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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGGATACTGGAAGTTCCTTTTGGCTTCCTCGCCAGAATCTGTTCCAGAGAAATTCTATGATGCCTACTTCAATGATTCAGATTGGGAGGCTTTGCCAGgcatgcatgctactacatcattacttgcttttattagatgcctttagttgatattgttctcattttttagtcagtagtgttcagtgtttgcttatatagc...

Basic information

species Oryza sativa
transcript LOC_Os01g72340.1
intron # 3
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|29621652|gb|CB626663.1|CB626663
EST:     GAAATTCTATGATGCCTACTTCAATGATTCAGATTGGGAGGCTTTGCCAG                         TTCCCTCAAACTGGCAAATGCATGGGTTTGACCGTCCAATCTACACAAATG
genomic: GAAATTCTATGATGCCTACTTCAATGATTCAGATTGGGAGGCTTTGCCAGgcatgcatgc ... ttggttgcagTTCCCTCAAACTGGCAAATGCATGGGTTTGACCGTCCAATCTACACAAATG
EST: gi|58690363|gb|CK079050.1|CK079050
EST:     GAAATTCTATGATGCCTACTTCAATGATTCAGATTGGGAGGCTTTGCCAG                         TTCCCTCAAACTGGCAAATGCATGGGTTTGACCGTCCAATCTACACAAATG
genomic: GAAATTCTATGATGCCTACTTCAATGATTCAGATTGGGAGGCTTTGCCAGgcatgcatgc ... ttggttgcagTTCCCTCAAACTGGCAAATGCATGGGTTTGACCGTCCAATCTACACAAATG
EST: gi|58668740|gb|CK057426.1|CK057426
EST:     GAAATTCTATGATGCCTACTTCAATGATTCAGATTGGGAGGCTTTGCCAG                         TTCCCTCAAACTGGCAAATGCATGGGTTTGACCGTCCAATCTACACAAATG
genomic: GAAATTCTATGATGCCTACTTCAATGATTCAGATTGGGAGGCTTTGCCAGgcatgcatgc ... ttggttgcagTTCCCTCAAACTGGCAAATGCATGGGTTTGACCGTCCAATCTACACAAATG
EST: gi|86904819|gb|CI310612.1|CI310612
EST:     GATTCAGATTGGGAGGCTTTGCCAG                         TTCCCTCAAACTGGCAAATGCATGGGTTTGACCGTCCAATCTACACAAATG
genomic: GATTCAGATTGGGAGGCTTTGCCAGgcatgcatgc ... ttggttgcagTTCCCTCAAACTGGCAAATGCATGGGTTTGACCGTCCAATCTACACAAATG

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: 52 (upstream exon), 75 (downstream exon)
Score: 18

AGTGGATACTGGAAGTTCCTTTTGGCTTCCTCGCCAGAATCTGTTCCAGAGAAATTCTATGATGCCTACTTCAATGATTCAGATTGGGAGGCTTTGCCAGgcatgcatgc ... ttggttgcagTTCCCTCAAACTGGCAAATGCATGGGTTTGACCGTCCAATCTACACAAATGTCACTTATCCTTTCACCATGAACCCGCCATTTGTGCCAAATGATAATCC




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