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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taataactatatagtagttggattgtttcttgttcattcagcttttatgatatgacctttttgattctgctgttaatattattattggatttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAATCTGCAACTCCTGAACCCAACTCTGAGGTTCTCTTCCTGTGCAGCTACGA

Basic information

species Zea mays
transcript GRMZM5G885700_T01
intron # 2
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|149088134|gb|EE177283.2|EE177283
EST:     AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG                         AGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
genomic: AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAGgtgcgcggaa ... ttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
EST: gi|50329241|gb|CO524367.1|CO524367
EST:     AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG                         AGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
genomic: AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAGgtgcgcggaa ... ttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
EST: gi|89762364|gb|DY689981.1|DY689981
EST:     AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG                         AGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
genomic: AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAGgtgcgcggaa ... ttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
EST: gi|211050924|gb|FL038266.1|FL038266
EST:     AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG                         AGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
genomic: AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAGgtgcgcggaa ... ttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
EST: gi|71444956|gb|DR826006.1|DR826006
EST:     AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG                         AGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
genomic: AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAGgtgcgcggaa ... ttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
EST: gi|211050923|gb|FL038265.1|FL038265
EST:     AGAACTGGTCGTCGCCGGA--SCCCTGCGTGCTGTACAAGTGGGTGCGAG                         AGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
genomic: AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAGgtgcgcggaa ... ttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
EST: gi|211484014|gb|FL012872.1|FL012872
EST:     AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG                         AGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
genomic: AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAGgtgcgcggaa ... ttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
EST: gi|71309036|gb|DR790783.1|DR790783
EST:     AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG                         AGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
genomic: AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAGgtgcgcggaa ... ttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
EST: gi|148935905|gb|EC879955.2|EC879955
EST:     AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG                         AGGACAGACTATCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT
genomic: AGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAGgtgcgcggaa ... ttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatatgacctttttgattctgctgttaatattattattggatttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAATCTGCAACTCCTGAACCCAACTCTGAGGTTCTCTTCCTGTGCAGCTACGA
                         tgttaat  putative branch site (score: 3)
                                            tttactt  putative PPT
                         tgttaatattattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taataactatatagtagttggattgtttcttgttcattcagcttttatgatatgacctttttgattctgctgttaatattattattggatttacttacagAGGACAGACTAGCAGCTTTGAAGGCTAAGGACAAGAAGCATGGGGCAGAATCTGCAACTCCTGAACCCAACTCTGAGGTTCTCTTCCTGTGCAGCTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - -tgtttct
- - - - - - - - - - - - - - - - - cattcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgctg