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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGGTAGCCAGGGTCAGAAATTAGATTCAGTTCTAGCAAAACCTTTGAAGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttcaacttcagtatataatgcaagcaaatatgaatgttttcccaaatgttatatcaagtggtttttcctgaacag

Basic information

species Zea mays
transcript GRMZM5G825854_T02
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825854_T01 (Zea mays), 5'ss of exon 23
lower sequence: LOC_Os08g34970.1 (Oryza sativa), 5'ss of exon 23
CTCTGGTAGCCAGGGTCAGAAATTAGATTCAGTTCTAGCAAAACCTTTGAAGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttcaacttcagtatataatgcaag-caaat-atgaatgttttcccaaatgttatatcaagtggtttttcctgaacag
||| |||||||||||||||||||| ||||| ||||| || |||||  | ||||||||||| ||||||||||||||||| ||||| ||||| ||||| |||||   ||   |          || ||||||| || || |||  | |||| |||  | ||  || ||      |||    |    
CTCGGGTAGCCAGGGTCAGAAATTGGATTCTGTTCTGGCTAAACCCCTTAAGACTCAAGCATTTGCTTCTCCTGATAAGGTTGCGGAGCTGGTTCAAAAGgtattttccaag---------atgatgcaagtcagatcatgcttctttttccatgtatttcataaaaatccctttttgtag---
















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|37392536|gb|CF633520.1|CF633520
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|37383203|gb|CF628592.1|CF628592
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|37389357|gb|CF631898.1|CF631898
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|86468964|gb|DY235334.1|DY235334
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|93281266|gb|EB673530.1|EB673530
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|6194992|gb|AW147096.1|AW147096
EST:     AGACTCAAGCTTTTGCTTTTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|211285685|gb|FL478243.1|FL478243
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|60348401|gb|DN215374.1|DN215374
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|32929996|gb|CF034808.1|CF034808
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|4776079|gb|AI665082.1|AI665082
EST:     TTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTCCCCCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: TTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|71432707|gb|DR813757.1|DR813757
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|60348441|gb|DN215414.1|DN215414
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|60341619|gb|DN208592.1|DN208592
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|60340575|gb|DN207548.1|DN207548
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGATAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|149104240|gb|EE289676.2|EE289676
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|211362787|gb|FL472151.1|FL472151
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|148953559|gb|EC898910.2|EC898910
EST:     AGACTCAAGCTTTTGCTTTTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|71432706|gb|DR813756.1|DR813756
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
EST: gi|211224223|gb|FK968322.1|FK968322
EST:     AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAG                         GTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG
genomic: AGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttc ... tcctgaacagGTTGCCGCTGCCATTCAACAAGATTTGCCCAAAGTAATGACCAAGATGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGGTAGCCAGGGTCAGAAATTAGATTCAGTTCTAGCAAAACCTTTGAAGACTCAAGCTTTTGCTTCTCCTGATAAAGTTGCTGAGCTAGTTCAGAAGgtgccttttcaacttcagtatataatgcaagcaaatatgaatgttttcccaaatgttatatcaagtggtttttcctgaacag

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