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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaatactctctcactccttttgtatacttcagtgacactccactaacatttttttccttgtaacctgaag

Basic information

species Zea mays
transcript GRMZM2G005082_T01
intron # 3
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|60397442|gb|DN230258.1|DN230258
EST:     GTTATGACACTTGCGTCTATTTGGCTGCCGG                         CAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
genomic: GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
EST: gi|71433996|gb|DR815046.1|DR815046
EST:     GTTATGACACTTGCGTCTATTTGGCTGCCGG                         CAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
genomic: GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
EST: gi|60355207|gb|DN222180.1|DN222180
EST:     GTTATGACACTTGCGTCTATTTGGCTGCCGG                         CAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
genomic: GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
EST: gi|60339494|gb|DN206467.1|DN206467
EST:     GTTATGACACTTGCGTCTATTTGGCTGCCGG                         CAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
genomic: GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
EST: gi|60343009|gb|DN209982.1|DN209982
EST:     GTTATGACACTTGCGTCTATTTGGCTGCCGG                         CAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
genomic: GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
EST: gi|60358660|gb|DN225633.1|DN225633
EST:     GTTATGACACTTGCGTCTATTTGGCTGCCGG                         CAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
genomic: GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
EST: gi|148943132|gb|EC888190.2|EC888190
EST:     GTTATGACACTTGCGTCTATTTGGCTGCCGG                         CAATAAGATGAGCACGACGAACTCAACATCTTTTCCAGCTCGCAGCGACTC
genomic: GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
EST: gi|60343691|gb|DN210664.1|DN210664
EST:     GTTATGACACTTGCGTCTATTTGGCTGCCGG                         CAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC
genomic: GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTC

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: 484

GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTCCGGTCCAGTCCCATGCGCCAAATGCTTCGCCACTTTGCTCCCCATGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 21

GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTCCGGTCCAGTCCCATGCGCCAAATGCTTCGCCACTTTGCTCCCCATGCTG


Block sizes: 48 (upstream exon), 22 (downstream exon)
Score: 2

GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTCCGGTCCAGTCCCATGCGCCAAATGCTTCGCCACTTTGCTCCCCATGCTG


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 6

GTTATGACACTTGCGTCTATTTGGCTGCCGGgtacgaaata ... taacctgaagCAATAAGATGAGCACGACGAACTCAACATCTCTTCCAGCTCGCAGCGACTCCGGTCCAGTCCCATGCGCCAAATGCTTCGCCACTTTGCTCCCCATGCTG