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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGTGCTCTCACACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttcttctttgcacacatgaatcagcagtatttgacgtggaacttgcaacttgcgggtgcatcatgtactaatgttcatttcgtgtag

Basic information

species Zea mays
transcript GRMZM2G020002_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020002_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 15
AGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGTGCTCTCACACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttcttctttgcacacatgaatcagcagtatttgacgtggaacttgcaacttgcgggtgcatcatgtactaatgttcatttcgtgtag
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AGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGTGCCCACACACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAGgtcggtccctcgttactcaca-------actgcatttgcaa--aagcttgaattcaacttatgttttctttttctct-ctcaatcggtgtag
















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|149070477|gb|EE158879.2|EE158879
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGAGGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|74240936|gb|DT648850.1|DT648850
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|211361841|gb|FL432810.1|FL432810
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|32809720|gb|CD961954.1|CD961954
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|28187829|gb|CB179439.1|CB179439
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|78079711|gb|DV508123.1|DV508123
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|148990302|gb|EE031901.2|EE031901
EST:     CACCCCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|18176646|gb|BM351579.1|BM351579
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|113703820|gb|EE681324.1|EE681324
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|148929734|gb|EC876616.2|EC876616
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGAGGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|149082367|gb|EE171551.2|EE171551
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGTGCTCTCACACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttcttctttgcacacatgaatcagcagtatttgacgtggaacttgcaacttgcgggtgcatcatgtactaatgttcatttcgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA