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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggggatccacaaattaggtagctaaattgaagtcacccgcgctaagtcgcaaaagcagctatcaacctctctgaccgactctattcttgcttcccctctccccttctgtatcttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCCCATGAAGAGCGACTCAT

Basic information

species Zea mays
transcript GRMZM2G130149_T04
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|29576784|gb|CB616896.1|CB616896
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGTCAAAGTATC-------A--G                         GGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
EST: gi|71317839|gb|DR795686.1|DR795686
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATC-------A--G                         GGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
EST: gi|211146081|gb|FL408662.1|FL408662
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGG---G----                         --CTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
EST: gi|211085128|gb|FL402170.1|FL402170
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGG                         GGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
EST: gi|76911849|gb|DV164464.1|DV164464
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATC-------A--G                         GGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
EST: gi|71419155|gb|DR804670.1|DR804670
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATC-------A--G                         GGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
EST: gi|37416590|gb|CF645947.1|CF645947
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGG---G----                         --CTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
EST: gi|13558921|gb|BG550276.1|BG550276
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGG---G----                         --CTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
EST: gi|211232178|gb|FL407887.1|FL407887
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGG                         GGCTCAACCGGACAGGCAAGAGCCTGCCGGCTGCGCTGGGTCAACTACCTC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGC-TGCCGGCTGCGCTGGGTCAACTACCTC
EST: gi|211343657|gb|FL392034.1|FL392034
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGG                         GGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
EST: gi|50337394|gb|CO532520.1|CO532520
EST:     GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGG---G----                         --CTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC
genomic: GTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTTTGAGGGgtggggatcc ... cttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctgaccgactctattcttgcttcccctctccccttctgtatcttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCCCATGAAGAGCGACTCAT
  ctctgac  putative branch site (score: 3)
            ctctattcttgcttcc  putative PPT
               tattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggggatccacaaattaggtagctaaattgaagtcacccgcgctaagtcgcaaaagcagctatcaacctctctgaccgactctattcttgcttcccctctccccttctgtatcttcatgcagGGCTCAACCGGACAGGCAAGAGCTGCCGGCTGCGCTGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCCCATGAAGAGCGACTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA