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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgctttgctttgttaaattcgctcgccgtagcaagcagtagtaacccgacccggcggtattggtggtactgactgagacgcccgtccgtccttgtctttgcttttgcgtgatgcagGAGCACCGCTCGCCGCGGGCGTCTCACCGGACGTCGACGGGCTCACGGCCGTCGCTTCTGTCGGAGAACGTCGGTGCCACCGACGACTCGGACAAGTCGA

Basic information

species Zea mays
transcript GRMZM2G043470_T02
intron # 4
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|76926181|gb|DV170751.1|DV170751
EST:     TGGGGCAGATCGTGCACATGCTCGAGGGTGACGAGTTCCCCTTCCGCACG                         GAGCACCGCTCGCCGCGGGCGTCTCACCGGACGTCGACGGGCTCACGGCCG
genomic: TGGGGCAGATCGTGCACATGCTCGAGGGTGACGAGTTCCCCTTCCGCACGgtattgcttt ... cgtgatgcagGAGCACCGCTCGCCGCGGGCGTCTCACCGGACGTCGACGGGCTCACGGCCG
EST: gi|76926179|gb|DV170750.1|DV170750
EST:     TGGGGCAGATCGTGCACATGCTCGAGGGTGACGAGTTCCCCTTCCGCACG                         GAGCACCGCTCGCCGCGGGCGTCTCACCGGACGTCGACGGGCTCACGGCCG
genomic: TGGGGCAGATCGTGCACATGCTCGAGGGTGACGAGTTCCCCTTCCGCACGgtattgcttt ... cgtgatgcagGAGCACCGCTCGCCGCGGGCGTCTCACCGGACGTCGACGGGCTCACGGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggtactgactgagacgcccgtccgtccttgtctttgcttttgcgtgatgcagGAGCACCGCTCGCCGCGGGCGTCTCACCGGACGTCGACGGGCTCACGGCCGTCGCTTCTGTCGGAGAACGTCGGTGCCACCGACGACTCGGACAAGTCGA
     tactgac  putative branch site (score: 1)
                                       cttttgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgctttgctttgttaaattcgctcgccgtagcaagcagtagtaacccgacccggcggtattggtggtactgactgagacgcccgtccgtccttgtctttgcttttgcgtgatgcagGAGCACCGCTCGCCGCGGGCGTCTCACCGGACGTCGACGGGCTCACGGCCGTCGCTTCTGTCGGAGAACGTCGGTGCCACCGACGACTCGGACAAGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA