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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACCATGCTTGTGTTTTCTGATCATGTCCGGAGCTTTGTGAACCCTGTTTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctacattcctgactactccaattcagtgctactttagttctgaatctaaactaatgtattttaagcttgtatagcttgtccagtttgttatttg...

Basic information

species Zea mays
transcript GRMZM5G891056_T02
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|211516010|gb|FL160576.1|FL160576
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516008|gb|FL160574.1|FL160574
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTTGTC-AGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCA
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTT-GTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCA
EST: gi|211516009|gb|FL160575.1|FL160575
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516003|gb|FL160569.1|FL160569
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516006|gb|FL160572.1|FL160572
EST:     TTGGACATCGTCAGGCAGACCAGCTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516004|gb|FL160570.1|FL160570
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTTGT-ATTTGCCAGTTGAGCAAGCACTGGGACTGAGACCA
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTT-GTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCA
EST: gi|211516012|gb|FL160578.1|FL160578
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516002|gb|FL160568.1|FL160568
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG

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: 21 (upstream exon), 48 (downstream exon)
Score: 26

GAGACCATGCTTGTGTTTTCTGATCATGTCCGGAGCTTTGTGAACCCTGTTTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA


Block sizes: 31 (upstream exon), 46 (downstream exon)
Score: 11

GAGACCATGCTTGTGTTTTCTGATCATGTCCGGAGCTTTGTGAACCCTGTTTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA


Block sizes: 26 (upstream exon), 46 (downstream exon)
Score: 10

GAGACCATGCTTGTGTTTTCTGATCATGTCCGGAGCTTTGTGAACCCTGTTTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA


Block sizes: 26 (upstream exon), 48 (downstream exon)
Score: 8

GAGACCATGCTTGTGTTTTCTGATCATGTCCGGAGCTTTGTGAACCCTGTTTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA