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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtgtctttgaggcctgtacagggagcattctcaaatctctgtcccttcgatggctaatgttttaaggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGAGCATTAGGATCCTGTAATGATAATAGTCTTTGTCCCAAGGGCACCTGGA

Basic information

species Zea mays
transcript GRMZM2G424181_T01
intron # 8
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|211044324|gb|FL126755.1|FL126755
EST:     CCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAG                         GTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGA
genomic: CCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAGgtaaatgtgt ... aggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGA
EST: gi|211099226|gb|FL470675.1|FL470675
EST:     CCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAG                         GTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGA
genomic: CCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAGgtaaatgtgt ... aggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGA
EST: gi|211099225|gb|FL470674.1|FL470674
EST:     CCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAG                         GTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGA
genomic: CCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAGgtaaatgtgt ... aggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGA
EST: gi|86470565|gb|DY236935.1|DY236935
EST:     CCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAG                         GTTTGGATGCGCGGCAGGTGTCCTTTTACGATTAAACTCTACTGGTGGTGA
genomic: CCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAGgtaaatgtgt ... aggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGA

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: 114

GCCTACCACTAATTCTCACCAAAATGAATAATCTTCCGCGGCTGCCACATCCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAGgtaaatgtgt ... aggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGAGCATTAGGATCCTGTAATGATAATAGTCTTTGTCCCAAGGGCACCTGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

GCCTACCACTAATTCTCACCAAAATGAATAATCTTCCGCGGCTGCCACATCCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAGgtaaatgtgt ... aggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGAGCATTAGGATCCTGTAATGATAATAGTCTTTGTCCCAAGGGCACCTGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GCCTACCACTAATTCTCACCAAAATGAATAATCTTCCGCGGCTGCCACATCCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAGgtaaatgtgt ... aggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGAGCATTAGGATCCTGTAATGATAATAGTCTTTGTCCCAAGGGCACCTGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

GCCTACCACTAATTCTCACCAAAATGAATAATCTTCCGCGGCTGCCACATCCACTGAGCTTCAGGAACTCGCGCTTGTGGTGGTGTTTCACAACAGATAGgtaaatgtgt ... aggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGAGCATTAGGATCCTGTAATGATAATAGTCTTTGTCCCAAGGGCACCTGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggagcattctcaaatctctgtcccttcgatggctaatgttttaaggttagcagGTTTGGATGCGCGGCAGGTGTCCTTCTACGACTAAACTCTACTGGTGGTGAGCATTAGGATCCTGTAATGATAATAGTCTTTGTCCCAAGGGCACCTGGA
                                ggctaat  putative branch site (score: 58)
                                   taatgttttaa  TA-rich tract