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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagaacgatgaaccaagctcctagatgaacttttgtgtgtgtgtgctttgcaacaattgttcttttcactcattgacaagatctctctccacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTTCCCTTCTCAGCACGTACCTCGAGTGGTGTCACACAAAGGCCGGTGTCAG

Basic information

species Zea mays
transcript GRMZM2G087598_T01
intron # 1
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|211104729|gb|FL156580.1|FL156580
EST:     CTCGGCTTCGCTCCCTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGCGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|13150589|gb|BG320911.1|BG320911
EST:     TTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
genomic: TTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|211104724|gb|FL156575.1|FL156575
EST:     CTCGGCTTCGCTCCCTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGCGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|149086843|gb|EE176391.2|EE176391
EST:     CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|13558285|gb|BG549641.1|BG549641
EST:     CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|78090968|gb|DV519342.1|DV519342
EST:     CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|74235283|gb|DT643197.1|DT643197
EST:     CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|211104727|gb|FL156578.1|FL156578
EST:     CTCGGCTTCGCTCCCTTCCCCTCCCTGCTCCGGCTCCGGTTTGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGCGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|149089172|gb|EE178360.2|EE178360
EST:     CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|211104728|gb|FL156579.1|FL156579
EST:     CTCGGCTTCGCTCCCTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGCGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT
EST: gi|211102262|gb|FL156574.1|FL156574
EST:     CTCGGCTTCGCTCCCTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAG                         TAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGCGGCAAAGGGTGTGCTT
genomic: CTCGGCTTCGCTCCTTTCCCCTCCCTGCTCCGGCTCCGGTTCGCACACAGgtgcgtgcgt ... cacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgcaacaattgttcttttcactcattgacaagatctctctccacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTTCCCTTCTCAGCACGTACCTCGAGTGGTGTCACACAAAGGCCGGTGTCAG
                          cattgac  putative branch site (score: 3)
                                     tctctctccacttttc  putative PPT
       aacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagaacgatgaaccaagctcctagatgaacttttgtgtgtgtgtgctttgcaacaattgttcttttcactcattgacaagatctctctccacttttcagTAAGAAAAGATGGCGCTGCCATCCATGAGTCTTGTGGCAAAGGGTGTGCTTCCCTTCTCAGCACGTACCTCGAGTGGTGTCACACAAAGGCCGGTGTCAG

- - - -gatgaac
- - - - - - - caagctc
- - - - - - - - - - - - - - - - - - - - - - - ctttgca