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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcattttggctgcattaattatgttgtgctaaaacggattaactgaaaaaacgaatatagattgttgacatgagtttctctctctctccttgctatagGTAAGCGCGAGCAGCACTTTTGGAGATTACCATCGAATTGTTGCGCCTGGTGAGACATATGAAG

Basic information

species Zea mays
transcript GRMZM2G106683_T02
intron # 13
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|60345819|gb|DN212792.1|DN212792
EST:     CGGGCAGGCCTGTACCCGGCTCAGTGATGATAAAGGGCATTGATTCCAAG                         GTAAGCGCGAGCAGCACTTTTGGAGATTACCATCGAATTGTTGCGCCTGGT
genomic: CGGGCAGGCCTGTACCCGGCTCAGTGATGATAAAGGGCATTGATTCCAAGgtgagctcat ... cttgctatagGTAAGCGCGAGCAGCACTTTTGGAGATTACCATCGAATTGTTGCGCCTGGT
EST: gi|5081117|gb|AI738163.1|AI738163
EST:     CGGGCAGGCCTGTACCCGGCTCAGTGATGATAAAGGGCATTGATTCCAAG                         GTAAGCGCGAGCAGCACTTTCGGAGATTACCATCGAATTGTTGCGCCTGGT
genomic: CGGGCAGGCCTGTACCCGGCTCAGTGATGATAAAGGGCATTGATTCCAAGgtgagctcat ... cttgctatagGTAAGCGCGAGCAGCACTTTTGGAGATTACCATCGAATTGTTGCGCCTGGT
EST: gi|78110109|gb|DV528524.1|DV528524
EST:     CGGGCAGGCCTGTACCCGGCTCAGTGATGATAAAGGGCATTGATTCCAAG                         GTAAGCGCGAGCAGCACTTTTGGAGATTACCATCGAATTGTTGCGCCTGGT
genomic: CGGGCAGGCCTGTACCCGGCTCAGTGATGATAAAGGGCATTGATTCCAAGgtgagctcat ... cttgctatagGTAAGCGCGAGCAGCACTTTTGGAGATTACCATCGAATTGTTGCGCCTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaaaacgaatatagattgttgacatgagtttctctctctctccttgctatagGTAAGCGCGAGCAGCACTTTTGGAGATTACCATCGAATTGTTGCGCCTGGTGAGACATATGAAG
                   tgttgac  putative branch site (score: 3)
                               tttctctctctctcct  putative PPT
          aatatagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctcattttggctgcattaattatgttgtgctaaaacggattaactgaaaaaacgaatatagattgttgacatgagtttctctctctctccttgctatagGTAAGCGCGAGCAGCACTTTTGGAGATTACCATCGAATTGTTGCGCCTGGTGAGACATATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT