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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgctttgctgtcatagagctagcgtcgagcataacttcatgcttggatcgtatgcttattgttcctcaatttcacgcacagtcatttttctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACACTGACAGCCTCCATGTTGCTAGAGGATTGTCTCATCCTGGGCTTTCGTCA

Basic information

species Zea mays
transcript GRMZM2G136389_T03
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|211505073|gb|FK974741.1|FK974741
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|89247752|gb|DY619538.1|DY619538
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|78114509|gb|DV532898.1|DV532898
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|76291396|gb|DV030964.1|DV030964
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|211505075|gb|FK974743.1|FK974743
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|89758710|gb|DY687791.1|DY687791
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|50323554|gb|CO518680.1|CO518680
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGA--TGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|18963822|gb|BM660649.1|BM660649
EST:     GCTTCCTCCACCGGCGCCTCGCGTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGGCAC
genomic: GCTTCCTCCACCGGCGCCTCGC-TACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|71431215|gb|DR812265.1|DR812265
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|101382964|gb|EB813535.1|EB813535
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|91878484|gb|EB408441.1|EB408441
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|91876453|gb|EB406410.1|EB406410
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|94472235|gb|EB701193.1|EB701193
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|87153075|gb|DY397864.1|DY397864
EST:     CGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGGCAC
genomic: CGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|71429124|gb|DR810174.1|DR810174
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|71307824|gb|DR790133.1|DR790133
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
EST: gi|149009815|gb|EE041700.2|EE041700
EST:     TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTAT                         GAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC
genomic: TTCCCCCGTGGACGAAGCTTCCTCCACCGGCGCCTCGCTACCTCGCCTATgtgagcactt ... tctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatcgtatgcttattgttcctcaatttcacgcacagtcatttttctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACACTGACAGCCTCCATGTTGCTAGAGGATTGTCTCATCCTGGGCTTTCGTCA
                                      tcatttttctctccc  CT-rich tract
            ttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgctttgctgtcatagagctagcgtcgagcataacttcatgcttggatcgtatgcttattgttcctcaatttcacgcacagtcatttttctctcccagGAAAGATGAATCTGTGATTTCCACAGATGGTGGAAATGAGGAGACAGACACTGACAGCCTCCATGTTGCTAGAGGATTGTCTCATCCTGGGCTTTCGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
cttgctt
- - - -tgctgtc
- - - - - - - - - - - - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -atgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacgcac