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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagtcatgcgcactgttgttacgctttctgtatgctgaatttaggcagcatgtagtagcgctactgatattcggttacctatttcatgggtttt...

Basic information

species Zea mays
transcript GRMZM2G069758_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|18166331|gb|BM336170.1|BM336170
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|33097992|gb|CF057952.1|CF057952
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|32823768|gb|CD963490.1|CD963490
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|33096068|gb|CF056062.1|CF056062
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|8102609|gb|AW927412.1|AW927412
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTTTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|17931888|gb|BM268848.1|BM268848
EST:     ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|67022839|gb|CO451588.1|CO451588
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|40303606|gb|CK347993.1|CK347993
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|16922789|gb|BM075781.1|BM075781
EST:     ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA

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: 43

AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 176

AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 240

AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 89

AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC