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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGAGGAAAAATATCGACTTTATGAGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgcaatagcttttgttgggttatgttgaaaaaaatatgctacagacagatacatctttgcatttttagttttaacccttttatcctggatctgtacag

Basic information

species Zea mays
transcript GRMZM5G825854_T01
intron # 5
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|93281267|gb|EB673531.1|EB673531
EST:     AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAG                         GTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC
genomic: AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgc ... atctgtacagGTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC
EST: gi|211087678|gb|FL052575.1|FL052575
EST:     AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCCTAAGCAG                         GTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC
genomic: AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgc ... atctgtacagGTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC
EST: gi|149104241|gb|EE289677.2|EE289677
EST:     AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAG                         GTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC
genomic: AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgc ... atctgtacagGTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC
EST: gi|148952057|gb|EC897846.2|EC897846
EST:     AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAG                         GTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC
genomic: AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgc ... atctgtacagGTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC
EST: gi|91872014|gb|EB401971.1|EB401971
EST:     AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAG                         GTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC
genomic: AGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgc ... atctgtacagGTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGC

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), 49 (downstream exon)
Score: 75

ACTGAGGAAAAATATCGACTTTATGAGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgc ... atctgtacagGTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

ACTGAGGAAAAATATCGACTTTATGAGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgc ... atctgtacagGTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

ACTGAGGAAAAATATCGACTTTATGAGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgc ... atctgtacagGTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

ACTGAGGAAAAATATCGACTTTATGAGAATACATTACAGGAGCGTGTCAACACATGTGACGTAATCCTTAAGCAGgtaagcctgc ... atctgtacagGTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT