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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagatttcggcttctgcttgtattagactagaacctggcatttgctgttgttcgattttacttacccaaagcaattttttggtatattttgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTAGATCTGAACCTTGTCGAGAGTATTCTGAACTCGTACTCCTCGCAACAAG

Basic information

species Zea mays
transcript GRMZM2G073988_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073988_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g34740.1 (Oryza sativa), 3'ss of exon 4
gcagatttcggcttctgcttgta-ttagactagaacctggcatt-tgctgttgttcgattttacttacccaa----agcaattttttggtatattttgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTAGATCTGAACCTTGTCGAGAGTATTCTGAACTCGTACTCCTCGCAACAAG
      |  |  | |||   | |  | |  ||  |  |  | |    |  |||||| |||| ||| | || |    |  ||  ||||||||||||||| ||| ||||||||||||| || ||||| ||||| ||  |||||||| ||||||||||| || ||||||||||| |||||  | || ||||| |||||||| ||||| |
-----atcagattcctgaaagaaacttggttacgatttttcgtagcacacttgttcaatttgactgatcctactctaagaaaattttggtatattttg-atttcagGGTCCATCAGGTGCTGCAGATACTGATGGGGAGATGACCCCAGTTGATGTGGACCTGAACCTTGTTGAGAGCTTCCTTAACTCTTACTCCTCTCAACAGG
















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|78088848|gb|DV517241.1|DV517241
EST:     CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAG                         GGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
genomic: CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAGgtagtccttg ... tgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
EST: gi|211146927|gb|FL134791.1|FL134791
EST:     CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAG                         GGTCCATCAGATGATGCAGCTACTGATGCAGAGATGACTCCAGTTGATGTA
genomic: CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAGgtagtccttg ... tgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
EST: gi|93014876|gb|EB640396.1|EB640396
EST:     CTCTTGAGAAAAGCTTTGCTCATGCCCCCCGCCCGGAAACTAACAATGAG                         GGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
genomic: CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAGgtagtccttg ... tgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
EST: gi|32866766|gb|CF006448.1|CF006448
EST:     CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAG                         GGTCCATCAGATGACGCTGCTACTGATGCAGAGATGACTCCAGTTGATGTA
genomic: CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAGgtagtccttg ... tgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
EST: gi|211028474|gb|FL443741.1|FL443741
EST:     AGCTTCGCTCATGCACCCCGACGGGAAACTAACAATGAG                         GGTCCATCAGATGATCCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
genomic: AGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAGgtagtccttg ... tgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
EST: gi|211528551|gb|FL441950.1|FL441950
EST:     CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAG                         GGTCCATCAGATGATGCAGCTACTGATGCAGAGATGACTCCAGTTGATGTA
genomic: CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAGgtagtccttg ... tgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
EST: gi|148943207|gb|EC888267.2|EC888267
EST:     CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAG                         GGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
genomic: CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAGgtagtccttg ... tgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
EST: gi|76018200|gb|DT945370.1|DT945370
EST:     CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAG                         GGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
genomic: CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAGgtagtccttg ... tgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
EST: gi|74237672|gb|DT645586.1|DT645586
EST:     CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAG                         GGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA
genomic: CTCTTGAGAAAAGCTTTGCTCATGCACCACGACCGGAAACTAACAATGAGgtagtccttg ... tgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgttcgattttacttacccaaagcaattttttggtatattttgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTAGATCTGAACCTTGTCGAGAGTATTCTGAACTCGTACTCCTCGCAACAAG
              tacttac  putative branch site (score: 1)
                            aattttttggtatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagatttcggcttctgcttgtattagactagaacctggcatttgctgttgttcgattttacttacccaaagcaattttttggtatattttgcattgcagGGTCCATCAGATGATGCAGCTACTGGTGCAGAGATGACTCCAGTTGATGTAGATCTGAACCTTGTCGAGAGTATTCTGAACTCGTACTCCTCGCAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC