN213588
EST:     TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACG                         TGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
genomic: TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACGgtgattcact ... ctcctcgcagTGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
EST: gi|8665311|gb|BE186127.1|BE186127
EST:     TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACG                         TGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
genomic: TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACGgtgattcact ... ctcctcgcagTGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
EST: gi|8665607|gb|BE186423.1|BE186423
EST:     TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACG                         TGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
genomic: TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACGgtgattcact ... ctcctcgcagTGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
EST: gi|60359372|gb|DN226345.1|DN226345
EST:     TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACG                         TGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA
genomic: TATCTGCCTAGAATTCTTGGCAAATATGGGAACCCCAAGTTTTGCCTACGgtgattcact ... ctcctcgcagTGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataccagtgtggtcctgtttcgatgtaagtaattccttgttttgctcctcgcagTGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCAAATTTTTTTTTCTGAGGGTAACAAATGTGGGCCCCCTGTTTTACTCTGA
 tattaat  putative branch site (score: 2)
                                 ttccttgttttgctcc  putative PPT
                          taagtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgcctaaaaacataatgcaattttagctaccttctttcttattaataccagtgtggtcctgtttcgatgtaagtaattccttgttttgctcctcgcagTGCTAACTCAACATGAATAGGGGCTGAAAGAAGCACAGCTCATTGGCTGCAAATTTTTTTTTCTGAGGGTAACAAATGTGGGCCCCCTGTTTTACTCTGA

- - - -aaaaaca
- - - - - - - -aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtcctg