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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAACAATGGGTCTCCTTGGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAGgtgcagttaatagttgattctacttagcttcaaattgaatttgcttacgttaagcactaagttattctgtgattcatttgtgttaaagttcttttgaaac...

Basic information

species Zea mays
transcript GRMZM2G157621_T03
intron # 15
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|60348856|gb|DN215829.1|DN215829
EST:     GGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAG                         GATAGCTTTGGTCGGGCGGGTGNNNNNNNTAAAGAAGCACTCAAGATGTCA
genomic: GGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAGgtgcagttaa ... gtcaatgcagGATAGCTTTGGTCGGGCGGGTGAAAAAAATAAAGAAGCACTCAAGATGTCA
EST: gi|60397550|gb|DN230366.1|DN230366
EST:     GGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAG                         GATAGCTTTGGTCGGGCGGGTGNNNNNNNTAAAGAAGCACTCAAGATGTCA
genomic: GGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAGgtgcagttaa ... gtcaatgcagGATAGCTTTGGTCGGGCGGGTGAAAAAAATAAAGAAGCACTCAAGATGTCA
EST: gi|31356419|gb|CD440776.1|CD440776
EST:     GGCTCAAGTTTTCATACAGCCAAGCAGCAATACTTGACCTTGCATTTCAG                         GATAGCTTTGGTCGGGTGGGTGNNNNNNNTAAAGAAGCACTCAAGATGTCA
genomic: GGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAGgtgcagttaa ... gtcaatgcagGATAGCTTTGGTCGGGCGGGTGAAAAAAATAAAGAAGCACTCAAGATGTCA

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: 47 (upstream exon), 47 (downstream exon)
Score: 107

TCAAACAATGGGTCTCCTTGGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAGgtgcagttaa ... gtcaatgcagGATAGCTTTGGTCGGGCGGGTGAAAAAAATAAAGAAGCACTCAAGATGTCAAAGCATATAACTAAACTTTTCCCAAATAAAGTGACAATTGAATCACCTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 106

TCAAACAATGGGTCTCCTTGGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAGgtgcagttaa ... gtcaatgcagGATAGCTTTGGTCGGGCGGGTGAAAAAAATAAAGAAGCACTCAAGATGTCAAAGCATATAACTAAACTTTTCCCAAATAAAGTGACAATTGAATCACCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

TCAAACAATGGGTCTCCTTGGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAGgtgcagttaa ... gtcaatgcagGATAGCTTTGGTCGGGCGGGTGAAAAAAATAAAGAAGCACTCAAGATGTCAAAGCATATAACTAAACTTTTCCCAAATAAAGTGACAATTGAATCACCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 142

TCAAACAATGGGTCTCCTTGGCTCAAGTTCTCATATAGCCAAGCAGCAATACTTGACCTTGCATTTCAGgtgcagttaa ... gtcaatgcagGATAGCTTTGGTCGGGCGGGTGAAAAAAATAAAGAAGCACTCAAGATGTCAAAGCATATAACTAAACTTTTCCCAAATAAAGTGACAATTGAATCACCTG