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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTATGCCTCACTCCAGAAAATTACAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatttttcatttcatttccagtctcctgcatctatctgttatttaatgcctgatgttcctctatgcag

Basic information

species Zea mays
transcript GRMZM2G120300_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120300_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g34100.1 (Oryza sativa), 5'ss of exon 6
ATGTATGCCTCACTCCAGAAAATTACAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagta----atttttcatttcatttccagtc----tcctgcatctatctgttatttaatgcctgatgttcctctatgcag
|||||  | |||||||||||||||| ||| || || ||||| |||| ||| || || || ||||||||||| ||||||| ||    |  ||   ||||| |||||         || |||  | |||||||||| ||| | | ||  || |  ||||
ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatccaacgttcattttcaattccacaaataaatcttcattgacctgttattta-tgcttcaagtatctatccgcag
















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|76286960|gb|DV026528.1|DV026528
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|111991062|gb|EE331971.1|EE331971
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|32925422|gb|CF030234.1|CF030234
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|32831167|gb|CD970845.1|CD970845
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|32926516|gb|CF031328.1|CF031328
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|89755327|gb|DY685795.1|DY685795
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCAGGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|76912678|gb|DV164843.1|DV164843
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|32925540|gb|CF030352.1|CF030352
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|78113025|gb|DV531419.1|DV531419
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGG
EST: gi|76290102|gb|DV029670.1|DV029670
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|32831772|gb|CD971450.1|CD971450
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|60400379|gb|DN233186.1|DN233186
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|60356731|gb|DN223704.1|DN223704
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|78113024|gb|DV531418.1|DV531418
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|32926815|gb|CF031627.1|CF031627
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|5770170|gb|AI973344.1|AI973344
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|60359081|gb|DN226054.1|DN226054
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|149112937|gb|EE295730.2|EE295730
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|211480476|gb|FL101272.1|FL101272
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|6445407|gb|AW179475.1|AW179475
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|148947425|gb|EC892845.2|EC892845
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|60352578|gb|DN219551.1|DN219551
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|149026716|gb|EE046118.2|EE046118
EST:     AGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTTG                         AGTAATGCAAAGTTTGC
genomic: AGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTT-Ggtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGC
EST: gi|149103111|gb|EE288478.2|EE288478
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|67017612|gb|CO446361.1|CO446361
EST:     CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: CAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
EST: gi|60399854|gb|DN232664.1|DN232664
EST:     AAAAGTATACTGTGGGCATGAATATACCTTG                         AGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG
genomic: AAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatt ... ctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTATGCCTCACTCCAGAAAATTACAGCTCTACCCGATGATACAAAAGTATACTGTGGGCATGAATATACCTTGgtgagtaatttttcatttcatttccagtctcctgcatctatctgttatttaatgcctgatgttcctctatgcag

- - - - - - - - - - - -  CAGCTC