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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgctgtacggctagctagtttttccttcagagagattgatcgagatgtgacgatgccgctgccttggttgctcgacag

Basic information

species Zea mays
transcript GRMZM5G836250_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836250_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g64660.3 (Oryza sativa), 5'ss of exon 1
---GCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgctgtacggctagctagtttttccttcagagagat-tgatcgagat-gtgacgatg----ccgctgccttggttgct-cgacag-
    |||| |    | |  | | |    ||  |  |||  |    | |  |   ||||||||||||| ||||||||||||| ||||||||||||||||| ||||||||||  |    |   || ||    | |   ||||     | |    ||||| | ||   ||    | |  | |||| ||| |  |||   
CTCACTCTACTGATTGGCACGCTGAACAAAACTTCTCGGGTTGTGCATGCA---GGCCGGGCTCGCCAAGCTCATCGGGCTGGCCGGCGAGACCAACGTTCAGgcaagtgtacctggcaa-taactgtcatctttctcagtttcttgtctctgagattgagatagtgaggactgaggacttgcttggtgtgaccag

upper sequence: GRMZM5G836250_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 5'ss of exon 1
------------------------------------------------GCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgctgtacggctagctagtttttccttcagagagattgatcgagatgtgacgatgccgctgccttggttgctcgacag
                                                 |||||||||||||| || |||||||||||||||||||||||||||||||||| |   |    ||  | | | |   ||  ||    |     ||| | |     |  | | |    |||   | |    |  | |   | | |  ||| | ||||   |||| |                    
GAACGAGCAGAGCCGCAACCCGGAGGCACGCGGCGACCTCACCATCCTCCTCTCCCACATCGTGCTTGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGgtcacacgaatcct-cccgttgt-ttcatcgttagg-----cgtacggatctctcggttctcactctactgattggcacgctgaacaaaacttctcgggttgtgc--atgcag--------------------

upper sequence: GRMZM5G836250_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 5'ss of exon 2
GCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgctgtacggctagctagtttttccttcagagagat-tgatcgagat-gtgacgatg----ccgctgccttggttgct-cgacag-
                                                    |||||||||||| ||||||||||||| ||||||||||||||||| ||||||||||  |    |   || ||    | |   ||||     | |    ||||| | ||   ||    | |  | |||| ||| |  |||   
----------------------------------------------------GCCGGGCTCGCCAAGCTCATCGGGCTGGCCGGCGAGACCAACGTTCAGgcaagtgtacctggcaa-taactgtcatctttctcagtttcttgtctctgagattgagatagtgaggactgaggacttgcttggtgtgaccag

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|91877968|gb|EB407925.1|EB407925
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|149064613|gb|EE286484.2|EE286484
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|149085230|gb|EE174737.2|EE174737
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|149056940|gb|EE156494.2|EE156494
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|33466970|gb|CF244019.1|CF244019
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|78106830|gb|DV525248.1|DV525248
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|148938587|gb|EC882914.2|EC882914
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|50327741|gb|CO522867.1|CO522867
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|89759142|gb|DY688055.1|DY688055
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|211007786|gb|FL012051.1|FL012051
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|149088446|gb|EE177549.2|EE177549
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|71314865|gb|DR794058.1|DR794058
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|149095912|gb|EE181574.2|EE181574
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|148983226|gb|EE029190.2|EE029190
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|71768089|gb|DR966026.1|DR966026
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|71770843|gb|DR968780.1|DR968780
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|148932776|gb|EE285437.2|EE285437
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|71317308|gb|DR795339.1|DR795339
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|211005021|gb|FL012048.1|FL012048
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|94476279|gb|EB705237.1|EB705237
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|91055488|gb|EB165906.1|EB165906
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|91877810|gb|EB407767.1|EB407767
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|149040104|gb|EE046754.2|EE046754
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|76282215|gb|DV021783.1|DV021783
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|74244032|gb|DT651946.1|DT651946
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|93284535|gb|EB676799.1|EB676799
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|37420508|gb|CF647945.1|CF647945
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAG
EST: gi|71438223|gb|DR819273.1|DR819273
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|78105897|gb|DV524315.1|DV524315
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|71757120|gb|DR955057.1|DR955057
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|78113532|gb|DV531923.1|DV531923
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAACCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgctgtacggctagctagtttttccttcagagagattgatcgagatgtgacgatgccgctgccttggttgctcgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA