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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAGCCGAATGTGAAGATAACATGTCTGATGATGGCTGCTCAGTAGCAGGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgccaacatctcaactttccacatctcttattccttaccatcatttcttttttgaattcaatgtcacatactagttacaatctgttgggctcccaataaattctttcgttacatgtgtcagcagcaaacaatcttccttttcccctttcagtaacgagtcctgctgtttaaactatgctctacaattacag

Basic information

species Zea mays
transcript GRMZM2G124883_T01
intron # 11
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|76018055|gb|DT945225.1|DT945225
EST:     GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGAT                         GCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
genomic: GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
EST: gi|211256989|gb|FL181069.1|FL181069
EST:     GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGAT                         GCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
genomic: GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
EST: gi|76281862|gb|DV021430.1|DV021430
EST:     GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGAT                         GCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
genomic: GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
EST: gi|211077349|gb|FK960593.1|FK960593
EST:     GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGAT                         GCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
genomic: GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
EST: gi|6827926|gb|AW331569.1|AW331569
EST:     GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGAT                         GCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGCCA
genomic: GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
EST: gi|211077347|gb|FK960591.1|FK960591
EST:     GGAACCGAGTATTCAGTAGGTGCTGCTTCAGAGGCGACAGCAGAACGGAT                         GCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
genomic: GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
EST: gi|32835742|gb|CD975420.1|CD975420
EST:     GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGAT                         GCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
genomic: GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA
EST: gi|37384588|gb|CF629383.1|CF629383
EST:     GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGAT                         GCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGGCA
genomic: GGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACA

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: 145

GTGAAGCCGAATGTGAAGATAACATGTCTGATGATGGCTGCTCAGTAGCAGGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACAGCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 23

GTGAAGCCGAATGTGAAGATAACATGTCTGATGATGGCTGCTCAGTAGCAGGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACAGCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCA


Block sizes: 35 (upstream exon), 48 (downstream exon)
Score: 5

GTGAAGCCGAATGTGAAGATAACATGTCTGATGATGGCTGCTCAGTAGCAGGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACAGCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 76

GTGAAGCCGAATGTGAAGATAACATGTCTGATGATGGCTGCTCAGTAGCAGGAACCGAGTATTCAGTAGGTGGTGCTTCAGAGGCGACAGCAGAACGGATgtatgttgcc ... acaattacagGCAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACAGCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCA