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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGACAGAAGATGTCCGAGAGGTCATTACACACCTGCATCACAGATATCCGAAAACCACACTGTTTTGCATTGGTACAAGCATAGGTGCCAATATTGTGgtatgcatctttctgcttggcataatcttttttcccccaatctgcatgtttcattatttgaacccaaatatcctgacatctgctatttcctgctaccaaa...

Basic information

species Zea mays
transcript GRMZM2G005444_T01
intron # 6
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|76011576|gb|DT938746.1|DT938746
EST:     CGAAAACCACACTGTTTTGCATTGGTACAAGCATAGGTGCCAATATTGTG                         GTCAAGTATCTTGGAGAAGAAGGCGAGAATACTCCTATAGCGGGTGCAGTA
genomic: CGAAAACCACACTGTTTTGCATTGGTACAAGCATAGGTGCCAATATTGTGgtatgcatct ... ctttttacagGTCAAGTATCTTGGAGAAGAAGGCGAGAATACTCCTATAGCGGGTGCAGTA
EST: gi|76017556|gb|DT944726.1|DT944726
EST:     CGAAAACCACACTGTTTTGCATTGGTACAAGCATAGGTGCCAATATTGTG                         GTCAAGTATCTTGGAGAAGAAGGCGAGAATACTCCTATAGCGGGTGCAGTA
genomic: CGAAAACCACACTGTTTTGCATTGGTACAAGCATAGGTGCCAATATTGTGgtatgcatct ... ctttttacagGTCAAGTATCTTGGAGAAGAAGGCGAGAATACTCCTATAGCGGGTGCAGTA

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: 65

TTGGACAGAAGATGTCCGAGAGGTCATTACACACCTGCATCACAGATATCCGAAAACCACACTGTTTTGCATTGGTACAAGCATAGGTGCCAATATTGTGgtatgcatct ... ctttttacagGTCAAGTATCTTGGAGAAGAAGGCGAGAATACTCCTATAGCGGGTGCAGTATCTATTTGTTCTCCATGGGATCTGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 195

TTGGACAGAAGATGTCCGAGAGGTCATTACACACCTGCATCACAGATATCCGAAAACCACACTGTTTTGCATTGGTACAAGCATAGGTGCCAATATTGTGgtatgcatct ... ctttttacagGTCAAGTATCTTGGAGAAGAAGGCGAGAATACTCCTATAGCGGGTGCAGTATCTATTTGTTCTCCATGGGATCTGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 196

TTGGACAGAAGATGTCCGAGAGGTCATTACACACCTGCATCACAGATATCCGAAAACCACACTGTTTTGCATTGGTACAAGCATAGGTGCCAATATTGTGgtatgcatct ... ctttttacagGTCAAGTATCTTGGAGAAGAAGGCGAGAATACTCCTATAGCGGGTGCAGTATCTATTTGTTCTCCATGGGATCTGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 378

TTGGACAGAAGATGTCCGAGAGGTCATTACACACCTGCATCACAGATATCCGAAAACCACACTGTTTTGCATTGGTACAAGCATAGGTGCCAATATTGTGgtatgcatct ... ctttttacagGTCAAGTATCTTGGAGAAGAAGGCGAGAATACTCCTATAGCGGGTGCAGTATCTATTTGTTCTCCATGGGATCTGTTG