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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAGTTGTTTTCATTGACAAATCTGACCTGTCATTCCAAGATAGATCATGGACACTAGCCAACGGTACTGGTGTGATTGATATTCAACACCCTTGCAGgtatttggacaccagacaatttgctaacaactttttgattgccattaaaatttttctttacaataatattattaattgctag

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 8
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|21809491|gb|BQ667809.1|BQ667809
EST:     TGGACACTAGCCAACGGTACTGGTGTGATTGATATTCAACACCCTTGCAG                         GTCTAATGTTGCTGTTCGGAAGGAGCTGCACAAACCAGCTTCAGATCGCTC
genomic: TGGACACTAGCCAACGGTACTGGTGTGATTGATATTCAACACCCTTGCAGgtatttggac ... taattgctagGTCTAATGTTGCTGTTCGGAAGGAGCTGCACAAACCAGCTTCAGATCGCTC
EST: gi|32848491|gb|CD988172.1|CD988172
EST:     GGTACTGGTGTGATTGATATTCAACACCCTTGCAG                         GTGTAATGTTGCTGTTCGGAAGGAGCTGCACAAGCCAGCTTCAGATCGCTC
genomic: GGTACTGGTGTGATTGATATTCAACACCCTTGCAGgtatttggac ... taattgctagGTCTAATGTTGCTGTTCGGAAGGAGCTGCACAAACCAGCTTCAGATCGCTC

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), 49 (downstream exon)
Score: 321

ACAGAGTTGTTTTCATTGACAAATCTGACCTGTCATTCCAAGATAGATCATGGACACTAGCCAACGGTACTGGTGTGATTGATATTCAACACCCTTGCAGgtatttggac ... taattgctagGTCTAATGTTGCTGTTCGGAAGGAGCTGCACAAACCAGCTTCAGATCGCTCTTGTATCCATCTCGAGTTTGACATTTCTGGCACTGGTCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 595

ACAGAGTTGTTTTCATTGACAAATCTGACCTGTCATTCCAAGATAGATCATGGACACTAGCCAACGGTACTGGTGTGATTGATATTCAACACCCTTGCAGgtatttggac ... taattgctagGTCTAATGTTGCTGTTCGGAAGGAGCTGCACAAACCAGCTTCAGATCGCTCTTGTATCCATCTCGAGTTTGACATTTCTGGCACTGGTCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 542

ACAGAGTTGTTTTCATTGACAAATCTGACCTGTCATTCCAAGATAGATCATGGACACTAGCCAACGGTACTGGTGTGATTGATATTCAACACCCTTGCAGgtatttggac ... taattgctagGTCTAATGTTGCTGTTCGGAAGGAGCTGCACAAACCAGCTTCAGATCGCTCTTGTATCCATCTCGAGTTTGACATTTCTGGCACTGGTCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 551

ACAGAGTTGTTTTCATTGACAAATCTGACCTGTCATTCCAAGATAGATCATGGACACTAGCCAACGGTACTGGTGTGATTGATATTCAACACCCTTGCAGgtatttggac ... taattgctagGTCTAATGTTGCTGTTCGGAAGGAGCTGCACAAACCAGCTTCAGATCGCTCTTGTATCCATCTCGAGTTTGACATTTCTGGCACTGGTCTTGT