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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcaaccaacaatcttgttgcttattggttcttcgatttggtttctttccagcgaattaatgtcgcagcaattgtttttttttgtttactcgtttgtagGATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGGATGCGGCAGTACAGGTCGCAGCTCGAACAGGAG

Basic information

species Zea mays
transcript GRMZM2G165945_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|149078161|gb|EE166908.2|EE166908
EST:     ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGG                         GATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGG
genomic: ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGGgtaagctctc ... tcgtttgtagGATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGG
EST: gi|78087675|gb|DV516068.1|DV516068
EST:     ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGG                         GATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGG
genomic: ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGGgtaagctctc ... tcgtttgtagGATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGG
EST: gi|211090433|gb|FL069853.1|FL069853
EST:     ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGG                         GATGGGATAGGTAAGAGCAACGGTGGTNGGAAGAGAGATGATAGACACAGG
genomic: ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGGgtaagctctc ... tcgtttgtagGATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGG
EST: gi|211090439|gb|FL069859.1|FL069859
EST:     ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGG                         GATGGGATAGGTWAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGG
genomic: ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGGgtaagctctc ... tcgtttgtagGATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGG
EST: gi|71308123|gb|DR790286.1|DR790286
EST:     ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGG                         GATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGG
genomic: ACGGCAACGCTCCGGCGCCGGCGGTGGAGGCCAGTTGCTCCTGGTCCGGGgtaagctctc ... tcgtttgtagGATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttccagcgaattaatgtcgcagcaattgtttttttttgtttactcgtttgtagGATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGGATGCGGCAGTACAGGTCGCAGCTCGAACAGGAG
          aattaat  putative branch site (score: 3)
                              tttttttttgtttact  putative PPT
                         aattgtttttttttgt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcaaccaacaatcttgttgcttattggttcttcgatttggtttctttccagcgaattaatgtcgcagcaattgtttttttttgtttactcgtttgtagGATGGGATAGGTAAGAGCAACGGTGGTGGGAAGAGAGATGATAGACACAGGATGCGGCAGTACAGGTCGCAGCTCGAACAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC