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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaactatccccgttcatctgaactttctgctttcactcatgctgctgctactaactgtttctatttgatgttggcatactaacgctcagtttcgtcttggtattctcagGTAGTTGTGTCCATGGGGGACAAGGTTAATCCCTGGTGCCACTGCCATTGGCATAATCCTGCATGGAAATCCGACACTGAAAGTTGTGCCGGCGATCTCC

Basic information

species Zea mays
transcript GRMZM2G412430_T01
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|33466899|gb|CF243948.1|CF243948
EST:     GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
genomic: GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
EST: gi|211122803|gb|FL103632.1|FL103632
EST:     GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
genomic: GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
EST: gi|211122804|gb|FL103633.1|FL103633
EST:     GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
genomic: GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
EST: gi|91048773|gb|EB159191.1|EB159191
EST:     GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
genomic: GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
EST: gi|211122802|gb|FL103631.1|FL103631
EST:     GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
genomic: GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
EST: gi|93014831|gb|EB640351.1|EB640351
EST:     GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
genomic: GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
EST: gi|38688088|gb|CK145119.1|CK145119
EST:     GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
genomic: GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
EST: gi|211122805|gb|FL103634.1|FL103634
EST:     GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
genomic: GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
EST: gi|37420778|gb|CF648085.1|CF648085
EST:     GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG
genomic: GAAGTGAAGACTTAGCACAGTCTGTGCTCGTCAAGTGCCCTGGCACTCTGGCAGGATGCGGTGGCTCGGTCTTTCGGTGGCACTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttctatttgatgttggcatactaacgctcagtttcgtcttggtattctcagGTAGTTGTGTCCATGGGGGACAAGGTTAATCCCTGGTGCCACTGCCATTGGCATAATCCTGCATGGAAATCCGACACTGAAAGTTGTGCCGGCGATCTCC
                      tactaac  putative branch site (score: 0)
                                              tattctc  putative PPT
       tatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaactatccccgttcatctgaactttctgctttcactcatgctgctgctactaactgtttctatttgatgttggcatactaacgctcagtttcgtcttggtattctcagGTAGTTGTGTCCATGGGGGACAAGGTTAATCCCTGGTGCCACTGCCATTGGCATAATCCTGCATGGAAATCCGACACTGAAAGTTGTGCCGGCGATCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA