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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGAACAAATCCACAGCCACCTCAACCTCCTTTACGGAATAAGCGAGCACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTGgtatgtgattgctaagttggtgtgccaaatcgcccctctgcttatgacaacgatacttgctgtagggacagagaccttatgttttctactgttctgttcacatattggctggcttgcagacctaatttcctgattctcttctatgtcatgttag

Basic information

species Zea mays
transcript GRMZM2G702026_T01
intron # 11
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|211284606|gb|FL307740.1|FL307740
EST:     ACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTG                         GTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGAC
genomic: ACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTGgtatgtgatt ... gtcatgttagGTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGAC
EST: gi|5555329|gb|AI881280.1|AI881280
EST:     ACGGCCTCCTTCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTG                         GTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGAC
genomic: ACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTGgtatgtgatt ... gtcatgttagGTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGAC
EST: gi|211531197|gb|FL317039.1|FL317039
EST:     ACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTGG                         GGTTT-GGAAATCCCCAGCTAAGCCTGCC-AAGCTTTC-CATTCTCAGGA-
genomic: ACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTGgtatgtgatt ... gtcatgttagGTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGAC
EST: gi|211498503|gb|FL359837.1|FL359837
EST:     ACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTG                         GTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGAC
genomic: ACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTGgtatgtgatt ... gtcatgttagGTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGAC

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: 48 (upstream exon), 45 (downstream exon)
Score: 196

GATCGAACAAATCCACAGCCACCTCAACCTCCTTTACGGAATAAGCGAGCACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTGgtatgtgatt ... gtcatgttagGTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGACTGCAGCGAACTCAGGAGCTATACCATTCAAGCCCCAGTTCAATGTTCTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 116

GATCGAACAAATCCACAGCCACCTCAACCTCCTTTACGGAATAAGCGAGCACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTGgtatgtgatt ... gtcatgttagGTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGACTGCAGCGAACTCAGGAGCTATACCATTCAAGCCCCAGTTCAATGTTCTC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 98

GATCGAACAAATCCACAGCCACCTCAACCTCCTTTACGGAATAAGCGAGCACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTGgtatgtgatt ... gtcatgttagGTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGACTGCAGCGAACTCAGGAGCTATACCATTCAAGCCCCAGTTCAATGTTCTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 111

GATCGAACAAATCCACAGCCACCTCAACCTCCTTTACGGAATAAGCGAGCACGGCCTCCTGCTTCACCTTCGATTGCTCCAGAACTTGCTCCAGTTTTTGgtatgtgatt ... gtcatgttagGTTTTTGGAAGTCCCCAGCTGAGCCTGCCCAAGCTTTCTCATTCTCAGGACTGCAGCGAACTCAGGAGCTATACCATTCAAGCCCCAGTTCAATGTTCTC