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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatttactgattgtaaccagttacggatgttaccactttccagcacttttttttgaaagttttttttgttccaatgtaatagtgtcctattcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTCACAGCGATAATTTGGCGAACTATGGAAAGTTATGCCGTGAAAGAACACA

Basic information

species Zea mays
transcript GRMZM2G060284_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060284_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 3'ss of exon 2
taatttactgattgtaaccagttacggatgttaccactttccagcactt--ttttttgaaagttttttttgttccaatgtaatagtgtcctattcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTCACAGCGATAATTTGGCGAACTATGGAAAGTTATGCCGTGAAAGAACACA
  ||  | |  || | || | ||||   | |    |  || ||    |   |    |  |||||||   | |  |     |||    |  | |  |||| |||||||||||||||||||||||||||||||||||||||||||||| | |||||||| |||||||||| ||||||||||||||||||||||||||| |||||
-tatggattttttattactacttacatttttggggatctttcaagtttcaatagcatctaagttttgactatcacccaaaaatgacctt-tgtgtgttgtagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGAAGCCTCACAGTGATAATTTGGTGAACTATGGAAAGTTATGCCGTGAAAGGACACA
















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|116816147|gb|EC858853.1|EC858853
EST:     TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAA                         GGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggatcca ... ttcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
EST: gi|28187707|gb|CB179317.1|CB179317
EST:     TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggatcca ... ttcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
EST: gi|211224212|gb|FK968311.1|FK968311
EST:     TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggatcca ... ttcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
EST: gi|149085565|gb|EE175077.2|EE175077
EST:     TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggatcca ... ttcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
EST: gi|13490745|gb|BG517509.1|BG517509
EST:     TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggatcca ... ttcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
EST: gi|76937460|gb|DV175147.1|DV175147
EST:     TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggatcca ... ttcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
EST: gi|211224215|gb|FK968314.1|FK968314
EST:     TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggatcca ... ttcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
EST: gi|211224214|gb|FK968313.1|FK968313
EST:     TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggatcca ... ttcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttttttgaaagttttttttgttccaatgtaatagtgtcctattcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTCACAGCGATAATTTGGCGAACTATGGAAAGTTATGCCGTGAAAGAACACA
                                        tcctattc  CT-rich tract
     tttttgaaagtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatttactgattgtaaccagttacggatgttaccactttccagcacttttttttgaaagttttttttgttccaatgtaatagtgtcctattcgttgcagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTCACAGCGATAATTTGGCGAACTATGGAAAGTTATGCCGTGAAAGAACACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC