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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcccgcatctccttcgcttgcgttactttctccctccggctcagagttctgtattgactagtttcccgctgtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG

Basic information

species Zea mays
transcript GRMZM2G115424_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|93282514|gb|EB674778.1|EB674778
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|21331604|gb|BQ486985.1|BQ486985
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|149088114|gb|EE177273.2|EE177273
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|94476635|gb|EB705593.1|EB705593
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347699|gb|FL126085.1|FL126085
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|91869344|gb|EB400345.1|EB400345
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|29130260|gb|CB380964.1|CB380964
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|76935015|gb|DV174136.1|DV174136
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347692|gb|FL126078.1|FL126078
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|148979152|gb|EE026541.2|EE026541
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|4753351|gb|AI657256.1|AI657256
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347698|gb|FL126084.1|FL126084
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211350088|gb|FL126088.1|FL126088
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347696|gb|FL126082.1|FL126082
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|149013491|gb|EE042992.2|EE042992
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|74232055|gb|DT639969.1|DT639969
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|31354599|gb|CD438956.1|CD438956
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|21390188|gb|BQ528237.1|BQ528237
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211350091|gb|FL126091.1|FL126091
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211350087|gb|FL126087.1|FL126087
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|86466339|gb|DY232710.1|DY232710
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCGGGGCGCTCACCACCG                         ATGTTGAAAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347688|gb|FL126074.1|FL126074
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|31910587|gb|CD651499.1|CD651499
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|28930828|gb|CB334189.1|CB334189
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|31406449|gb|CD485181.1|CD485181
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347693|gb|FL126079.1|FL126079
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211350089|gb|FL126089.1|FL126089
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|28931208|gb|CB334569.1|CB334569
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|89252072|gb|DY623858.1|DY623858
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|93017250|gb|EB642770.1|EB642770
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|60355952|gb|DN222925.1|DN222925
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211350090|gb|FL126090.1|FL126090
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGASCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347697|gb|FL126083.1|FL126083
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347690|gb|FL126076.1|FL126076
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347691|gb|FL126077.1|FL126077
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|149110861|gb|EE294360.2|EE294360
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211347689|gb|FL126075.1|FL126075
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         ATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... gtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctccctccggctcagagttctgtattgactagtttcccgctgtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG
                          tattgac  putative branch site (score: 2)
                                              tcgcttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcccgcatctccttcgcttgcgttactttctccctccggctcagagttctgtattgactagtttcccgctgtcgcttcagATGTTGAGAAGTTCTACGTGATGTGCGACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT