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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAGGCGACGACGGGTAGGCCACCGCCGCCGGCGCCGTCCCACTACGACAACTGCTGAGGCCTTCATCGCTTTCTTCGCCGGCGACGAGCACCCACCAAgtatccccaccgcttctcttcccttcctaagcgccaaaccctaccttaacgctatttagctatttgatgtcccctaacttcgaactttttgccaaaaaaa...

Basic information

species Zea mays
transcript GRMZM2G035922_T02
intron # 1
splice site 5'
intron type U12 (go to U12 genes for details)

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|211411852|gb|FL441860.1|FL441860
EST:     AACTGCTGAGGCCGTCATCGCTTTCTTCGCCGGCGACGAGCACCCACCAA                         TTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCC
genomic: AACTGCTGAGGCCTTCATCGCTTTCTTCGCCGGCGACGAGCACCCACCAAgtatccccac ... ttgtctatagTTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCC
EST: gi|211184198|gb|FL244917.1|FL244917
EST:     AACTGCTGAGGCCTTCATCGCTTTCTTCGCCGGCGACGAGCACCCACCAA                         TTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCC
genomic: AACTGCTGAGGCCTTCATCGCTTTCTTCGCCGGCGACGAGCACCCACCAAgtatccccac ... ttgtctatagTTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCC

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: 357

ACAAGGCGACGACGGGTAGGCCACCGCCGCCGGCGCCGTCCCACTACGACAACTGCTGAGGCCTTCATCGCTTTCTTCGCCGGCGACGAGCACCCACCAAgtatccccac ... ttgtctatagTTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCCATGAAGATAACTCTATTTTCTCATTTGAAATTGGACAAGGCGCTGTCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 251

ACAAGGCGACGACGGGTAGGCCACCGCCGCCGGCGCCGTCCCACTACGACAACTGCTGAGGCCTTCATCGCTTTCTTCGCCGGCGACGAGCACCCACCAAgtatccccac ... ttgtctatagTTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCCATGAAGATAACTCTATTTTCTCATTTGAAATTGGACAAGGCGCTGTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

ACAAGGCGACGACGGGTAGGCCACCGCCGCCGGCGCCGTCCCACTACGACAACTGCTGAGGCCTTCATCGCTTTCTTCGCCGGCGACGAGCACCCACCAAgtatccccac ... ttgtctatagTTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCCATGAAGATAACTCTATTTTCTCATTTGAAATTGGACAAGGCGCTGTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

ACAAGGCGACGACGGGTAGGCCACCGCCGCCGGCGCCGTCCCACTACGACAACTGCTGAGGCCTTCATCGCTTTCTTCGCCGGCGACGAGCACCCACCAAgtatccccac ... ttgtctatagTTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCCATGAAGATAACTCTATTTTCTCATTTGAAATTGGACAAGGCGCTGTCAT