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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctatcaagcatttttttttcagttatagccagaaaattatttgttaattagtttctccaatgcaggctagctaatttgattgaactctactgttggatgaatgtttgaattaattcagGGGTTGCGCGAGGAGCCGGCGTTCGGGTTCGTGGACAACACCGGCGGCGGGTGGGACGGCGGCGCCGGCGCCGGCGCGGCGGCGGACATGTTCGCCTTCC

Basic information

species Oryza sativa
transcript LOC_Os06g49840.2
intron # 7
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|58666206|gb|CK054892.1|CK054892
EST:     GTGAAGCACTCCTACGAGGCGTACAAGACTCTGCAGCAGGAGCTG                         GGGTTGTGCGAGGAGCCGGCGT--GG-TTCGTGGACAACACCGGCGGCGGG
genomic: GTGAAGCACTCCTACGAGGCGTACGAGACTCTGCAGCAGGAGCTGgtaacctatc ... attaattcagGGGTTGCGCGAGGAGCCGGCGTTCGGGTTCGTGGACAACACCGGCGGCGGG
EST: gi|29621840|gb|CB626851.1|CB626851
EST:     GTGAAGCACTCCTACGAGGCGTACAAGACTCTGCAGCAGGAGCTG                         GGGTTGTGCGAGGAGCCGGCGT--GG-TTCGTGGACAACACCGGCGGCGGG
genomic: GTGAAGCACTCCTACGAGGCGTACGAGACTCTGCAGCAGGAGCTGgtaacctatc ... attaattcagGGGTTGCGCGAGGAGCCGGCGTTCGGGTTCGTGGACAACACCGGCGGCGGG
EST: gi|38483278|gb|CF967080.1|CF967080
EST:     GTGAAGCACTCCTACGAGGCGTACAAGACTCTGCAGCAGGAGCTG                         GGGTTGTGCGAAGAGCCGGCGT
genomic: GTGAAGCACTCCTACGAGGCGTACGAGACTCTGCAGCAGGAGCTGgtaacctatc ... attaattcagGGGTTGCGCGAGGAGCCGGCGT
EST: gi|58660818|gb|CK049498.1|CK049498
EST:     GTGAAGCACTCCTACGAGGCGTACAAGACTCTGCAGCAGGAGCTG                         GGGTTGTGCGAGGAGCCGGCGT--GG-TTCGTGGACAACACCGGCGGCGGG
genomic: GTGAAGCACTCCTACGAGGCGTACGAGACTCTGCAGCAGGAGCTGgtaacctatc ... attaattcagGGGTTGCGCGAGGAGCCGGCGTTCGGGTTCGTGGACAACACCGGCGGCGGG
EST: gi|58671677|gb|CK060363.1|CK060363
EST:     GTGAAGCACTCCTACGAGGCGTACAAGACTCTGCAGCAGGAGCTG                         GGGTTGTGCGAGGAGCCGGCGT
genomic: GTGAAGCACTCCTACGAGGCGTACGAGACTCTGCAGCAGGAGCTGgtaacctatc ... attaattcagGGGTTGCGCGAGGAGCCGGCGT

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: 75 (upstream exon), 28 (downstream exon)
Score: 2

GTGAAGCACTCCTACGAGGCGTACGAGACTCTGCAGCAGGAGCTGgtaacctatc ... attaattcagGGGTTGCGCGAGGAGCCGGCGTTCGGGTTCGTGGACAACACCGGCGGCGGGTGGGACGGCGGCGCCGGCGCCGGCGCGGCGGCGGACATGTTCGCCTTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggctagctaatttgattgaactctactgttggatgaatgtttgaattaattcagGGGTTGCGCGAGGAGCCGGCGTTCGGGTTCGTGGACAACACCGGCGGCGGGTGGGACGGCGGCGCCGGCGCCGGCGCGGCGGCGGACATGTTCGCCTTCC
                                            aattaat  putative branch site (score: 2)
                                    aatgtttgaattaatt  TA-rich tract