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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCATCGCCATGCTTGAGAAGACCGGGACTCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttgaatgaaacaatatacaaattatctattttgtaccaattctaaccagtgatgctctcctcttcttcaacgacatactag

Basic information

species Zea mays
transcript GRMZM2G003096_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003096_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g07090.1 (Oryza sativa), 5'ss of exon 6
AATCATCGCCATGCTTGAGAAGACCGGGACTCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttgaatgaaacaatatacaaattatctattttgtaccaattctaaccagtgatgctctcctcttcttcaacgacatactag
|||||| || |||||||||||||| |||| |||||||||||||||||||||||||||||| |||||||| ||| | ||||||   | ||||  ||   ||| |    |||   | ||| |    || || | |     || |||| ||||| |              
AATCATTGCAATGCTTGAGAAGACAGGGATTCTAAAAATTGCAAGTGTGGGAGATTGTGGTTTGAAAGTAATTAGAAAAGgttagcatgaacaaatttatagatttcttaa--agtttattagcatacttatc-----tgttctcttcttcctag------------
















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|50334525|gb|CO529651.1|CO529651
EST:     GGGTTGAAAGTTATTCGTAAAG                         GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
genomic: GGGTTGAAAGTTATTCGTAAAGgtagacttga ... gacatactagGGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
EST: gi|89249663|gb|DY621449.1|DY621449
EST:     AGTTATTTGTAAAG                         GGCAAGTAATGTTTTCTATATCCCCTCAAGAACATTATTTTTGACTGCCCA
genomic: AGTTATTCGTAAAGgtagacttga ... gacatactagGGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTA-TTTTGACTGCCCA
EST: gi|50334526|gb|CO529652.1|CO529652
EST:     TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAG                         GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
genomic: TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttga ... gacatactagGGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
EST: gi|211439719|gb|FL188857.1|FL188857
EST:     TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAG                         GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
genomic: TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttga ... gacatactagGGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
EST: gi|211439722|gb|FL188860.1|FL188860
EST:     TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAG                         GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
genomic: TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttga ... gacatactagGGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
EST: gi|211439720|gb|FL188858.1|FL188858
EST:     TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTGGRG                         GGCAAGTAATGTTCTCTATATCCCCATCAAGAACATTATTTTGACTGCCCA
genomic: TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttga ... gacatactagGGCAAGTAATGTTCTCTATATCCCC-TCAAGAACATTATTTTGACTGCCCA
EST: gi|211537751|gb|FL446842.1|FL446842
EST:     TAAAAATGGCAAATGTGGGAGATTGGTGGG-TGAAAGTTATTCGTAAAAG                         GGCAAGTAATGTTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCC
genomic: TAAAAATTGCAAGTGTGGGAGATT-GTGGGTTGAAAGTTATTCGT-AAAGgtagacttga ... gacatactagGGCAAGTAATG-TTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCC
EST: gi|211439718|gb|FL188856.1|FL188856
EST:     TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAG                         GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
genomic: TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttga ... gacatactagGGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
EST: gi|13178513|gb|BG349771.1|BG349771
EST:     TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAG                         GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTAT
genomic: TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttga ... gacatactagGGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTAT
EST: gi|89249664|gb|DY621450.1|DY621450
EST:     TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAG                         GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT
genomic: TCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttga ... gacatactagGGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCATCGCCATGCTTGAGAAGACCGGGACTCTAAAAATTGCAAGTGTGGGAGATTGTGGGTTGAAAGTTATTCGTAAAGgtagacttgaatgaaacaatatacaaattatctattttgtaccaattctaaccagtgatgctctcctcttcttcaacgacatactag

- - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT