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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTAAAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcacgagcccttctacactttgttaatatcctagatccattttttttggattgctgttcagatttagtgacccgatttctcgctgcag

Basic information

species Zea mays
transcript GRMZM2G120115_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 6
TGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTAAAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcacgagcccttctacactttgttaatatcctagatc--cattttttttggattgctgttcagatttagtgacccgatttctcgctgcag
|||||||||  ||||||| |||||||||||| |||||||| | || || ||||| || || || || ||||| || ||||||||||||||||||||||||||| ||| | ||  ||||   ||||   |||||||  |  |    || |   ||     ||     ||   || |   | | ||||   | |||||
TGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAAAAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtactttta-gactcctttagcactc-attaatatatttcactggcactcacttcaacatgtgaaacattgttcgattctc-attttatgttgcag
















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|71444906|gb|DR825956.1|DR825956
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
EST: gi|71310156|gb|DR791369.1|DR791369
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
EST: gi|211365944|gb|FL391110.1|FL391110
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
EST: gi|76290013|gb|DV029581.1|DV029581
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATTTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
EST: gi|60394595|gb|DN227465.1|DN227465
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
EST: gi|78108843|gb|DV527260.1|DV527260
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
EST: gi|37392993|gb|CF633751.1|CF633751
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
EST: gi|88749057|gb|DY533198.1|DY533198
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATTTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
EST: gi|84977510|gb|DW475932.1|DW475932
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
EST: gi|6952519|gb|AW424587.1|AW424587
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGCTACTGGCTATCTTC
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTC
EST: gi|50328759|gb|CO523885.1|CO523885
EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTAAAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcacgagcccttctacactttgttaatatcctagatccattttttttggattgctgttcagatttagtgacccgatttctcgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT