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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattcttttctgagttgcagttttaatgttctattttgtactattttattgattgccactaactaatccattgcgctggtgctag

Basic information

species Zea mays
transcript GRMZM2G069676_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069676_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 5'ss of exon 11
GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattcttttctgagttgcagttttaatgttctattttgtactattttattgattgccact----aactaatccattgc--gctggtgctag-----
|||||| ||||||||||| || ||||||||||| || |||||| ||||||||||||||||| |||||||||||||||| || |||||||        |    |  | |    ||     ||||||     |||  |    | ||||    ||||    |||       |||  ||       
GTCTGCTGCTGTTGATTCAAGTGGTCGTGAGTTAAACCGTAACAGATTGATTGCTTTGATGTCTGCCATAGTTCTTGAAGAGgtaagatctcacaaggcaaagttggtcgtgtgactagttttgtgggcatttgctatgagacactctagaactgtggcatgattaaatggcactctgaaaa
















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|211441851|gb|FL182588.1|FL182588
EST:     TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA                         CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT
genomic: TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattct ... ctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT
EST: gi|32933693|gb|CF038505.1|CF038505
EST:     TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA                         CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT
genomic: TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattct ... ctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT
EST: gi|60341753|gb|DN208726.1|DN208726
EST:     TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA                         CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT
genomic: TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattct ... ctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT
EST: gi|32832812|gb|CD972490.1|CD972490
EST:     TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA                         CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT
genomic: TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattct ... ctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT
EST: gi|33094155|gb|CF054149.1|CF054149
EST:     TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA                         CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT
genomic: TGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattct ... ctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACT

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), 47 (downstream exon)
Score: 163

GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattct ... ctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 184

GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattct ... ctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 151

GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattct ... ctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAAgtaagattct ... ctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG