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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgtgaagagtgtagaagcactttttccctaacggtgtgctatttctcaggctattatggttcattggcattcccctcagttttaacttttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCTCTCAATGGTGCTGGTCTTTGTCCTGCTAGTAGATCATTTAGCACCCAGG

Basic information

species Zea mays
transcript GRMZM2G040209_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|211169299|gb|FL375027.1|FL375027
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|78086164|gb|DV514557.1|DV514557
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211504997|gb|FL428972.1|FL428972
EST:     CGATGCGACGGGCGCTCCTCAGATCGGTCGACTTCTCCCCCGACAGCAAG                         GCTGCAGTTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|37416811|gb|CF646057.1|CF646057
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|28910304|gb|CB331372.1|CB331372
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211225728|gb|FL398690.1|FL398690
EST:     CGATGCGACGGGCGCTCCTCAGATCGGTCGACTTCTCCCCCGACAGCAAG                         GCTGCAGTTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211360524|gb|FL385277.1|FL385277
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|60345785|gb|DN212758.1|DN212758
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|149080018|gb|EE169038.2|EE169038
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211496244|gb|FL383704.1|FL383704
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211279377|gb|FL428423.1|FL428423
EST:     GCTGCGACGGGCGCTCCTCAGATCGGSTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: GCTGCGACGGGCGCTCCTCAGATCGG-TCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211506477|gb|FL386350.1|FL386350
EST:     CGATGCGACGGGCGCTCCTCAGATCGGTCGACTTCTCCCCCGACAGCAAG                         GCTGCAGTTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211413498|gb|FL407164.1|FL407164
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211438872|gb|FL372183.1|FL372183
EST:     CGATGCGACGGGCGCTCCTCAGATCGGTCGACTTCTCCCCCGACAGCAAG                         GCTGCAGTTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211498787|gb|FL369824.1|FL369824
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|71318463|gb|DR795997.1|DR795997
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211125424|gb|FL376741.1|FL376741
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211240619|gb|FL389150.1|FL389150
EST:     CGATGCGACGGGCGCTCCTCAGATCGGTCGACTTCTCCCCCGACAGCAAG                         GCTGCAGTTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211201667|gb|FL383393.1|FL383393
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211464176|gb|FL410755.1|FL410755
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCGACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211060366|gb|FL403446.1|FL403446
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|211065293|gb|FL377931.1|FL377931
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|9952646|gb|BE639334.1|BE639334
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCGACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
EST: gi|31250314|gb|CD219338.1|CD219338
EST:     CGCTGCGACGGGCGCTCCTCAGATCGGTCGACTTCTCCCCCGACAGCAAG                         GCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT
genomic: CGCTGCGACGGGCGCTCCTCAGATCGGTCAACTTCTCCCCCGACAGCAAGgtccgctccc ... tttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcaggctattatggttcattggcattcccctcagttttaacttttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCTCTCAATGGTGCTGGTCTTTGTCCTGCTAGTAGATCATTTAGCACCCAGG
                                     ttttaac  putative branch site (score: 2)
                                     ttttaacttttttttc  CT-rich tract
                                   agttttaacttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgtgaagagtgtagaagcactttttccctaacggtgtgctatttctcaggctattatggttcattggcattcccctcagttttaacttttttttcagGCTGCAATTGAGTACTTTTATTCTTTCTCAAGGGCACAGTCTGCTTGTTCTCTCAATGGTGCTGGTCTTTGTCCTGCTAGTAGATCATTTAGCACCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - gaagcac
- - - - - - - - - - - - - - - - - - -tgtgcta