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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctccatttgattgcttccgagctatgcagatttagtagtatattttattcctctggaaaacattgctgtacaggttcctgtatggtgacacataatggattgcgatagcattctgtgctgttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG

Basic information

species Zea mays
transcript GRMZM2G025854_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025854_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 2
gttctccatttgattgcttccgagctatgcagatttagtagtatattttattcctctggaaaacattgctgtacaggttcctgtat-ggtgacacataatggattgcg-atagcattctgtgctgttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
                          | | |      ||  ||| ||  |      || |     || |  |||   ||  | | | ||      | |||    | |  | | | || | || |||||||||||||||||||| |||||||||||||| ||||| |||||||||||||||
------------------------gcaagtaccagctgttttatgttccacgatcttgcacccatttccgatacgctttttttttttgggtgtgtacaattcccttcatacatctttttttggtgttcttttcagGTGAAAGTGTTCCAGCAGGAGAATTACCTCGCTAATTGGATTCAG
















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|211456111|gb|FL153032.1|FL153032
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCNTANT-GGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGC-TAATTGGATTCAG
EST: gi|211456112|gb|FL153033.1|FL153033
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211022165|gb|FL153038.1|FL153038
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTGTTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211456113|gb|FL153034.1|FL153034
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTGTTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211022172|gb|FL153045.1|FL153045
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAGAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211024619|gb|FL153052.1|FL153052
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211022174|gb|FL153047.1|FL153047
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211456114|gb|FL153035.1|FL153035
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTGTTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211022173|gb|FL153046.1|FL153046
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211456115|gb|FL153036.1|FL153036
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTGTTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|89759099|gb|DY688027.1|DY688027
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|50333167|gb|CO528293.1|CO528293
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|74238594|gb|DT646508.1|DT646508
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211022178|gb|FL153051.1|FL153051
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211022177|gb|FL153050.1|FL153050
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211022175|gb|FL153048.1|FL153048
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
EST: gi|211022168|gb|FL153041.1|FL153041
EST:     CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG                         GTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
genomic: CCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGgttctccatt ... ttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgtatggtgacacataatggattgcgatagcattctgtgctgttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG
                                          ctgttcttttc  CT-rich tract
              acataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctccatttgattgcttccgagctatgcagatttagtagtatattttattcctctggaaaacattgctgtacaggttcctgtatggtgacacataatggattgcgatagcattctgtgctgttcttttcagGTGAAAGTATTCCAGCAGGAGAACTACCTTGCTAATTGGATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA