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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTAGATGTATGCCTGATTTAATGGATGTTGACTCGCCCAATTGCTTATCGAAAACACCAGTGAAAAAAAAGCATGTGACTCTTGTGCTTGATTTGGACGgtgagcagcactaacttctcgtggaatattacttttgaatgtgtcttctaatttctggttctttattgttcactagctactggcatgttaccattatttt...

Basic information

species Zea mays
transcript GRMZM2G162347_T02
intron # 5
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|78179711|gb|DV550084.1|DV550084
EST:     GAAAACACCAGTGNNNNNNNNGCATGTGACTCTTGTGCTTGATTTGGACG                         AGACTCTGGTACATTCAACATTGGATCACTGCGACAATGCTGATTTTACCC
genomic: GAAAACACCAGTGAAAAAAAAGCATGTGACTCTTGTGCTTGATTTGGACGgtgagcagca ... tcatatgcagAGACTCTGGTACATTCAACATTGGATCACTGCGACAATGCTGATTTTACCC
EST: gi|71533678|gb|DR784437.1|DR784437
EST:     GACTCTTGTGCTTGATTTGGACG                         AGACTCTGGTACATTCAACATTGGATCACTGCGACAATGCTGATTTTACCC
genomic: GACTCTTGTGCTTGATTTGGACGgtgagcagca ... tcatatgcagAGACTCTGGTACATTCAACATTGGATCACTGCGACAATGCTGATTTTACCC
EST: gi|116825971|gb|EC869721.1|EC869721
EST:     AAAGCATGTGACTCTTGTGCTTGATTAGGACG                         AGACTC-GGTACATTCAACATTGGATCAC-GCGACAATGCTGATTTTACCC
genomic: AAAGCATGTGACTCTTGTGCTTGATTTGGACGgtgagcagca ... tcatatgcagAGACTCTGGTACATTCAACATTGGATCACTGCGACAATGCTGATTTTACCC

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: 72

TCTAGATGTATGCCTGATTTAATGGATGTTGACTCGCCCAATTGCTTATCGAAAACACCAGTGAAAAAAAAGCATGTGACTCTTGTGCTTGATTTGGACGgtgagcagca ... tcatatgcagAGACTCTGGTACATTCAACATTGGATCACTGCGACAATGCTGATTTTACCCTAGAAGTTTTCTTTAATATGAAAAATCACACAGTGTATGTGAGAAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

TCTAGATGTATGCCTGATTTAATGGATGTTGACTCGCCCAATTGCTTATCGAAAACACCAGTGAAAAAAAAGCATGTGACTCTTGTGCTTGATTTGGACGgtgagcagca ... tcatatgcagAGACTCTGGTACATTCAACATTGGATCACTGCGACAATGCTGATTTTACCCTAGAAGTTTTCTTTAATATGAAAAATCACACAGTGTATGTGAGAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

TCTAGATGTATGCCTGATTTAATGGATGTTGACTCGCCCAATTGCTTATCGAAAACACCAGTGAAAAAAAAGCATGTGACTCTTGTGCTTGATTTGGACGgtgagcagca ... tcatatgcagAGACTCTGGTACATTCAACATTGGATCACTGCGACAATGCTGATTTTACCCTAGAAGTTTTCTTTAATATGAAAAATCACACAGTGTATGTGAGAAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78

TCTAGATGTATGCCTGATTTAATGGATGTTGACTCGCCCAATTGCTTATCGAAAACACCAGTGAAAAAAAAGCATGTGACTCTTGTGCTTGATTTGGACGgtgagcagca ... tcatatgcagAGACTCTGGTACATTCAACATTGGATCACTGCGACAATGCTGATTTTACCCTAGAAGTTTTCTTTAATATGAAAAATCACACAGTGTATGTGAGAAAAAG