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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttctcttgctttgtgtgtgggcaaccaagatcagcacaagactgtgtcagctaacagcggcaatggcgggaaaccaaacaaaaacaaaaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACCTCGTCGCGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCG

Basic information

species Zea mays
transcript GRMZM2G046743_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g03350.1 (Oryza sativa), 3'ss of exon 1
tctttctcttgctttgtgtgtgggcaaccaagatcagcacaagactgtgtcagctaacagcggcaa--tggcggg---aaaccaaacaaaaacaaaa----acttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACCTCGTCGCGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCG
    | |||||| | | |||| | |       |  || ||  |      ||| | | | |  ||||  | ||  |    ||  || |||   | |||      | ||||||||   ||||||| | ||||||||| |||||||| ||||| || ||||| |||||  ||||||||||||||||||||||||||||||||||||||||||
----tttcttgcatagagtgtagtctgt----actagtact-gttgagatcaaccatctgtagcaaagtagcaagcttgaattaatcaatggcgaaacaatggtggcagGATGGCCGGAGCGCGCAGGAGAAGGCGATCGACGACTGGCTTCCCATCACGTCGTCCAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCG
















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|149000253|gb|EE037406.2|EE037406
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|71428207|gb|DR809257.1|DR809257
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|50336114|gb|CO531240.1|CO531240
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|74244994|gb|DT652908.1|DT652908
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|94478524|gb|EB707482.1|EB707482
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|88757930|gb|DY542071.1|DY542071
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|74235966|gb|DT643880.1|DT643880
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|76285930|gb|DV025498.1|DV025498
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|94473958|gb|EB702916.1|EB702916
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|149078147|gb|EE166895.2|EE166895
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|88753088|gb|DY537229.1|DY537229
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
EST: gi|78092655|gb|DV521029.1|DV521029
EST:     CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAG                         GATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC
genomic: CGGCCATGGAGACCCAAGCGCCGGAGAAGGAGAACTACCTCCCTGAAAAGgtaccgtctc ... aaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcagctaacagcggcaatggcgggaaaccaaacaaaaacaaaaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACCTCGTCGCGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCG
      agctaac  putative branch site (score: 2)
                                 aaacaaaaacaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttctcttgctttgtgtgtgggcaaccaagatcagcacaagactgtgtcagctaacagcggcaatggcgggaaaccaaacaaaaacaaaaacttgcagGATGCGAGGAGCGCACGGGAGAAGGCCATCGACGAGTGGCTCCCGATCACCTCGTCGCGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG