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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGTCCGAGATTTGGCTCTAGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgttgtagtttctcagatgccatccagttggttttttcaagctctaatccctatgtttcctatttgcatctttttacgcag

Basic information

species Zea mays
transcript GRMZM2G173682_T01
intron # 7
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|86473490|gb|DY239860.1|DY239860
EST:     AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAG                         ACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
genomic: AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
EST: gi|148949197|gb|EC894635.2|EC894635
EST:     AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAG                         ACGATTTCGATGATTTCTGTTTTCGGGCATCTGAGTTGGCAGAGAAAGCCA
genomic: AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
EST: gi|211435917|gb|FL467684.1|FL467684
EST:     AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAG                         ACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
genomic: AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
EST: gi|110210894|gb|EC892791.1|EC892791
EST:     TTGGTTTTTTCTGTCGCGACAAAG                         ACGATTTCGATGATTTCTGTTTTCGGGCATCTGAGTTGGCAGAGAAAGCCA
genomic: TTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
EST: gi|87157629|gb|DY402418.1|DY402418
EST:     AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAG                         ACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
genomic: AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
EST: gi|84969916|gb|DV170881.2|DV170881
EST:     AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAG                         ACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
genomic: AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
EST: gi|22715457|gb|BU197774.1|BU197774
EST:     AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAG                         ACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
genomic: AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
EST: gi|211435918|gb|FL467685.1|FL467685
EST:     AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAG                         ACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA
genomic: AGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCA

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: 47 (upstream exon), 46 (downstream exon)
Score: 23

TGTTGTCCGAGATTTGGCTCTAGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCAATGGAGCGCCACTCTTTACTGTCATGCAGTCAGTCCAGCCATCGAAGCA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 36

TGTTGTCCGAGATTTGGCTCTAGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCAATGGAGCGCCACTCTTTACTGTCATGCAGTCAGTCCAGCCATCGAAGCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 26

TGTTGTCCGAGATTTGGCTCTAGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCAATGGAGCGCCACTCTTTACTGTCATGCAGTCAGTCCAGCCATCGAAGCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 35

TGTTGTCCGAGATTTGGCTCTAGAACAAATAGACCCATCCCTAGCCATTGGTTTTTACTGTCGCGACAAAGgtgagccgtt ... ttttacgcagACGATTTCGATGATTTCTGTTCTCGGGCATCTGAGTTGGCAGAGAAAGCCAATGGAGCGCCACTCTTTACTGTCATGCAGTCAGTCCAGCCATCGAAGCA