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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactggtgaccattcctaatatttcttttttgcatttcgggaagcaaacatccattaatgttcccctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC

Basic information

species Zea mays
transcript GRMZM2G151268_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151268_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g01170.1 (Oryza sativa), 3'ss of exon 3
gtaactggtgaccattcctaatatttcttttttgcat-ttcgggaagcaaacatccattaatgttccc------------ctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC
||||| | | |||| || ||| |||| || || | || |||||| ||||| | | ||||| |||||| ||||||| ||||||||||||||||||||| | || || || ||||||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||
gtaacagtttgccatatctcataaatcttggatggatatgtccaaaatcaacatctgctaatgctgctattgattgttggctgttgcatttgtaaatcagCCAAAGGACTTCTGGAAGAATGAATTAAAGGATTTTTCTAACAAAAGCGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCCATGCTTCTAGATGTTC

upper sequence: GRMZM2G151268_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 3'ss of exon 3
gtaactggtgaccattcctaatatttcttttttgcat-ttcgggaagcaaacatccattaatgttccc------------ctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC
||||| | | |||| || ||| |||| || || | || |||||| ||||| | | ||||| |||||| ||||||| ||||||||||||||||||||| | || || || ||||||||||| |||||||||||||||||||||||||||||||| || ||||| |||||||||
gtaacagtttgccatatctcataaatcttggatggatatgtccaaaatcaacatctgctaatgctgctattgattgttggctgttgcatttgtaaatcagCCAAAGGACTTCTGGAAGAATGAATTAAAGGATTTTTCTAACAAAAGCGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGCCCCATGCTTCTAGATGTTC
















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|211533622|gb|FL412539.1|FL412539
EST:     GGGCGCAATTWAGTCACACAATGAWAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGG
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGG
EST: gi|9028689|gb|BE238729.1|BE238729
EST:     GGGCGCAATTAAGTCACACAATGAAAGTT-ACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAG
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAG
EST: gi|211029306|gb|FL370361.1|FL370361
EST:     GGGCGCAATTAAGTCACACAATGAA-GTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGATAGACTTCTCT
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCT
EST: gi|29945213|gb|CB815527.1|CB815527
EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA
EST: gi|211511056|gb|FL378831.1|FL378831
EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAMC-TG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAAC
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAAC
EST: gi|211355840|gb|FL403701.1|FL403701
EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGT
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGT
EST: gi|211317656|gb|FL416767.1|FL416767
EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAMC-TG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGA
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGA
EST: gi|211156585|gb|FL395419.1|FL395419
EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttcgggaagcaaacatccattaatgttcccctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC
                      cattaat  putative branch site (score: 3)
 ttcccctgttttgttt  CT-rich tract
 ttttgtttgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactggtgaccattcctaatatttcttttttgcatttcgggaagcaaacatccattaatgttcccctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG