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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGACACAGGCGCTGGCGCCCTCCCTCCGCCTCCTCCTGCTGCTACCGCTGCTCGCCGCCGCCGCCGCCGCCGCCGCGTTGTCTCACCCAGCGCACGAGgtgggtgtgctttgattctgttctgtcgtcgcatgctttgtctgctctggctgctcgcctcgcctgacgtggctggattcggctgcgcgcgtggcag

Basic information

species Zea mays
transcript GRMZM2G020002_T03
intron # 1
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|149082368|gb|EE171552.2|EE171552
EST:     CGCCGCCGCCGCGTTGTCTCACCCAGCGCACGAG                         TTCTGCGCGGTCGGGGGTGACGCCTCCGGCTGCGGCGGCGGAGGAGACGGC
genomic: CGCCGCCGCCGCGTTGTCTCACCCAGCGCACGAGgtgggtgtgc ... cgcgtggcagTTCTGCGCGGTCGGGGGTGACGCCTCCGGCTGCGGCGGCGGAGGAGACGGC
EST: gi|87152398|gb|DY397187.1|DY397187
EST:     GTCTCACCCAGCGCACGAG                         TTCTGCGCGGTCGGGGGTGACGCCTCCGGCTGCGGCGGCGGAGGAGACGGC
genomic: GTCTCACCCAGCGCACGAGgtgggtgtgc ... cgcgtggcagTTCTGCGCGGTCGGGGGTGACGCCTCCGGCTGCGGCGGCGGAGGAGACGGC

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: 42 (upstream exon), 49 (downstream exon)
Score: 59

GGCGACACAGGCGCTGGCGCCCTCCCTCCGCCTCCTCCTGCTGCTACCGCTGCTCGCCGCCGCCGCCGCCGCCGCCGCGTTGTCTCACCCAGCGCACGAGgtgggtgtgc ... cgcgtggcagTTCTGCGCGGTCGGGGGTGACGCCTCCGGCTGCGGCGGCGGAGGAGACGGCACGAGGATCCTGATCAAGGGCGGGACGGTGGTCAACGCGCACCTCGCGG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 338

GGCGACACAGGCGCTGGCGCCCTCCCTCCGCCTCCTCCTGCTGCTACCGCTGCTCGCCGCCGCCGCCGCCGCCGCCGCGTTGTCTCACCCAGCGCACGAGgtgggtgtgc ... cgcgtggcagTTCTGCGCGGTCGGGGGTGACGCCTCCGGCTGCGGCGGCGGAGGAGACGGCACGAGGATCCTGATCAAGGGCGGGACGGTGGTCAACGCGCACCTCGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

GGCGACACAGGCGCTGGCGCCCTCCCTCCGCCTCCTCCTGCTGCTACCGCTGCTCGCCGCCGCCGCCGCCGCCGCCGCGTTGTCTCACCCAGCGCACGAGgtgggtgtgc ... cgcgtggcagTTCTGCGCGGTCGGGGGTGACGCCTCCGGCTGCGGCGGCGGAGGAGACGGCACGAGGATCCTGATCAAGGGCGGGACGGTGGTCAACGCGCACCTCGCGG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 122

GGCGACACAGGCGCTGGCGCCCTCCCTCCGCCTCCTCCTGCTGCTACCGCTGCTCGCCGCCGCCGCCGCCGCCGCCGCGTTGTCTCACCCAGCGCACGAGgtgggtgtgc ... cgcgtggcagTTCTGCGCGGTCGGGGGTGACGCCTCCGGCTGCGGCGGCGGAGGAGACGGCACGAGGATCCTGATCAAGGGCGGGACGGTGGTCAACGCGCACCTCGCGG