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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgttccatatttcatgaagacgtcgaacatgcatctacaaatacatttaaattgaatggacgctttaatcatgcaatccttttatccgtttcttgtagGGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA

Basic information

species Zea mays
transcript GRMZM5G814279_T01
intron # 5
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|60359649|gb|DN226622.1|DN226622
EST:     GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG                         GGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
genomic: GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAGgtgagaaatg ... tttcttgtagGGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
EST: gi|60341355|gb|DN208328.1|DN208328
EST:     GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG                         GGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
genomic: GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAGgtgagaaatg ... tttcttgtagGGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
EST: gi|91871951|gb|EB401908.1|EB401908
EST:     GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG                         GGCACACAGCTAGAAGATGGGAACAGGCGTCTAAAAGAACAA
genomic: GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAGgtgagaaatg ... tttcttgtagGGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
EST: gi|91871952|gb|EB401909.1|EB401909
EST:     GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG                         GGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
genomic: GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAGgtgagaaatg ... tttcttgtagGGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
EST: gi|71312209|gb|DR792627.1|DR792627
EST:     GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG                         GGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
genomic: GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAGgtgagaaatg ... tttcttgtagGGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
EST: gi|60355305|gb|DN222278.1|DN222278
EST:     GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG                         GGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
genomic: GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAGgtgagaaatg ... tttcttgtagGGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttaaattgaatggacgctttaatcatgcaatccttttatccgtttcttgtagGGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA
                   ctttaat  putative branch site (score: 4)
                                 tccttttatccgtttc  putative PPT
     aaattgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgttccatatttcatgaagacgtcgaacatgcatctacaaatacatttaaattgaatggacgctttaatcatgcaatccttttatccgtttcttgtagGGCACACAGCTAGAAGATGAGAACAGGCGTCTAAAAGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC