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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgataatataacctcagtataaccacggttgttttgacgtcctttatgttttgtaattccaagttccttttcttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCGCGGTTGACAGTGTTGAGACCCCTGACCCTTGTAAATGAAGCCTGAGAGC

Basic information

species Zea mays
transcript GRMZM2G025340_T01
intron # 27
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|211018176|gb|FL213621.1|FL213621
EST:     GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAG                         CATGGTGAANGCTGGGGATAGGATCAAGAAGCAGCAAATGG
genomic: GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGG
EST: gi|211388989|gb|FL456719.1|FL456719
EST:     GCTGTCGCMCAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAG                         CATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
genomic: GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
EST: gi|211018177|gb|FL213622.1|FL213622
EST:     GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAG                         CATGGTGAAGGCTGGGGATAGGATCAAGAAGCAKCAAATGGCTGCTCCTCG
genomic: GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
EST: gi|32932707|gb|CF037519.1|CF037519
EST:     GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAG                         CATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
genomic: GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
EST: gi|211018178|gb|FL213623.1|FL213623
EST:     GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAG                         CATGGTGAAGGCTGGGGATAGGA
genomic: GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGA
EST: gi|32931357|gb|CF036169.1|CF036169
EST:     GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAG                         CATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
genomic: GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
EST: gi|32930376|gb|CF035188.1|CF035188
EST:     GCCGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAG                         CATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
genomic: GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
EST: gi|32931744|gb|CF036556.1|CF036556
EST:     GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAG                         CATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
genomic: GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
EST: gi|113651777|gb|DW810508.1|DW810508
EST:     ATTTATAACCCCTCATGATATCAG                         CATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
genomic: ATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
EST: gi|5608199|gb|AI901866.1|AI901866
EST:     GCTGTCGCCCAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAG                         CATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG
genomic: GCTGTCGCACAAGGGTCTCAATGGATATTTATAACCCCTCATGATATCAGgtttgataat ... ttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttttgacgtcctttatgttttgtaattccaagttccttttcttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCGCGGTTGACAGTGTTGAGACCCCTGACCCTTGTAAATGAAGCCTGAGAGC
    ttttgac  putative branch site (score: 3)
                             ttccaagttccttttc  putative PPT
               tttatgttttgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgataatataacctcagtataaccacggttgttttgacgtcctttatgttttgtaattccaagttccttttcttttcctcagCATGGTGAAGGCTGGGGATAGGATCAAGAAGCAGCAAATGGCTGCTCCTCGCGGTTGACAGTGTTGAGACCCCTGACCCTTGTAAATGAAGCCTGAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC