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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgacgataaattacatgtgatcttgttcgcagttcgtgcatatgtgcctatacggacctgacagtgcgaagcactcaaatacctttttttccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG

Basic information

species Zea mays
transcript GRMZM2G038848_T01
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|91878697|gb|EB408654.1|EB408654
EST:     GACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGCGCTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: GACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCG-GTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345290|gb|FL126063.1|FL126063
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345286|gb|FL126059.1|FL126059
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345287|gb|FL126060.1|FL126060
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345285|gb|FL126058.1|FL126058
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|30705270|gb|CD058727.1|CD058727
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|101390742|gb|EB817305.1|EB817305
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|71448245|gb|DR829295.1|DR829295
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345293|gb|FL126066.1|FL126066
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTSGGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|148946555|gb|EC884293.2|EC884293
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345288|gb|FL126061.1|FL126061
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|148942779|gb|EC887806.2|EC887806
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctatacggacctgacagtgcgaagcactcaaatacctttttttccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG
          acctgac  putative branch site (score: 3)
                                  tacctttttttccctg  putative PPT
                               aaataccttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgacgataaattacatgtgatcttgttcgcagttcgtgcatatgtgcctatacggacctgacagtgcgaagcactcaaatacctttttttccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA