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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAGgtgtgaagttactaaatatgttgctctcctattcatctcttgacaccttcaattggttctgaactgttaagttttgccaacacctactgcag

Basic information

species Zea mays
transcript GRMZM2G124918_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|16926475|gb|BM079543.1|BM079543
EST:     GCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAG                         CGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGG
genomic: GCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAGgtgtgaagtt ... cctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGG
EST: gi|14243814|gb|BG841530.2|BG841530
EST:     GCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAG                         CGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGG
genomic: GCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAGgtgtgaagtt ... cctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGG
EST: gi|95107983|gb|EB740212.1|EB740212
EST:     GCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAG                         CGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGG
genomic: GCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAGgtgtgaagtt ... cctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGG
EST: gi|28984995|gb|BQ539599.2|BQ539599
EST:     GCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAG                         CGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGG
genomic: GCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAGgtgtgaagtt ... cctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGG

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: 46 (upstream exon), 43 (downstream exon)
Score: 19

ATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAGgtgtgaagtt ... cctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGGGAAGCAGCACGCAGTGCTGCGAGGGCAGCATTTTGACGAACCGTGTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

ATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAGgtgtgaagtt ... cctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGGGAAGCAGCACGCAGTGCTGCGAGGGCAGCATTTTGACGAACCGTGTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

ATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAGgtgtgaagtt ... cctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGGGAAGCAGCACGCAGTGCTGCGAGGGCAGCATTTTGACGAACCGTGTGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 97

ATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAGgtgtgaagtt ... cctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGGGAAGCAGCACGCAGTGCTGCGAGGGCAGCATTTTGACGAACCGTGTGTG