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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGCCTGCGCGACCAGGGAGGCAGGGCACGCGGCAACCACGTGGGGAGGCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAGgtatggaatcgattcctgtgtctgtgtcctcgcctctacgcgccgcgcgcttttttttgtgtgtgtgtgtgtgtgcgcacgcgccctgtctctgcggagg...

Basic information

species Zea mays
transcript GRMZM2G178822_T02
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|149077869|gb|EE166597.2|EE166597
EST:     GCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCA--G---G                         ATTGCAGCACCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGA
genomic: GCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAGgtatggaatc ... tgttgactagATTGCAGCAGCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGA
EST: gi|149089320|gb|EE178543.2|EE178543
EST:     GCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAG                         ATTGCAGCAGCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGA
genomic: GCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAGgtatggaatc ... tgttgactagATTGCAGCAGCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGA
EST: gi|71328344|gb|DR800801.1|DR800801
EST:     GCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAG                         ATTGCAGCAGCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGA
genomic: GCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAGgtatggaatc ... tgttgactagATTGCAGCAGCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGA

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), 45 (downstream exon)
Score: 181

GGCTGCCTGCGCGACCAGGGAGGCAGGGCACGCGGCAACCACGTGGGGAGGCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAGgtatggaatc ... tgttgactagATTGCAGCAGCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGAAAAAGTGATCTGCCGGGCATATCTCCTTCAATGCAAGCGATTCTTTTCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 152

GGCTGCCTGCGCGACCAGGGAGGCAGGGCACGCGGCAACCACGTGGGGAGGCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAGgtatggaatc ... tgttgactagATTGCAGCAGCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGAAAAAGTGATCTGCCGGGCATATCTCCTTCAATGCAAGCGATTCTTTTCG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 71

GGCTGCCTGCGCGACCAGGGAGGCAGGGCACGCGGCAACCACGTGGGGAGGCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAGgtatggaatc ... tgttgactagATTGCAGCAGCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGAAAAAGTGATCTGCCGGGCATATCTCCTTCAATGCAAGCGATTCTTTTCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 228

GGCTGCCTGCGCGACCAGGGAGGCAGGGCACGCGGCAACCACGTGGGGAGGCGACGACACCACACCACCCTATGCTCTCTGTCCTCGCCCGCAGGGTAAGgtatggaatc ... tgttgactagATTGCAGCAGCAGTGAATTTGGGAGCTTGAAGCGTTCATCCGAGACATGGAAAAAGTGATCTGCCGGGCATATCTCCTTCAATGCAAGCGATTCTTTTCG