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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttggttgttcgtaaatcagaattatgagttgtgttattattttgaaaagacacactttacatcaccttcacagtgcttcgtatgttgctttttccagGACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCAAGATATGTACAATACCAGCAATAATATGGTAGTTCCGAAACTGCTTGTT

Basic information

species Oryza sativa
transcript LOC_Os01g62410.2
intron # 6
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|33675025|gb|CF303264.1|CF303264
EST:     CGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAG                         GACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA
genomic: CGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAGgtacgtttat ... ctttttccagGACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA
EST: gi|25799828|gb|CA755789.1|CA755789
EST:     CGGATTTATGGGAATAAATGGGCAGAGATAGCANAAGTTCTTCCTGGAAG                         GACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA
genomic: CGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAGgtacgtttat ... ctttttccagGACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA
EST: gi|66922024|gb|CX108872.1|CX108872
EST:     CGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAG                         GACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA
genomic: CGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAGgtacgtttat ... ctttttccagGACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA
EST: gi|58668776|gb|CK057462.1|CK057462
EST:     CGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAG                         GACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA
genomic: CGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAGgtacgtttat ... ctttttccagGACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA
EST: gi|58655298|gb|CK043978.1|CK043978
EST:     CGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAG                         GACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA
genomic: CGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAGgtacgtttat ... ctttttccagGACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCA

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: 65 (upstream exon), 58 (downstream exon)
Score: 9

GGAAAGATGCTTGGACTACTGAGGAGGAACAGGCACTCATAAATGCTCATCGGATTTATGGGAATAAATGGGCAGAGATAGCAAAAGTTCTTCCTGGAAGgtacgtttat ... ctttttccagGACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCAAGATATGTACAATACCAGCAATAATATGGTAGTTCCGAAACTGCTTGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaagacacactttacatcaccttcacagtgcttcgtatgttgctttttccagGACTGATAATTCTATAAAGAATCATTGGAATAGTTCTCTCAGAAAGAAGCAAGATATGTACAATACCAGCAATAATATGGTAGTTCCGAAACTGCTTGTT
                                          ttgctttttcc  CT-rich tract
             tttacat  TA-rich tract