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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttccagccatctttcacttttttttttggttcctaatctttcactgtgtaaatctacatatagtttccatcaccactaacccttgctggaggaactaatgaaacggctttctcctcctaccttgcctgccgcag

Basic information

species Zea mays
transcript GRMZM2G134930_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134930_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g49500.2 (Oryza sativa), 5'ss of exon 1
AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttccagccatctttcacttttttttttggttcctaatctttcactgtgtaa--atctacatatagtttccatcaccactaacccttgctggaggaactaatgaaacggctttctcctcctaccttgcctgccgcag
                 |  | |  | |  || |||  |||||   | |    |   |||  |  |     ||   ||     ||      |  || | |  |      ||||| | |||   ||| |    |  | | | ||  |     |   ||||      |   ||  | |    |||| ||||                 
-----------------TCGCCCTCCTCGCCCCCGCCGCCTTCTTCCGCGAGCGCCGCACCCGCCGCCCCCTCACCCCTCACCTCCTCGCCTCCTTCGCTCTCCTCGGCTTCACCGGgtattcatcgattcctcctcttcttcttcttctccttctgctcatcttatcgatcgatc--tcttcttctccag---------------
















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|148963460|gb|EE014479.2|EE014479
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCCCTGG                         GATCTTTCGG-AACCAGCTCCCTCTT
genomic: C-GGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTT-CGGGAACCAGCTCC-TCTT
EST: gi|71434594|gb|DR815644.1|DR815644
EST:     CGGTGACTCCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCCGGCTCCTCTTCCTCCTGGGGCCTCGG
genomic: CGGTGACTCC-TCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAG-CTCCTCTTCCTCCTGGG-CCTCGG
EST: gi|18384215|gb|BM417414.1|BM417414
EST:     CCGGTGACGCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGC
EST: gi|94476183|gb|EB705141.1|EB705141
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|88758283|gb|DY542424.1|DY542424
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|148951696|gb|EC897448.2|EC897448
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|149058751|gb|EE156769.2|EE156769
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|78106564|gb|DV524982.1|DV524982
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|89762148|gb|DY689879.1|DY689879
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|148971932|gb|EE022716.2|EE022716
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|148966599|gb|EE017634.2|EE017634
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|78114582|gb|DV532970.1|DV532970
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|87153844|gb|DY398633.1|DY398633
EST:     CCGGTGACGCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|149101866|gb|EE287429.2|EE287429
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttccagccatctttcacttttttttttggttcctaatctttcactgtgtaaatctacatatagtttccatcaccactaacccttgctggaggaactaatgaaacggctttctcctcctaccttgcctgccgcag

- - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - CTCCTC