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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGCCCCCGTGAGGAGCTCCCACACCTCGACGGCTGGCCTGCTCGCGTGGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgctcttctgttcctccgccacccgccccgcgcggcgcgctgcttgtgatcgtcgttgatctcttgtggtccctctctcgccctgcag

Basic information

species Zea mays
transcript GRMZM2G128491_T01
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|87157807|gb|DY402596.1|DY402596
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|71307158|gb|DR789750.1|DR789750
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|148956639|gb|EC902493.2|EC902493
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|9254985|gb|BE345453.1|BE345453
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|78114333|gb|DV532722.1|DV532722
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|71430885|gb|DR811935.1|DR811935
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|211018202|gb|FL215892.1|FL215892
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|78118764|gb|DV537148.1|DV537148
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|211015418|gb|FL215877.1|FL215877
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|211018200|gb|FL215890.1|FL215890
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|211018199|gb|FL215889.1|FL215889
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|22819528|gb|BU499618.1|BU499618
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|76936903|gb|DV174954.1|DV174954
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|71327882|gb|DR800570.1|DR800570
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
EST: gi|211018201|gb|FL215891.1|FL215891
EST:     GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAG                         CCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG
genomic: GGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGG

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), 48 (downstream exon)
Score: 77

AGCGGCCCCCGTGAGGAGCTCCCACACCTCGACGGCTGGCCTGCTCGCGTGGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGGGCCGACGGCCTCAACAAGACGAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 24

AGCGGCCCCCGTGAGGAGCTCCCACACCTCGACGGCTGGCCTGCTCGCGTGGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGGGCCGACGGCCTCAACAAGACGAAGAG


Block sizes: 31 (upstream exon), 46 (downstream exon)
Score: 13

AGCGGCCCCCGTGAGGAGCTCCCACACCTCGACGGCTGGCCTGCTCGCGTGGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGGGCCGACGGCCTCAACAAGACGAAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

AGCGGCCCCCGTGAGGAGCTCCCACACCTCGACGGCTGGCCTGCTCGCGTGGCCTCACCCCGATGGCGCCGGGTCGCTGCCAGCACGCCGGCCTAACCAGgtgacccgct ... cgccctgcagCCGACGGAGGAATTCAGGAATGTGGTGTTTGGGGGGCAGCTCACGGAGGGGGCCGACGGCCTCAACAAGACGAAGAG