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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGTTTTGCATGAACTATTGGTGTTGGCTATCTAAAGGACAGAAAGGCAGACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaagcataccttcgccttcaaatttgcgtagcttcgtttttattctgcaagttgtttggtctatcgttcaaatgccttattattctgcgagctgttttaagactgggcctcaatttttttccag

Basic information

species Zea mays
transcript GRMZM2G158584_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|149103360|gb|EE288742.2|EE288742
EST:     CAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATG                         GCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
genomic: CAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
EST: gi|78114495|gb|DV532884.1|DV532884
EST:     GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATG                         GCAGAAAGTGCTACTGTCGCTCTCATTTGTAGCGGTGTGGTACTGGGATCC
genomic: GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
EST: gi|148949507|gb|EC894971.2|EC894971
EST:     GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATG                         GCAGAGAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
genomic: GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
EST: gi|29544577|gb|CB604957.1|CB604957
EST:     GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATG                         GCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
genomic: GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
EST: gi|149028385|gb|EE154636.2|EE154636
EST:     CAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATG                         GCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
genomic: CAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
EST: gi|149011824|gb|EE042427.2|EE042427
EST:     GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATG                         GCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
genomic: GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
EST: gi|30087079|gb|CB885287.1|CB885287
EST:     GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATG                         GCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC
genomic: GACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCC

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), 35 (downstream exon)
Score: 30

ATAGTTTTGCATGAACTATTGGTGTTGGCTATCTAAAGGACAGAAAGGCAGACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCCTTGCCAATAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 13

ATAGTTTTGCATGAACTATTGGTGTTGGCTATCTAAAGGACAGAAAGGCAGACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCCTTGCCAATAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 27

ATAGTTTTGCATGAACTATTGGTGTTGGCTATCTAAAGGACAGAAAGGCAGACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCCTTGCCAATAAG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 12

ATAGTTTTGCATGAACTATTGGTGTTGGCTATCTAAAGGACAGAAAGGCAGACATGAGCAACAGATCCCGCTCCATGGGCTGAAACTGGGATTCGTGATGgtcagctaag ... ttttttccagGCAGAAAGTGCTACTGTCGCTCTCAATTGTAGCGGTGTGGTACTGGGATCCTTGCCAATAAG