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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattttgttgaagatgtttcactctttcacctgttgtttcaccattgctgaatttttactcctgcatgggttgcttattttgtttctttagCTCGAGACCCGTATTGGTAAAAGGGAAGCAGAAGCAAGAAAACTTGAGAAAAAAATTAATGACATTGTGGACAAGGTGTACAGAGATTTTAGCATTTCAG

Basic information

species Zea mays
transcript GRMZM2G416069_T01
intron # 3
splice site 3'
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|76010848|gb|DT938018.1|DT938018
EST:     GGAGTAATATTGAGACAGAGATTAATCGTCTGAAGCCTGGAGAGGAGGAG                         CTCGAGACCCGTATTGGTAAAAGGGAAGCAGAAGCAAGAAAACTTGAGNNN
genomic: GGAGTAATATTGAGACAGAGATTAATCGTCTGAAGCCTGGAGAGGAGGAGgtaatatttt ... gtttctttagCTCGAGACCCGTATTGGTAAAAGGGAAGCAGAAGCAAGAAAACTTGAGAAA




















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: 830

AATAACCTTAGAGGGAAACTAGCTAAATTAGCATCTGAGAGGAGTAATATTGAGACAGAGATTAATCGTCTGAAGCCTGGAGAGGAGGAGgtaatatttt ... gtttctttagCTCGAGACCCGTATTGGTAAAAGGGAAGCAGAAGCAAGAAAACTTGAGAAAAAAATTAATGACATTGTGGACAAGGTGTACAGAGATTTTAGCATTTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 384

AATAACCTTAGAGGGAAACTAGCTAAATTAGCATCTGAGAGGAGTAATATTGAGACAGAGATTAATCGTCTGAAGCCTGGAGAGGAGGAGgtaatatttt ... gtttctttagCTCGAGACCCGTATTGGTAAAAGGGAAGCAGAAGCAAGAAAACTTGAGAAAAAAATTAATGACATTGTGGACAAGGTGTACAGAGATTTTAGCATTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 408

AATAACCTTAGAGGGAAACTAGCTAAATTAGCATCTGAGAGGAGTAATATTGAGACAGAGATTAATCGTCTGAAGCCTGGAGAGGAGGAGgtaatatttt ... gtttctttagCTCGAGACCCGTATTGGTAAAAGGGAAGCAGAAGCAAGAAAACTTGAGAAAAAAATTAATGACATTGTGGACAAGGTGTACAGAGATTTTAGCATTTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 330

AATAACCTTAGAGGGAAACTAGCTAAATTAGCATCTGAGAGGAGTAATATTGAGACAGAGATTAATCGTCTGAAGCCTGGAGAGGAGGAGgtaatatttt ... gtttctttagCTCGAGACCCGTATTGGTAAAAGGGAAGCAGAAGCAAGAAAACTTGAGAAAAAAATTAATGACATTGTGGACAAGGTGTACAGAGATTTTAGCATTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaccattgctgaatttttactcctgcatgggttgcttattttgtttctttagCTCGAGACCCGTATTGGTAAAAGGGAAGCAGAAGCAAGAAAACTTGAGAAAAAAATTAATGACATTGTGGACAAGGTGTACAGAGATTTTAGCATTTCAG
                                     cttattttgtttcttt  CT-rich tract
                                      ttattttgtttcttta  TA-rich tract