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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAACATTGGCCCTGATACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACAgtgagttttcagataatgtttatacatatgtatttggccggaaaaatatttcatgggatctatcggctgtatttatgcatatgcttatacatatgtagatcctttgtaacattctgattaccttttttgctag

Basic information

species Oryza sativa
transcript LOC_Os01g21820.1
intron # 16
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|218484584|gb|FG955879.1|FG955879
EST:     ACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACA                         GTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
genomic: ACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACAgtgagttttc ... tttttgctagGTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
EST: gi|29676134|gb|CB672409.1|CB672409
EST:     AGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACA                         GTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
genomic: AGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACAgtgagttttc ... tttttgctagGTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
EST: gi|29615684|gb|CB620696.1|CB620696
EST:     ACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACA                         GTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
genomic: ACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACAgtgagttttc ... tttttgctagGTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
EST: gi|29676704|gb|CB672979.1|CB672979
EST:     AGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACA                         GTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
genomic: AGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACAgtgagttttc ... tttttgctagGTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
EST: gi|27577941|gb|CB000636.1|CB000636
EST:     ACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACA                         GTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
genomic: ACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACAgtgagttttc ... tttttgctagGTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
EST: gi|58593464|gb|CF991772.1|CF991772
EST:     ACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACA                         GTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC
genomic: ACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACAgtgagttttc ... tttttgctagGTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATC

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 1 RNA-Seqlibrary.


Block sizes: 48 (upstream exon), 63 (downstream exon)
Score: 14

GCAAACATTGGCCCTGATACCCCGAGAGAAGATTGGGATCTTAGCAAACTGATAGCTAAACTTCAACAgtgagttttc ... tttttgctagGTATTGCTATCTATTAGATGATTTGACACCAGAATTGTTGGAGGGCAAATCGTCAAGCTATGAGGATTTGCAAGAGTACCTTCGTACCCGAGGACGTGAA




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