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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgggtctcgtcctctcctagttcctcggttccgtgccctccgtgatggccgtcgcggtcttgacggtatttcattgttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAACTGCATCTTCGTGTTCAAGTTCCGAACCAACTTCGGAGGCGGCAAGTCCA

Basic information

species Zea mays
transcript GRMZM2G029685_T01
intron # 1
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|211011481|gb|FL283787.1|FL283787
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGA-STCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|211008701|gb|FL283770.1|FL283770
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGA-STCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|211014258|gb|FL283800.1|FL283800
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|211008706|gb|FL283775.1|FL283775
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|211011487|gb|FL283793.1|FL283793
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGASSTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|211014263|gb|FL283805.1|FL283805
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|211014266|gb|FL283808.1|FL283808
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|211008700|gb|FL283769.1|FL283769
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|37376305|gb|CF624665.1|CF624665
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|211008710|gb|FL283779.1|FL283779
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|60397441|gb|DN230257.1|DN230257
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|211014259|gb|FL283801.1|FL283801
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCSAACGTCTCCAAG                         GCGGA-CTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
EST: gi|60355885|gb|DN222858.1|DN222858
EST:     AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAG                         GCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC
genomic: AGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAAC

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), 44 (downstream exon)
Score: 99

GGTGACGCTCCGCACACGCAAGTTCATGACCAACCGTCTTCTCTCCCGCAAGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAACTGCATCTTCGTGTTCAAGTTCCGAACCAACTTCGGAGGCGGCAAGTCCA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 81

GGTGACGCTCCGCACACGCAAGTTCATGACCAACCGTCTTCTCTCCCGCAAGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAACTGCATCTTCGTGTTCAAGTTCCGAACCAACTTCGGAGGCGGCAAGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GGTGACGCTCCGCACACGCAAGTTCATGACCAACCGTCTTCTCTCCCGCAAGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAACTGCATCTTCGTGTTCAAGTTCCGAACCAACTTCGGAGGCGGCAAGTCCA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 109

GGTGACGCTCCGCACACGCAAGTTCATGACCAACCGTCTTCTCTCCCGCAAGCAGTTCGTGCTCGAGGTCATCCACCCCGGCCGCCCCAACGTCTCCAAGgttgtgggtc ... gttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAACTGCATCTTCGTGTTCAAGTTCCGAACCAACTTCGGAGGCGGCAAGTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtgccctccgtgatggccgtcgcggtcttgacggtatttcattgttcgcgcagGCGGAGCTCAAGGAGAGGCTGGCGAAGATCTACGAGGTGAAGGACCCAAACTGCATCTTCGTGTTCAAGTTCCGAACCAACTTCGGAGGCGGCAAGTCCA
                           tcttgac  putative branch site (score: 109)
                                    tatttcatt  TA-rich tract