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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagttccacacactttaaatctacatgttcagatgctcttctcacctgttatgcttattgtttcagcattttgtacatcaaagccttttctttcttgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG

Basic information

species Zea mays
transcript GRMZM2G131667_T04
intron # 2
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|20208213|gb|BQ134302.1|BQ134302
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTTCATCACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|211365709|gb|FL031158.1|FL031158
EST:     TGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|32797174|gb|CD949410.1|CD949410
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTA
EST: gi|91877199|gb|EB407156.1|EB407156
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|4776649|gb|AI665652.1|AI665652
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTCGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|44900457|gb|CK827002.1|CK827002
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA
EST: gi|5006220|gb|AI712282.1|AI712282
EST:     TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGNAG                         GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACNCA
genomic: TATCTATACTCACTGATTATGAAATTGCAGAGGACTACCTCGACTGGGAGgtatagttcc ... tgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttattgtttcagcattttgtacatcaaagccttttctttcttgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG
                                 ccttttctttcttgt  CT-rich tract
     tattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagttccacacactttaaatctacatgttcagatgctcttctcacctgttatgcttattgtttcagcattttgtacatcaaagccttttctttcttgtgaatcagGTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG