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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcacagttcaattcctcgggcataaagctttcctgagacctattcaacaccgtgtgtatgcatgcatggtagATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCGAGGCTCCCTGCCGTCGCCGAGTCGTTCTGCTCGTGGTCATCGCTATCTGGACCTCGCCAAGTT

Basic information

species Oryza sativa
transcript LOC_Os01g27449.1
intron # 1
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|33689302|gb|CF317541.1|CF317541
EST:     TCTTCCCCAATTCCGGCCGTCAAGCTCCACCTTCGATTTCTCCCTCTCCG                         ATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCGAGGCTCCCTGCCGT
genomic: TCTTCCCCAATTCCGGCCGTCAAGCTCCACCTTCGATTTCTCCCTCTCCGgtgagtcaca ... tgcatggtagATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCGAGGCTCCCTGCCGT
EST: gi|218479206|gb|FG957478.1|FG957478
EST:     TCTTCCCCAATTCCGGCCGTCAAGCTCCACCTTCGATTTCTCCCTCTCCG                         ATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCGAGGCTCCCTGCCGT
genomic: TCTTCCCCAATTCCGGCCGTCAAGCTCCACCTTCGATTTCTCCCTCTCCGgtgagtcaca ... tgcatggtagATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCGAGGCTCCCTGCCGT
EST: gi|33822376|gb|CF337000.1|CF337000
EST:     TCTTCCCCAATTCCGGCCGTCAAGCTCCACCTTCGATTTCTCCCTCTCCG                         ATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCGAGGCTCCCTGCCGT
genomic: TCTTCCCCAATTCCGGCCGTCAAGCTCCACCTTCGATTTCTCCCTCTCCGgtgagtcaca ... tgcatggtagATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCGAGGCTCCCTGCCGT
EST: gi|88328426|gb|CI676631.1|CI676631
EST:     TCTTCCCCAATTCCGGCCGTCAAGCTCCACCTTCGATTTCTCCCTCTCCG                         ATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCG
genomic: TCTTCCCCAATTCCGGCCGTCAAGCTCCACCTTCGATTTCTCCCTCTCCGgtgagtcaca ... tgcatggtagATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCG

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: 66 (upstream exon), 56 (downstream exon)
Score: 39

TCCCTCATGAACCCCTGCCAGTGGTGCAGCGAGCTTGGAGATCGGCATCGTCTTCCCCAATTCCGGCCGTCAAGCTCCACCTTCGATTTCTCCCTCTCCGgtgagtcaca ... tgcatggtagATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCGAGGCTCCCTGCCGTCGCCGAGTCGTTCTGCTCGTGGTCATCGCTATCTGGACCTCGCCAAGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggcataaagctttcctgagacctattcaacaccgtgtgtatgcatgcatggtagATCATCAGCCATATCAAGCCGGCGTCGTCATCGAGCGAGGCTCCCTGCCGTCGCCGAGTCGTTCTGCTCGTGGTCATCGCTATCTGGACCTCGCCAAGTT
                       tattcaa  TA-rich tract