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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgggttgaacttatgttgatttcactctctgaatgctttaggcatgtgctgagtctagcactggttaagctttcttttgaaactagtatcttatcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCTGACATTGATAGGAGTAATTTTGATTCATCTGATCAGTCTGCAAATGTCA

Basic information

species Zea mays
transcript GRMZM2G000749_T02
intron # 11
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|21987416|gb|BQ778944.1|BQ778944
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|211021453|gb|FL457596.1|FL457596
EST:     ATGCCTTTGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAG
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAG
EST: gi|60341236|gb|DN208209.1|DN208209
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|149097304|gb|EE183133.2|EE183133
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|211203712|gb|FL472035.1|FL472035
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|71761192|gb|DR959129.1|DR959129
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|89246871|gb|DY618657.1|DY618657
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|22543109|gb|BU093547.1|BU093547
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT

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: 49 (upstream exon), 48 (downstream exon)
Score: 119

CAATCTTGAGCTAATTGCTTACACTGTCTGGAATGCACTTGAGTATTCTTATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCTGACATTGATAGGAGTAATTTTGATTCATCTGATCAGTCTGCAAATGTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 183

CAATCTTGAGCTAATTGCTTACACTGTCTGGAATGCACTTGAGTATTCTTATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCTGACATTGATAGGAGTAATTTTGATTCATCTGATCAGTCTGCAAATGTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 287

CAATCTTGAGCTAATTGCTTACACTGTCTGGAATGCACTTGAGTATTCTTATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCTGACATTGATAGGAGTAATTTTGATTCATCTGATCAGTCTGCAAATGTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 185

CAATCTTGAGCTAATTGCTTACACTGTCTGGAATGCACTTGAGTATTCTTATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCTGACATTGATAGGAGTAATTTTGATTCATCTGATCAGTCTGCAAATGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagtctagcactggttaagctttcttttgaaactagtatcttatcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCTGACATTGATAGGAGTAATTTTGATTCATCTGATCAGTCTGCAAATGTCA
                                        tcttatcttct  CT-rich tract
                      tttctttt  TA-rich tract