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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTCCAGTTTTTCTGCTAACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAGgtatctgagctatgatacgtatctgtatgtctgtatcgattgaagttttcttgaatgaagttttcaatcttacacccttgtttttctatttacag

Basic information

species Zea mays
transcript GRMZM2G138125_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138125_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os04g59624.3 (Oryza sativa), 5'ss of exon 12
GAGCTCCAGTTTTTCTGCTAACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAGgtatctgagctatgatacgtatctgtatgtctgtatcga-ttgaagttttcttgaatgaagttttcaat-------cttacacccttgtttttctatttacag
|||||||| | ||| |||| |||||||||||||||||||||||||||||||||||||||||| |||||||||| |||||||||||||| ||||| || ||||| |||| | | |     |   |   ||  | ||| |  ||    ||||  ||||||    | ||  |       || |  | | |||||  | || | |||
GAGCTCCAATATTTTTGCTGACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAGCTCGTGTCATAGTAGTTGATCCTGCTTGGAATCCAAGgtacctgaacaacgccgtttccttac-tgagtttattgcctttttattttactgaatgtttgtctctgtatgtttactaatgctcctgtttccc-atcttcag

upper sequence: GRMZM2G138125_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA08G00400.1 (Glycine max), 5'ss of exon 15
GAGCTCCAGTTTTTCTGCTAACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAGgtat---ctgagctatgata----cgtatctgtatgtctgtatcgattgaagttttcttga-atgaagttttcaatcttacacccttgtttttctatttacag
|||||||  | |||||  | ||  | || ||||| ||  | ||||| ||||| || |  |||  |||||| ||||||||||||||||| |||||||| |||||     | |  |||        | |  || ||||||| |||  || |     | | ||     ||   ||   | ||  ||| || |||     |||||  
GAGCTCCTATATTTCTCTTGACATCTCAGGTTGGCGGTTTAGGACTAACACTTACAAGAGCAGATCGTGTGATTGTAGTTGATCCTGCTTGGAACCCAAGgtacatcttaaagtattcctttcccttgactatatgtctatatacatcgttaactgcctgttgctaaaactttttttttttaccatt-tttccagttttac--
















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|28873896|gb|CB329825.1|CB329825
EST:     CTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAG                         TACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA
genomic: CTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAGgtatctgagc ... ctatttacagTACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA
EST: gi|67035224|gb|CO463757.1|CO463757
EST:     TCACCAAGGCAACTCGTGTCATTGTTAGT-GATCCTGCATGGGACCCTAG                         TACAGACNATCAAAGTGTTGATCGTGCTTACCGAAT-GGACAGACTAAAA-
genomic: TCACCAAGGCAACTCGTGTCATTGT-AGTTGATCCTGCATGGAACCCTAGgtatctgagc ... ctatttacagTACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA
EST: gi|28987103|gb|CB351465.1|CB351465
EST:     CTCACCAAGGCAACTCGTGTCATTGCAGTTGATCCTGCATGGAACCCTAG                         TACAGACAATCAAAGGGTTGATCGGGCTTACCGAATTGGACAGACTAAAAA
genomic: CTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAGgtatctgagc ... ctatttacagTACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA
EST: gi|94475969|gb|EB704927.1|EB704927
EST:     CTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAG                         TACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA
genomic: CTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAGgtatctgagc ... ctatttacagTACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA
EST: gi|31909131|gb|CD650765.1|CD650765
EST:     CTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAG                         TACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA
genomic: CTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAGgtatctgagc ... ctatttacagTACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA
EST: gi|28930971|gb|CB334332.1|CB334332
EST:     CTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAG                         TACAGACAATCAAAGGGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA
genomic: CTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAGgtatctgagc ... ctatttacagTACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTCCAGTTTTTCTGCTAACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAACTCGTGTCATTGTAGTTGATCCTGCATGGAACCCTAGgtatctgagctatgatacgtatctgtatgtctgtatcgattgaagttttcttgaatgaagttttcaatcttacacccttgtttttctatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA