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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtccatttttgtgtgtgcactataatatctttttctctgtattaaattatgggcaattattaacttacctttttcttttcgacattttacagGGGAACAATTAGATACGCTAGCGTCCATGCCCACTTAGGTCGTACAGGTAGCAGGAGGGATGATTTAGAGTCACTGGCTTACACCCTAATCTTTTTAATA

Basic information

species Oryza sativa
transcript LOC_Os03g57940.1
intron # 9
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|58680153|gb|CK068840.1|CK068840
EST:     GATGTCTTTAG                         GGGAACAATTAGATACGCTAGCGTCCATGCCCACTTAGGTCGTACAGGTAG
genomic: GATGTCTTTAGgttcgtccat ... cattttacagGGGAACAATTAGATACGCTAGCGTCCATGCCCACTTAGGTCGTACAGGTAG
EST: gi|58599847|gb|CK010375.1|CK010375
EST:     GCATCATCTGGTCAGCATGTTGACTATGATCAGAGGCCAGATGTCTTTAG                         GGGAACAATTAGATACGCTAGCGTCCATGCCCACTTAGGTCGTACAGGTAG
genomic: GCATCATCTGGTCAGCATGTTGACTATGATCAGAGGCCAGATGTCTTTAGgttcgtccat ... cattttacagGGGAACAATTAGATACGCTAGCGTCCATGCCCACTTAGGTCGTACAGGTAG
EST: gi|58689275|gb|CK077962.1|CK077962
EST:     GCATCATCTGGTCAGCATGTTGACTATGATCAGAGGCCAGATGTCTTTAG                         GGGAACAATTAGATACGCTAGCGTCCATGCCCACTTAGGTCGTACAGGTAG
genomic: GCATCATCTGGTCAGCATGTTGACTATGATCAGAGGCCAGATGTCTTTAGgttcgtccat ... cattttacagGGGAACAATTAGATACGCTAGCGTCCATGCCCACTTAGGTCGTACAGGTAG

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: 67 (upstream exon), 75 (downstream exon)
Score: 26

CATCCAGGTGGAAAGAAGCATCATCTGGTCAGCATGTTGACTATGATCAGAGGCCAGATGTCTTTAGgttcgtccat ... cattttacagGGGAACAATTAGATACGCTAGCGTCCATGCCCACTTAGGTCGTACAGGTAGCAGGAGGGATGATTTAGAGTCACTGGCTTACACCCTAATCTTTTTAATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtattaaattatgggcaattattaacttacctttttcttttcgacattttacagGGGAACAATTAGATACGCTAGCGTCCATGCCCACTTAGGTCGTACAGGTAGCAGGAGGGATGATTTAGAGTCACTGGCTTACACCCTAATCTTTTTAATA
                              cctttttcttttcgac  CT-rich tract
                 aattattaactta  TA-rich tract