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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgcgcgctaccgcctccctccctctcccgtcgatgcgatcttctagctccagattgcatctccttcttcttcctccttcggccagggcagaatggctcctcgcgggctgcggttttgtgctcaaaggcgcgatctttacgctcgggatggcttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGATTTGCTTGGGAGTGAGAGGAGAGAGCGAGTAATAGGGTGAAGGAGTCTTG

Basic information

species Zea mays
transcript GRMZM2G135568_T04
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|71757755|gb|DR955692.1|DR955692
EST:     AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAG                         GAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
genomic: AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAGgttggtgcgc ... ttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
EST: gi|211033696|gb|FL002057.1|FL002057
EST:     AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAG                         GAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
genomic: AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAGgttggtgcgc ... ttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
EST: gi|211036134|gb|FL002061.1|FL002061
EST:     AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAG                         GAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
genomic: AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAGgttggtgcgc ... ttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
EST: gi|149061139|gb|EE157399.2|EE157399
EST:     AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAG                         GAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
genomic: AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAGgttggtgcgc ... ttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
EST: gi|149083911|gb|EE173287.2|EE173287
EST:     AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAG                         GAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
genomic: AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAGgttggtgcgc ... ttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
EST: gi|211036133|gb|FL002060.1|FL002060
EST:     AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAG                         GAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
genomic: AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAGgttggtgcgc ... ttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
EST: gi|211033697|gb|FL002058.1|FL002058
EST:     AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAG                         GAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
genomic: AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAGgttggtgcgc ... ttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
EST: gi|211036135|gb|FL002062.1|FL002062
EST:     AG-MCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAG                         GAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
genomic: AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAGgttggtgcgc ... ttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
EST: gi|211033698|gb|FL002059.1|FL002059
EST:     AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAG                         GAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT
genomic: AGACCAAACCTACTAGCAGCGCGTCGGGGGTGCACCTGCGGCCGATCTAGgttggtgcgc ... ttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcggttttgtgctcaaaggcgcgatctttacgctcgggatggcttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGATTTGCTTGGGAGTGAGAGGAGAGAGCGAGTAATAGGGTGAAGGAGTCTTG
                                            cttcgtt  CT-rich tract
                         atcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtgcgcgctaccgcctccctccctctcccgtcgatgcgatcttctagctccagattgcatctccttcttcttcctccttcggccagggcagaatggctcctcgcgggctgcggttttgtgctcaaaggcgcgatctttacgctcgggatggcttcgttacagGAGACAGGGATTTCTTCTCGTCCTGTCCTGTGGATTATTACGGGCCTGGATTTGCTTGGGAGTGAGAGGAGAGAGCGAGTAATAGGGTGAAGGAGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG