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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttcttcaaacaatttcaacgatcatgataaggagtaatatagtaacattttccccatattttagactaagattgctaacattttgctgctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCACCTGCAAGCGAACCTGGCGATAGCAGCGGAAACAACACTCCAAAGGACG

Basic information

species Zea mays
transcript GRMZM2G050861_T01
intron # 6
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|67012855|gb|CO441604.1|CO441604
EST:     TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGAT                         GAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
genomic: TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGATgtaagttaag ... ctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
EST: gi|6601756|gb|AW256197.1|AW256197
EST:     GATTTCCCGTACAGAGAT                         GAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
genomic: GATTTCCCGTACAGAGATgtaagttaag ... ctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
EST: gi|6760613|gb|AW324712.1|AW324712
EST:     TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTTCCGTACAGAGAT                         GAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
genomic: TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGATgtaagttaag ... ctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
EST: gi|71762004|gb|DR959941.1|DR959941
EST:     TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGAT                         GAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
genomic: TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGATgtaagttaag ... ctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
EST: gi|6742388|gb|AW313203.1|AW313203
EST:     TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTTCCGTACAGAGAT                         GAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
genomic: TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGATgtaagttaag ... ctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
EST: gi|76011103|gb|DT938273.1|DT938273
EST:     TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGAT                         GAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
genomic: TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGATgtaagttaag ... ctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
EST: gi|50327546|gb|CO522672.1|CO522672
EST:     TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGAT                         GAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
genomic: TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGATgtaagttaag ... ctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
EST: gi|78087662|gb|DV516055.1|DV516055
EST:     TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGAT                         GAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA
genomic: TTGGGCATGTCATTCACATGCTTGAGGTTGACGATTTCCCGTACAGAGATgtaagttaag ... ctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacattttccccatattttagactaagattgctaacattttgctgctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCACCTGCAAGCGAACCTGGCGATAGCAGCGGAAACAACACTCCAAAGGACG
                             tgctaac  putative branch site (score: 1)
                                     ttttgctgctctcccc  CT-rich tract
            atattttagactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttcttcaaacaatttcaacgatcatgataaggagtaatatagtaacattttccccatattttagactaagattgctaacattttgctgctctccccagGAGCGCCGGGGTGGCAAAGCTCCAGCCCAAGCAAGATCGGTGGAAACGCCACCTGCAAGCGAACCTGGCGATAGCAGCGGAAACAACACTCCAAAGGACG

- - - - aaacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgctg