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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCACgtatgatttctttctttgccttcaattgcattgctaaattctaatattcatacttgttctcaccaccataatttagttttaacctttttttatttgttatatggtgtag

Basic information

species Oryza sativa
transcript LOC_Os01g60650.1
intron # 4
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|86859142|gb|CI277052.1|CI277052
EST:     CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCAC                         TATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
genomic: CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCACgtatgatttc ... tatggtgtagTATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
EST: gi|86598102|gb|CI278492.1|CI278492
EST:     CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCAC                         TATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
genomic: CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCACgtatgatttc ... tatggtgtagTATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
EST: gi|38480393|gb|CF964482.1|CF964482
EST:     CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCAC                         TATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
genomic: CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCACgtatgatttc ... tatggtgtagTATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
EST: gi|86858811|gb|CI275060.1|CI275060
EST:     CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCAC                         TATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
genomic: CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCACgtatgatttc ... tatggtgtagTATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
EST: gi|25804201|gb|CA760162.1|CA760162
EST:     CAATTGCAAGTGTCATCTTTTTCAGGGAATTATTAATTTTCTTCCAC                         TATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
genomic: CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCACgtatgatttc ... tatggtgtagTATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
EST: gi|88245896|gb|CI245745.1|CI245745
EST:     TCATCTTCTTCAGGGAATTATTAATTTTCTTCCAC                         TATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
genomic: TCATCTTCTTCAGGGAATTATTAATTTTCTTCCACgtatgatttc ... tatggtgtagTATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
EST: gi|27576402|gb|CA999096.1|CA999096
EST:     ATTTTCTTCCAC                         TATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
genomic: ATTTTCTTCCACgtatgatttc ... tatggtgtagTATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
EST: gi|33807572|gb|CF329679.1|CF329679
EST:     TTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCC-C                         TATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG
genomic: TTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCACgtatgatttc ... tatggtgtagTATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG

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: 47 (upstream exon), 72 (downstream exon)
Score: 22

CAATTGCAAGTGTCATCTTCTTCAGGGAATTATTAATTTTCTTCCACgtatgatttc ... tatggtgtagTATGGGTGGTTTCCAAATATTTTCGTGGTCCTTCTCAG




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