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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggtatatatatttacacatcgttcttttgccagagctacacagctgtagtattgtttctggtgcggacaaaatgctaatgtttttaaactggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAACCTTCAGAAGAATACGGTTGCTTCGATATTTCATACTTCA

Basic information

species Zea mays
transcript GRMZM2G086484_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|60400869|gb|DN233676.1|DN233676
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|83278326|gb|DV942334.1|DV942334
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|6022289|gb|AW067217.1|AW067217
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|19770206|gb|BQ034927.1|BQ034927
EST:     CAGAGAAAGCATCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|19351231|gb|BM895763.1|BM895763
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|19770249|gb|BQ034970.1|BQ034970
EST:     CAGAGAAAGCATCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|18649762|gb|BM498581.1|BM498581
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|60355351|gb|DN222324.1|DN222324
EST:     CAGAGAAAGCATCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|19769590|gb|BQ034311.1|BQ034311
EST:     CAGAGAAAGCATCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|71311912|gb|DR792439.1|DR792439
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|87153971|gb|DY398760.1|DY398760
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|211121251|gb|FL454290.1|FL454290
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|78024638|gb|DV493025.1|DV493025
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|71762836|gb|DR960773.1|DR960773
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|19351230|gb|BM895762.1|BM895762
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|71315320|gb|DR794272.1|DR794272
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|22491304|gb|BU051227.1|BU051227
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|19822448|gb|BQ048472.1|BQ048472
EST:     CAGAGAAAGCATCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC
EST: gi|37374586|gb|CF623668.1|CF623668
EST:     CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGAT                         GTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAT
genomic: CAGAGAAAGCTTCCAAAGAATCCACTCCTACCATTGTTATAAGAAACGATgtatgttttc ... ctggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtagtattgtttctggtgcggacaaaatgctaatgtttttaaactggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAACCTTCAGAAGAATACGGTTGCTTCGATATTTCATACTTCA
                             tgctaat  putative branch site (score: 2)
                                taatgtttttaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggtatatatatttacacatcgttcttttgccagagctacacagctgtagtattgtttctggtgcggacaaaatgctaatgtttttaaactggtagcagGTTGGTAAAATCCTCCTGAATGCTCTGATCTACAAGGGGATAAAAATGAACCTTCAGAAGAATACGGTTGCTTCGATATTTCATACTTCA

- - - - - - - - - - - - -cttttgc
- - - - - - - - - - - - - - - - - - gctacac
- - - - - - - - - - - - - - - - - - - - - - gctgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgcgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg