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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCGCTTTCGGTGGCTTCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgcgctatcacgagtacttgcccagccaagtgtgttctcggcttaccaaagtttgtgctgtccgcag

Basic information

species Zea mays
transcript GRMZM5G824600_T01
intron # 2
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|161587047|gb|EY954209.1|EY954209
EST:     CGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAGAAG                         GAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATC
genomic: CGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATC
EST: gi|6526663|gb|AW215954.1|AW215954
EST:     TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAG                         GAAATTAAGGTGGACGAGTACATTACGCCCAACATGAACCTGGCTGACATC
genomic: TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATC
EST: gi|91873469|gb|EB403426.1|EB403426
EST:     TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAG                         GAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATC
genomic: TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATC
EST: gi|91053435|gb|EB163853.1|EB163853
EST:     TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAG                         GAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATC
genomic: TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATC
EST: gi|166698096|gb|EG135847.1|EG135847
EST:     TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAGAAG                         GAAATTAAGGTGGACGAGTAC
genomic: TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTAC
EST: gi|83278957|gb|DV942965.1|DV942965
EST:     TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAG                         GAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATC
genomic: TCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATC

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), 49 (downstream exon)
Score: 840

ATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCGCTTTCGGTGGCTTCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATCAACGACGCCTTCCACCTGCTGCACGAAGGTGGCTGTCTGCGTTGTGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 852

ATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCGCTTTCGGTGGCTTCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATCAACGACGCCTTCCACCTGCTGCACGAAGGTGGCTGTCTGCGTTGTGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 541

ATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCGCTTTCGGTGGCTTCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATCAACGACGCCTTCCACCTGCTGCACGAAGGTGGCTGTCTGCGTTGTGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 534

ATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCGCTTTCGGTGGCTTCAAGAGCCGGACCCAGGTCCCATGGCTTGTTGACAAGTACATGAAAAAGgtactgctgc ... ctgtccgcagGAAATTAAGGTGGACGAGTACATTACGCACAACATGAACCTGGCTGACATCAACGACGCCTTCCACCTGCTGCACGAAGGTGGCTGTCTGCGTTGTGTGC