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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAAAGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTGgtatgttcaggctagtgcaaatttcttaagcttttgctattgtaaccatttctctaccttgataaatcatcttgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g47440.2
intron # 6
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|86506555|gb|CI149188.1|CI149188
EST:     AGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTG                         CTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
genomic: AGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTGgtatgttcag ... ttgtttgcagCTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
EST: gi|89193405|gb|CI050703.1|CI050703
EST:     AGACAGAACTCGCGAAAGCGTCCCAGACTCAGAAATCGAATTCATCACTG                         CTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
genomic: AGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTGgtatgttcag ... ttgtttgcagCTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
EST: gi|58606351|gb|CK034384.1|CK034384
EST:     AGACAGAAATCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTG                         CTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
genomic: AGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTGgtatgttcag ... ttgtttgcagCTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
EST: gi|86500468|gb|CI143101.1|CI143101
EST:     AGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTG                         CTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
genomic: AGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTGgtatgttcag ... ttgtttgcagCTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
EST: gi|58667527|gb|CK056213.1|CK056213
EST:     AGACAGAAATCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTG                         CTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
genomic: AGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTGgtatgttcag ... ttgtttgcagCTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
EST: gi|88848755|gb|CI087277.1|CI087277
EST:     GACTCAGAAATCGAATTCATCACTG                         CTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
genomic: GACTCAGAAATCGAATTCATCACTGgtatgttcag ... ttgtttgcagCTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
EST: gi|88520897|gb|CI448551.1|CI448551
EST:     TCGAATTCATCACTG                         CTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
genomic: TCGAATTCATCACTGgtatgttcag ... ttgtttgcagCTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
EST: gi|29646264|gb|CB651271.1|CB651271
EST:     AGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTG                         CTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA
genomic: AGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTGgtatgttcag ... ttgtttgcagCTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATA

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: 31 (upstream exon), 20 (downstream exon)
Score: 1

GAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAAAGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACTGgtatgttcag ... ttgtttgcagCTCTGCATTCTTCTGGTGATCTTCGGGGTTGTCTTGCTAATTGTGATAATAGTTTTGGCAACTTGAGGCGCGACGTAGAGATTACTGGTGCACTCGGTAG




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