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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaacataagaaaattaagattttcatcacggtggagtttgagcccaaatgtaccttaggggctgtgtttccttaccatgttttactgtgtcttttacagGTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTGCTCAAAAA

Basic information

species Zea mays
transcript GRMZM2G015730_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|211506874|gb|FL291277.1|FL291277
EST:     CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAG                         GTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG
genomic: CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAGgtgatcctct ... tcttttacagGTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG
EST: gi|149111657|gb|EE190801.2|EE190801
EST:     CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAG                         GTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG
genomic: CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAGgtgatcctct ... tcttttacagGTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG
EST: gi|211509239|gb|FL291293.1|FL291293
EST:     CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAG                         GTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG
genomic: CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAGgtgatcctct ... tcttttacagGTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG
EST: gi|211506879|gb|FL291282.1|FL291282
EST:     CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAG                         GTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG
genomic: CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAGgtgatcctct ... tcttttacagGTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG
EST: gi|211509232|gb|FL291286.1|FL291286
EST:     CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAG                         GTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG
genomic: CGAGCCAGAACGCGCTCTAGAGGAGAACGGACCCACCGGCGCTGCAAGAGgtgatcctct ... tcttttacagGTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatgtaccttaggggctgtgtttccttaccatgttttactgtgtcttttacagGTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTGCTCAAAAA
                        tccttac  putative branch site (score: 2)
                                           tgtctttt  putative PPT
                                atgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaacataagaaaattaagattttcatcacggtggagtttgagcccaaatgtaccttaggggctgtgtttccttaccatgttttactgtgtcttttacagGTGAAGCATCCTTGAAGAATTGTGCATCAGAGCTAGTGGGCGCTCCAACTGCTCAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT