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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGTGCATGGAGACGTCAAACCTGAGAACTTTCTTCTGGGGCAGCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaagactgttccaattaacttgcatttttttgtgaaattgtccccctttcttatttctgctagattactggtggtctagagcattaggtcttttgatcagcttaacagcttctttgttaattttcacttgccag

Basic information

species Zea mays
transcript GRMZM2G017835_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017835_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G47680.2 (Glycine max), 5'ss of exon 7
ATATGTGCATGGAGACGTCAAACCTGAGAACTTTCTTCTGGGGCAGCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaagactgttccaattaacttgcatttt-tttgtgaaattgtccccctttcttatttctgctagattactg-gtggtctagagcattaggtcttttgatcagcttaacagcttctttgttaattttcacttgccag
 |||||||||||||| || ||||| ||||||||| | || || || ||||| || || || ||||||||| | | |||||| || |||||||||||| |  |       | |||  |   |||||||  || ||         | ||||| | |  | |   | || |    ||  | |  ||                                                     
CTATGTGCATGGAGATGTAAAACCAGAGAACTTTTTACTTGGTCAACCTTCTACACCACAAGAAAAGAAATTGTTTCTTGTAGACCTTGGATTAGgttagtagttgcaattcaaggatgatgcatttcattcgtatttacactctcctttttgacctttctcatataagcacgtattttgcag-----------------------------------------------------
















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|31355100|gb|CD439457.1|CD439457
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|211242969|gb|FL282602.1|FL282602
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|22819487|gb|BU499577.1|BU499577
EST:     CCTTCAACGCCTCATGAAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGCTATGATCAAC
genomic: CCTTCAACGCCTCATGAAAA-GAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|211242967|gb|FL282600.1|FL282600
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|76015692|gb|DT942862.1|DT942862
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|32832258|gb|CD971936.1|CD971936
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|87156608|gb|DY401397.1|DY401397
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|31440950|gb|CD510381.1|CD510381
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|6587599|gb|AW244917.1|AW244917
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGC
EST: gi|32832272|gb|CD971950.1|CD971950
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|211242968|gb|FL282601.1|FL282601
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|26559748|gb|CA831983.1|CA831983
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|32832300|gb|CD971978.1|CD971978
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|148988749|gb|EE031658.2|EE031658
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|60345255|gb|DN212228.1|DN212228
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|32832043|gb|CD971721.1|CD971721
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|32835538|gb|CD975216.1|CD975216
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
EST: gi|32835900|gb|CD975578.1|CD975578
EST:     GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAG                         CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC
genomic: GCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaaga ... cacttgccagCAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGTGCATGGAGACGTCAAACCTGAGAACTTTCTTCTGGGGCAGCCTTCAACGCCTCATGAAAAGAAACTTTATCTTGTGGATCTTGGATTAGgtaaacaagactgttccaattaacttgcatttttttgtgaaattgtccccctttcttatttctgctagattactggtggtctagagcattaggtcttttgatcagcttaacagcttctttgttaattttcacttgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA