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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcatttgtgttcctgcttctatgttattctttgatgatgttgttgcatggtatcaaagagaatttattttacaaagtgaataagtgatgccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCCCCCAAAACTGCTGACGATAGTGATGATGATGACACACTGGAAATCTGGG

Basic information

species Zea mays
transcript GRMZM2G092497_T04
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|78088679|gb|DV517072.1|DV517072
EST:     GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG                         GAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
genomic: GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
EST: gi|78109829|gb|DV528245.1|DV528245
EST:     GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG                         GAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
genomic: GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
EST: gi|28873635|gb|CB329598.1|CB329598
EST:     GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG                         GAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
genomic: GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
EST: gi|211528668|gb|FL445662.1|FL445662
EST:     GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG                         GAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
genomic: GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
EST: gi|71325873|gb|DR799620.1|DR799620
EST:     GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG                         GAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
genomic: GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
EST: gi|76913046|gb|DV164985.1|DV164985
EST:     GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG                         GAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
genomic: GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
EST: gi|71447185|gb|DR828235.1|DR828235
EST:     GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG                         GAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
genomic: GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
EST: gi|74238865|gb|DT646779.1|DT646779
EST:     GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG                         GAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
genomic: GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
EST: gi|89762158|gb|DY689885.1|DY689885
EST:     GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG                         GAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC
genomic: GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 8

GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCCCCCAAAACTGCTGACGATAGTGATGATGATGACACACTGGAAATCTGGG


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 7

GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCCCCCAAAACTGCTGACGATAGTGATGATGATGACACACTGGAAATCTGGG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 10

GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAGgtattcattt ... ccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCCCCCAAAACTGCTGACGATAGTGATGATGATGACACACTGGAAATCTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatggtatcaaagagaatttattttacaaagtgaataagtgatgccaaatgcagGAACTAGGCAATGACCTCAAAGTGGATAATGACTTTGCTTCTAGTTGTGCCCCCAAAACTGCTGACGATAGTGATGATGATGACACACTGGAAATCTGGG
                aatttattttacaaag  TA-rich tract