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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACAAATTAGTGGAGCAAGCTGTTGGAATGCCTTCAGTTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggttactgaatttttctggtacagacatcctcaagtactctctctgatttatagcgtttgtcattttttattccttaacgcccaaagctggaagctctggcttatgatttacctttctttgtgcttcatgccttgcag

Basic information

species Zea mays
transcript GRMZM2G161566_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161566_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g51410.2 (Oryza sativa), 5'ss of exon 5
TGACAAATTAGTGGAGCAAGCTGTTGGAATGCCTTCAGTTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggttactgaatttttctggtacagacatcctcaagtactctctctgatttatagcgtttgtcattttttattccttaacgcccaaagctggaagctctggcttatgatttacctttctttgtgcttcatgccttgcag
||| ||||| || || |||||||| || ||||||||||| |||||||| ||||| ||||| ||||||||||||||| ||||||||||||||||  ||       |||||||   |   | ||  | |  |   |||   || | |||| |||||    || || |  | |      ||| |||  |   |||  ||||  |||  || |   | |  || |||| || |||
TGATAAATTGGTCGAACAAGCTGTGGGCATGCCTTCAGTCGCTCAAATTTTCAAGGTTCATAGTGAAGCCTTCTTTAGGGATAATGAGgtaatcttt-------ttttctgaatccatcttctgctaacatgatctactatct-tagcatttgtttacttgtagttatcagaaggaaaatctgaga---ctga-ttat--tttctctgtggctctcttttatgcattacag
















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|13237004|gb|BG355018.1|BG355018
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|5343250|gb|AI795555.1|AI795555
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|24934599|gb|CA452817.1|CA452817
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|37392587|gb|CF633545.1|CF633545
EST:     ATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: ATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|30087805|gb|CB886011.1|CB886011
EST:     CTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCNCC
genomic: CTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|32164833|gb|CD670151.1|CD670151
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|32928190|gb|CF033002.1|CF033002
EST:     TTGCTCAAATATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|56461974|gb|CK986272.1|CK986272
EST:     TTGCTCAAATATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|37398941|gb|CF636791.1|CF636791
EST:     TTGCTCAAATATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|211307747|gb|FL198214.1|FL198214
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|60342476|gb|DN209449.1|DN209449
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|213191774|gb|FM182092.1|FM182092
EST:     TTGCTCAAATATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|60395600|gb|DN228470.1|DN228470
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|44900819|gb|CK827364.1|CK827364
EST:     TTGCTCAAATATTCAAAGTTCACAGCGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
EST: gi|60355769|gb|DN222742.1|DN222742
EST:     TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAG                         AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC
genomic: TTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggtta ... tgccttgcagAGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACAAATTAGTGGAGCAAGCTGTTGGAATGCCTTCAGTTGCTCAAATATTCAAAGTTCACAGTGAAGCCTTCTTTCGGGATAATGAGgtaatggttactgaatttttctggtacagacatcctcaagtactctctctgatttatagcgtttgtcattttttattccttaacgcccaaagctggaagctctggcttatgatttacctttctttgtgcttcatgccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC