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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgacatccatgctgttcactgtttaggatcgtgaggatgctattgcgataatagctgatggacaaatgggaatgattttcaaatgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA

Basic information

species Zea mays
transcript GRMZM2G060842_T01
intron # 3
splice site 3'
intron type U2

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|211288681|gb|FL312632.1|FL312632
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAA
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAA
EST: gi|76280845|gb|DV020413.1|DV020413
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
EST: gi|50327397|gb|CO522523.1|CO522523
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
EST: gi|211271929|gb|FL194754.1|FL194754
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAA
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAA
EST: gi|76280844|gb|DV020412.1|DV020412
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
EST: gi|91875732|gb|EB405689.1|EB405689
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAC                         GAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
EST: gi|211290817|gb|FL312641.1|FL312641
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCT
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCT
EST: gi|76912690|gb|DV164849.1|DV164849
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
EST: gi|101386086|gb|EB815086.1|EB815086
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
EST: gi|50323043|gb|CO518169.1|CO518169
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
EST: gi|50326968|gb|CO522094.1|CO522094
EST:     GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAG                         GAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT
genomic: GGGTGTCCGGTGACAGCAGCCCTCCTTTAAGCAAGAGGCTTTCTGCCGAGgtgtgacatc ... atgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctattgcgataatagctgatggacaaatgggaatgattttcaaatgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA
               agctgat  putative branch site (score: 4)
                                 aatgattttcaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgacatccatgctgttcactgtttaggatcgtgaggatgctattgcgataatagctgatggacaaatgggaatgattttcaaatgctgacagGAAAGGCAGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC