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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctattttaagcagtatctttatttacacagcctcacctatgcacagtcccatacttcctttgtttggctgcaccctaatccacataggtgcattggagtgcagccaaacaagtcattttattacctcactggctactaacgtgctactgatattctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG

Basic information

species Zea mays
transcript GRMZM2G058910_T01
intron # 16
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|87156017|gb|DY400806.1|DY400806
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|30031854|gb|CB833705.1|CB833705
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCCCTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|71768892|gb|DR966829.1|DR966829
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|33102453|gb|CF062413.1|CF062413
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGT
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGT
EST: gi|60396043|gb|DN228913.1|DN228913
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATGCCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|60351631|gb|DN218604.1|DN218604
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|16377225|gb|BI991828.1|BI991828
EST:     CGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTGCGAGAAAGTACTAATGAC
genomic: CGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|60352256|gb|DN219229.1|DN219229
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|26559777|gb|CA832012.1|CA832012
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|33101846|gb|CF061806.1|CF061806
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGT
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGT
EST: gi|87157808|gb|DY402597.1|DY402597
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|84977217|gb|DW475639.1|DW475639
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|24767313|gb|CA402457.1|CA402457
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|32941635|gb|CF046454.1|CF046454
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGT
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGT
EST: gi|31359889|gb|CD444246.1|CD444246
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|32851026|gb|CD990707.1|CD990707
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|22935980|gb|BU572255.1|BU572255
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC
EST: gi|32850827|gb|CD990508.1|CD990508
EST:     CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAG                         TCTTGCACACTCTGA
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGA
EST: gi|67016167|gb|CO444916.1|CO444916
EST:     CTTGGTGCAGTCTCAAACACCGCTTCATACCTTCGCCTTTGGGCTCTGAG                         TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAACCACTTATGAC
genomic: CTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGAC

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 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 184

AGTTCGGTGAAGTTTTTGTTCACCAACTGATTCACACGATAGAATTTGTTCTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 424

AGTTCGGTGAAGTTTTTGTTCACCAACTGATTCACACGATAGAATTTGTTCTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 391

AGTTCGGTGAAGTTTTTGTTCACCAACTGATTCACACGATAGAATTTGTTCTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 318

AGTTCGGTGAAGTTTTTGTTCACCAACTGATTCACACGATAGAATTTGTTCTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctat ... ctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtcattttattacctcactggctactaacgtgctactgatattctcctttcagTCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG
                                         tattctcctttc  CT-rich tract
     attttatta  TA-rich tract