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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcctctgcacgctctgccgattgggctcctgattctgtcccggctgcgtggattcgtgcgattgatgcgggggttttctcttatgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG

Basic information

species Zea mays
transcript GRMZM2G080917_T02
intron # 1
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|60356472|gb|DN223445.1|DN223445
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520810|gb|FL147604.1|FL147604
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520816|gb|FL147610.1|FL147610
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|148945591|gb|EC890845.2|EC890845
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520809|gb|FL147603.1|FL147603
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211455959|gb|FL147587.1|FL147587
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211455961|gb|FL147589.1|FL147589
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211455967|gb|FL147595.1|FL147595
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520807|gb|FL147601.1|FL147601
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520803|gb|FL147597.1|FL147597
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211523805|gb|FL147613.1|FL147613
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|148997618|gb|EE035837.2|EE035837
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211455963|gb|FL147591.1|FL147591
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520815|gb|FL147609.1|FL147609
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|50326049|gb|CO521175.1|CO521175
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520805|gb|FL147599.1|FL147599
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211455964|gb|FL147592.1|FL147592
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211455965|gb|FL147593.1|FL147593
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520813|gb|FL147607.1|FL147607
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|78106946|gb|DV525364.1|DV525364
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520814|gb|FL147608.1|FL147608
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520811|gb|FL147605.1|FL147605
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211455962|gb|FL147590.1|FL147590
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520806|gb|FL147600.1|FL147600
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGA-GGTTCTTCAAGCTCTGTGACCCCG
EST: gi|211520808|gb|FL147602.1|FL147602
EST:     CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCG                         ATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
genomic: CCGCGACTACAAAGCCCGCCGCGCCGGCATGATCAAGGCACTCACCACCGgtacgcctct ... tgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccggctgcgtggattcgtgcgattgatgcgggggttttctcttatgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG
                     gattgat  putative branch site (score: 4)
                                   ttttctcttatgct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcctctgcacgctctgccgattgggctcctgattctgtcccggctgcgtggattcgtgcgattgatgcgggggttttctcttatgctgtgcagATGTGGAGAGGTTCTTCAAGCTCTGTGACCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT