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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctccctctcctatctcctccctccctatctctcagcataatctcatattgcaacgatcaaatttag

Basic information

species Zea mays
transcript GRMZM2G031053_T01
intron # 12
splice site 5'
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|211261660|gb|FK945684.1|FK945684
EST:     TAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG                         GCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
genomic: TAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
EST: gi|211025431|gb|FL195734.1|FL195734
EST:     CAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG                         GCCACTGAAGCGAAGTCGAAAGAACCATGAGTCTGATTCGTTGGCTTTGAG
genomic: CAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCG-AAGAGCCATGAGTCTGATTCGTTGGCTTTGAG
EST: gi|87154018|gb|DY398807.1|DY398807
EST:     AACTTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG                         GCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
genomic: AACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
EST: gi|211025432|gb|FL195735.1|FL195735
EST:     AACTTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG                         GCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
genomic: AACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
EST: gi|18384448|gb|BM417647.1|BM417647
EST:     AACTTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG                         GCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
genomic: AACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
EST: gi|18649914|gb|BM498733.1|BM498733
EST:     AACTTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG                         GCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
genomic: AACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
EST: gi|211027876|gb|FL195737.1|FL195737
EST:     AACTTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG                         GCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
genomic: AACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
EST: gi|211025427|gb|FL195730.1|FL195730
EST:     CAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG                         GCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
genomic: CAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
EST: gi|22489641|gb|BU049564.1|BU049564
EST:     AACTTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG                         GCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG
genomic: AACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGG

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), 47 (downstream exon)
Score: 145

GAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGGGAGGAGATCAGATTACTGACTGATAACCTGGAGTCTATTAGAAGTGAAG


Block sizes: 34 (upstream exon), 47 (downstream exon)
Score: 52

GAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGGGAGGAGATCAGATTACTGACTGATAACCTGGAGTCTATTAGAAGTGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 56

GAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGGGAGGAGATCAGATTACTGACTGATAACCTGGAGTCTATTAGAAGTGAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 59

GAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAGgtatgtctcc ... tcaaatttagGCCACTGAAGCGAAGTCGAAGAGCCATGAGTCTGATTCGTTGGCTTTGAGGGAGGAGATCAGATTACTGACTGATAACCTGGAGTCTATTAGAAGTGAAG