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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgagattgtttcaactttgcttgttcacataaagtttaacacttacaatcgtaatgcacgattttgatacatggttgttgaacttttcttcatctattcctacaaggctcagAAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG

Basic information

species Zea mays
transcript GRMZM2G094444_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094444_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g11510.1 (Oryza sativa), 3'ss of exon 2
gtgtgagattgtttcaactttgcttgttcacataaagtttaacacttacaatcgtaatgcacgattttgatacatggttgttg-aacttttcttcatctattcctacaaggctcagAAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG
|| |||||| ||||  ||||| | ||| |||  | |||  ||   ||      | ||| |  ||||| ||||||||| |  || | | ||  ||  | | | |  |  |||||||||| ||||||||||||||| |||||||||| ||||  ||||||||||| | ||
gtatgagatagttt--actttacatgtgcacggacagt--aatgtttcttgctgcaattcgtgattt-gatacatggatactgcatccttcttttctttgtgctgagcagGCTCAGAAAAATATATTCCAGATGATCAGGACAGTCTGGGTCTCTGATGGTCTGAAAG
















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|5566944|gb|AI881855.1|AI881855
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGGCTCAG                    
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCT-A-----AGgtgtgagatt ... caagg
EST: gi|101396104|gb|EB819979.1|EB819979
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|101396104|gb|EB819979.1|EB819979
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|101396104|gb|EB819979.1|EB819979
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|101396104|gb|EB819979.1|EB819979
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|101396104|gb|EB819979.1|EB819979
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|31355816|gb|CD440173.1|CD440173
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGGCTCAG                    
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCT-A-----AGgtgtgagatt ... caagg
EST: gi|93013218|gb|EB638738.1|EB638738
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         AAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGA
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcagAAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGA
EST: gi|71328899|gb|DR801132.1|DR801132
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGGCTCAG                    
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCT-A-----AGgtgtgagatt ... caagg
EST: gi|91049487|gb|EB159905.1|EB159905
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGGCTCAG                    
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCT-A-----AGgtgtgagatt ... caagg
EST: gi|211518405|gb|FL045671.1|FL045671
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518405|gb|FL045671.1|FL045671
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518405|gb|FL045671.1|FL045671
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518405|gb|FL045671.1|FL045671
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518405|gb|FL045671.1|FL045671
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|91055834|gb|EB166252.1|EB166252
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGGCTCAG                    
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCT-A-----AGgtgtgagatt ... caagg
EST: gi|74244669|gb|DT652583.1|DT652583
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGGCTCAG                    
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCT-A-----AGgtgtgagatt ... caagg
EST: gi|211518397|gb|FL045663.1|FL045663
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518397|gb|FL045663.1|FL045663
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518397|gb|FL045663.1|FL045663
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518397|gb|FL045663.1|FL045663
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518397|gb|FL045663.1|FL045663
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518399|gb|FL045665.1|FL045665
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518399|gb|FL045665.1|FL045665
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518399|gb|FL045665.1|FL045665
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518399|gb|FL045665.1|FL045665
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518399|gb|FL045665.1|FL045665
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|93284067|gb|EB676331.1|EB676331
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|93284067|gb|EB676331.1|EB676331
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|93284067|gb|EB676331.1|EB676331
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|93284067|gb|EB676331.1|EB676331
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|93284067|gb|EB676331.1|EB676331
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518406|gb|FL045672.1|FL045672
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGGCTCAG                    
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCT-A-----AGgtgtgagatt ... caagg
EST: gi|76288143|gb|DV027711.1|DV027711
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         AAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGA
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcagAAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGA
EST: gi|149089237|gb|EE178440.2|EE178440
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGGCTCAG                    
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCT-A-----AGgtgtgagatt ... caagg
EST: gi|78117346|gb|DV535733.1|DV535733
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         AAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGA
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcagAAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGA
EST: gi|211518403|gb|FL045669.1|FL045669
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518403|gb|FL045669.1|FL045669
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518403|gb|FL045669.1|FL045669
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518403|gb|FL045669.1|FL045669
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-
EST: gi|211518403|gb|FL045669.1|FL045669
EST:     ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAG                         G
genomic: ACACTCTGAAAACAAGGCTTCAGAGTCAAGCTATAATGACAGGGGCTAAGgtgtgagatt ... caaggctcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgattttgatacatggttgttgaacttttcttcatctattcctacaaggctcagAAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG
    ttttgat  putative branch site (score: 4)
                         cttttcttcatctatt  putative PPT
     tttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgagattgtttcaactttgcttgttcacataaagtttaacacttacaatcgtaatgcacgattttgatacatggttgttgaacttttcttcatctattcctacaaggctcagAAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG