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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacattgctaccttgcagcttcttcttcgctattatttatgtcataaaaagagatctaactgggacactttttttctcctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT

Basic information

species Zea mays
transcript GRMZM2G029566_T02
intron # 9
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|76920585|gb|DV168249.1|DV168249
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|149099313|gb|EE185349.2|EE185349
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|31355627|gb|CD439984.1|CD439984
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GTCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|32851376|gb|CD991057.1|CD991057
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|148929744|gb|EC876669.2|EC876669
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|29545139|gb|CB605317.1|CB605317
EST:     CACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: CACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|211248919|gb|FL466732.1|FL466732
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|71328227|gb|DR800747.1|DR800747
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|78124352|gb|DV542736.1|DV542736
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|60346412|gb|DN213385.1|DN213385
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|83278342|gb|DV942350.1|DV942350
EST:     AGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: AGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|4730752|gb|AI649918.1|AI649918
EST:     TTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|211273143|gb|FL031466.1|FL031466
EST:     ATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: ATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|211059340|gb|FL474462.1|FL474462
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|91052882|gb|EB163300.1|EB163300
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|211273141|gb|FL031464.1|FL031464
EST:     TTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|149042086|gb|EE047064.2|EE047064
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|211273140|gb|FL031463.1|FL031463
EST:     TTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|148946153|gb|EC891447.2|EC891447
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|86465953|gb|DY232326.1|DY232326
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|211228559|gb|FL433551.1|FL433551
EST:     CGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: CGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
EST: gi|149076832|gb|EE165487.2|EE165487
EST:     TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA                         GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT
genomic: TACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAAgtatgacatt ... cctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttatgtcataaaaagagatctaactgggacactttttttctcctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT
                     atctaac  putative branch site (score: 2)
                                 cactttttttctcctt  putative PPT
         tcataaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacattgctaccttgcagcttcttcttcgctattatttatgtcataaaaagagatctaactgggacactttttttctcctttgaaagGCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA