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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctggagcgcacggttctgtgcccgttcctctccatctctctccagtttgattaccatttaccagttttgattctgacgcggggtttacatttttagGGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAACCAACAAG

Basic information

species Zea mays
transcript GRMZM2G126218_T02
intron # 2
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|211366522|gb|FL182994.1|FL182994
EST:     GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAG                         GGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAAC
genomic: GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAGgtatcctgga ... acatttttagGGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAAC
EST: gi|67020298|gb|CO449047.1|CO449047
EST:     GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAG                         GGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAAC
genomic: GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAGgtatcctgga ... acatttttagGGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAAC
EST: gi|211178131|gb|FL062332.1|FL062332
EST:     GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAG                         GGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAAC
genomic: GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAGgtatcctgga ... acatttttagGGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAAC

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: 48 (upstream exon), 38 (downstream exon)
Score: 34

GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAGgtatcctgga ... acatttttagGGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAACCAACAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 23

GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAGgtatcctgga ... acatttttagGGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAACCAACAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 14

GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAGgtatcctgga ... acatttttagGGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAACCAACAAG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 19

GCTACGGTGGGCGCCGCCGGCAGGCCGGCGAACCGCACCGTCGTGTTCAGgtatcctgga ... acatttttagGGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAACCAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagtttgattaccatttaccagttttgattctgacgcggggtttacatttttagGGGTTTTCAGGAACTCTGTGATAAGATTCAGATTAACACGGACGCCCGAACCAACAAG
                             ttctgac  putative branch site (score: 19)
                                              cattttt  putative PPT
                                          tttacattttta  TA-rich tract