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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctagagcttgcgttttggatgtttttttcgagattgatggtggtttggtcctgttgttgatcgatgtggctgatatgtacttcttaattcgtgtcacagCACTGGGTTAGCGACAGTGATGGCAGTGATAACTTCGAATGGGACAGTGATGGTAACGGGGAGCAGACAGTGAGCTTCAACGCTGCTGGTGCTGGTTCAT

Basic information

species Zea mays
transcript GRMZM2G092497_T03
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|149074707|gb|EE163131.2|EE163131
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|149074707|gb|EE163131.2|EE163131
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|149074707|gb|EE163131.2|EE163131
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|149074707|gb|EE163131.2|EE163131
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|89762158|gb|DY689885.1|DY689885
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|89762158|gb|DY689885.1|DY689885
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|89762158|gb|DY689885.1|DY689885
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|89762158|gb|DY689885.1|DY689885
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|91873568|gb|EB403525.1|EB403525
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGGTG                       
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAA---TGgtggtgagag ... cgtgtcac
EST: gi|71325873|gb|DR799620.1|DR799620
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGGTG                       
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAA---TGgtggtgagag ... cgtgtcac
EST: gi|211134850|gb|FL400322.1|FL400322
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|211134850|gb|FL400322.1|FL400322
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|211134850|gb|FL400322.1|FL400322
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|211134850|gb|FL400322.1|FL400322
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|78109829|gb|DV528245.1|DV528245
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGGTG                       
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAA---TGgtggtgagag ... cgtgtcac
EST: gi|28873635|gb|CB329598.1|CB329598
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGGTG                       
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAA---TGgtggtgagag ... cgtgtcac
EST: gi|76913046|gb|DV164985.1|DV164985
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGGTG                       
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAA---TGgtggtgagag ... cgtgtcac
EST: gi|74238865|gb|DT646779.1|DT646779
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGGTG                       
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAA---TGgtggtgagag ... cgtgtcac
EST: gi|78088679|gb|DV517072.1|DV517072
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGGTG                       
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAA---TGgtggtgagag ... cgtgtcac
EST: gi|211400336|gb|FL375597.1|FL375597
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|211400336|gb|FL375597.1|FL375597
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|211400336|gb|FL375597.1|FL375597
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|211400336|gb|FL375597.1|FL375597
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         G
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacag-
EST: gi|71447185|gb|DR828235.1|DR828235
EST:     GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATG                         CACTGGGTTAGCGACAGTGATGGCAGTGATAACTTCGAATGGGACAGTGAT
genomic: GCCGCGTCGGAGAGGTAGCCCCCGGAGCTCTTCGCGGAGGCTCGGGAATGgtggtgagag ... cgtgtcacagCACTGGGTTAGCGACAGTGATGGCAGTGATAACTTCGAATGGGACAGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtcctgttgttgatcgatgtggctgatatgtacttcttaattcgtgtcacagCACTGGGTTAGCGACAGTGATGGCAGTGATAACTTCGAATGGGACAGTGATGGTAACGGGGAGCAGACAGTGAGCTTCAACGCTGCTGGTGCTGGTTCAT
                                     tcttaat  putative branch site (score: 3)
                                    ttcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctagagcttgcgttttggatgtttttttcgagattgatggtggtttggtcctgttgttgatcgatgtggctgatatgtacttcttaattcgtgtcacagCACTGGGTTAGCGACAGTGATGGCAGTGATAACTTCGAATGGGACAGTGATGGTAACGGGGAGCAGACAGTGAGCTTCAACGCTGCTGGTGCTGGTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT