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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGTTCCAGGCGCAAAATGGGCGTGTATGGTTCATCCAAATTCATGAAAGCAGCAGAGTTCAATGGAATACTCAGCAATGACCAACAACTGAATTCTGgtacatgcatttatctcgaaaaaaaattctggtacatgcagataacagatgtgggtccttaattttagtccctatactaatttcctttactaatgctttggataattttgatgtccttttactaatttcaatcattgtcgattag

Basic information

species Oryza sativa
transcript LOC_Os01g66830.1
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|163928559|gb|EG710868.1|EG710868
EST:     AGCAGCAGAGTTCAATGGAATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTATAACTGGAACAAAGTTGCCATAAGGTATTGCGATGGGGCATCGT
genomic: AGCAGCAGAGTTCAATGGAATACTCAGCAATGACCAACAACTGAATTCTGgtacatgcat ... tgtcgattagATTTTTATAACTGGAACAAAGTTGCCATAAGGTATTGCGATGGGGCATCGT
EST: gi|88385983|gb|CI568651.1|CI568651
EST:     AGCACAGTTCAACTGGAATACTCAGCAACTGACCAACACCTGAATTCCTG                         ATTTTTATAACCTGGAACAAAGTTGCCATAAGGTATTGCGATGGGGC-TC
genomic: AGCAGAGTTCAA-TGGAATACTCAGCAA-TGACCAACAACTGAATTC-TGgtacatgcat ... tgtcgattagATTTTTATAAC-TGGAACAAAGTTGCCATAAGGTATTGCGATGGGGCATC
EST: gi|88426051|gb|CI604340.1|CI604340
EST:     GCAGCAGAGTTCAATGGAATACTCACCCAATGACCAACAACTGAATTCTG                         ATTTTTATAACTGGAACAAAGTTGCCATAAGGTATTGCGATGGGGCATCGT
genomic: GCAGCAGAGTTCAATGGAATACTCAGC-AATGACCAACAACTGAATTCTGgtacatgcat ... tgtcgattagATTTTTATAACTGGAACAAAGTTGCCATAAGGTATTGCGATGGGGCATCGT

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: 74 (upstream exon), 73 (downstream exon)
Score: 18

AGTTGTTCCAGGCGCAAAATGGGCGTGTATGGTTCATCCAAATTCATGAAAGCAGCAGAGTTCAATGGAATACTCAGCAATGACCAACAACTGAATTCTGgtacatgcat ... tgtcgattagATTTTTATAACTGGAACAAAGTTGCCATAAGGTATTGCGATGGGGCATCGTTTTCTGGTGATGCGGAGGCCCAAGATAAG




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