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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGAACCAGGCAGAGGTGGTCTTGTTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggtttgaaatagcattcttgttctcattccatgtttctgctgtttcttttacttatatttgattttgcag

Basic information

species Zea mays
transcript GRMZM2G030280_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 4
CTTGAACCAGGCAGAGGTGGTCTTGTTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggtttg-aaatagcattcttgttctcattccatgtttctgctgtttcttt---tacttatatt-tgattttgcag
|||||||||||      || ||||| |||| ||     |  |||||||||||| |||||||||| ||||||||||||  |  |||| || ||||  |||  || |  || ||| ||   | |||| |      || ||   || | | |||| ||
CTTGAACCAGGTCAGCTTGCTCTTGCTGCTGCTTCTGACTCTGACAGATCCAAGGACAAACATGAAGATCAAAAGgtaaaattttgcaagtagctctctcctttttgtttcatattatcgttgttgcaacaaatattttccttatcactttgtag
















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|50331700|gb|CO526826.1|CO526826
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|89249315|gb|DY621101.1|DY621101
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCACAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211521271|gb|FL055174.1|FL055174
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211524263|gb|FL055178.1|FL055178
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211524264|gb|FL055179.1|FL055179
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|71305566|gb|DR788926.1|DR788926
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|74232819|gb|DT640733.1|DT640733
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|91872807|gb|EB402764.1|EB402764
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|60396273|gb|DN229142.1|DN229142
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211521265|gb|FL055168.1|FL055168
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211521263|gb|FL055166.1|FL055166
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211521270|gb|FL055173.1|FL055173
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|94472378|gb|EB701336.1|EB701336
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211521262|gb|FL055165.1|FL055165
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|71426016|gb|DR807066.1|DR807066
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|76290001|gb|DV029569.1|DV029569
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211524261|gb|FL055176.1|FL055176
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211521267|gb|FL055170.1|FL055170
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCTTCGCCTTGCTCAAAATCGTGAGGCTGCAA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAA
EST: gi|88753042|gb|DY537183.1|DY537183
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTTGCGTCGCCTTGCTCAAAA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATT-GCGTCGCCTTGCTCAAAA
EST: gi|211521272|gb|FL055175.1|FL055175
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|211524262|gb|FL055177.1|FL055177
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
EST: gi|101385511|gb|EB814802.1|EB814802
EST:     TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAG                         ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA
genomic: TTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggttt ... gattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGAACCAGGCAGAGGTGGTCTTGTTGCTTCTGACTCCAGTGACAGATCCAAAGACAAACATGGAGATCAAAAGgtgcaggtttgaaatagcattcttgttctcattccatgtttctgctgtttcttttacttatatttgattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA