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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggcctctccttccatcctctgcatgtactgacaaggatatatacacgcttcatgtccacgttctctgatcaagttctctgctactctgtttggtcaccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACTCATAAG

Basic information

species Zea mays
transcript GRMZM5G896082_T01
intron # 4
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|149051802|gb|EE155929.2|EE155929
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|149070758|gb|EE159171.2|EE159171
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|71325794|gb|DR799576.1|DR799576
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|76293829|gb|DV033397.1|DV033397
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|50329134|gb|CO524260.1|CO524260
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|148959398|gb|EC905432.2|EC905432
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|78092904|gb|DV521278.1|DV521278
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|71449206|gb|DR830256.1|DR830256
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|74239749|gb|DT647663.1|DT647663
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|71435282|gb|DR816332.1|DR816332
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|50328983|gb|CO524109.1|CO524109
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAG
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAG
EST: gi|93014353|gb|EB639873.1|EB639873
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|71773101|gb|DR971019.1|DR971019
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|149097127|gb|EE182939.2|EE182939
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|211033504|gb|FL333366.1|FL333366
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAA-G                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|149111107|gb|EE294603.2|EE294603
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|149058763|gb|EE156781.2|EE156781
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|71322554|gb|DR797954.1|DR797954
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|148971891|gb|EE022659.2|EE022659
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|78114034|gb|DV532423.1|DV532423
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|71775245|gb|DR973123.1|DR973123
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|89757906|gb|DY687292.1|DY687292
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCCGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|13516143|gb|BG518419.1|BG518419
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|149011246|gb|EE042332.2|EE042332
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|78107802|gb|DV526220.1|DV526220
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
EST: gi|148949267|gb|EC894710.2|EC894710
EST:     ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAG                         ACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT
genomic: ACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAAGgtttggcctc ... ccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtccacgttctctgatcaagttctctgctactctgtttggtcaccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACTCATAAG
           ctctgat  putative branch site (score: 4)
                                          tcaccttcttt  putative PPT
                                               ttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggcctctccttccatcctctgcatgtactgacaaggatatatacacgcttcatgtccacgttctctgatcaagttctctgctactctgtttggtcaccttctttagACAGACGGCAGTGTCATTGTGAAGGAGGGTCCCAGGTGCAGCCTAAGGACTCATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG