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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCCGGCTGGAAGGCCATGGGGGCTAGGGCTACCTCCCCTCCGCCATGGAGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgcacttcttgccggttcttatggttctttcgctccacccgtaattttagttcatcgattcgttggagttgtactattttgcagggtttcccg...

Basic information

species Zea mays
transcript GRMZM2G028307_T02
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|211005860|gb|FL395309.1|FL395309
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACGAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|71436528|gb|DR817578.1|DR817578
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|211079341|gb|FL392675.1|FL392675
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAATGAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|50328271|gb|CO523397.1|CO523397
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|71444847|gb|DR825897.1|DR825897
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|74237284|gb|DT645198.1|DT645198
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG

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: 257

TGTCCGGCTGGAAGGCCATGGGGGCTAGGGCTACCTCCCCTCCGCCATGGAGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 83

TGTCCGGCTGGAAGGCCATGGGGGCTAGGGCTACCTCCCCTCCGCCATGGAGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG


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

TGTCCGGCTGGAAGGCCATGGGGGCTAGGGCTACCTCCCCTCCGCCATGGAGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

TGTCCGGCTGGAAGGCCATGGGGGCTAGGGCTACCTCCCCTCCGCCATGGAGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG