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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttccctttccccgtcttctatggtgaaccgtgtggatctgagggtttttgctgacctgtgggtttctctttgattcgctgcag

Basic information

species Oryza sativa
transcript LOC_Os09g08430.1
intron # 2
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|218489030|gb|FG957547.1|FG957547
EST:     CGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAAG
genomic: CGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTC-AAG
EST: gi|117233205|gb|CT848038.1|CT848038
EST:     AGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
genomic: AGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
EST: gi|5607427|gb|AU076125.1|AU076125
EST:     GTNAAGTACTC-AAGGAAGCGACCAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
genomic: GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
EST: gi|33660730|gb|CF291697.1|CF291697
EST:     AGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
genomic: AGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
EST: gi|163920102|gb|EG712032.1|EG712032
EST:     TCAGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
genomic: TCAGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
EST: gi|33669752|gb|CF297991.1|CF297991
EST:     AGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAATG
genomic: AGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAA-G
EST: gi|33660061|gb|CF291028.1|CF291028
EST:     AGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
genomic: AGCCATGGTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
EST: gi|38471990|gb|CF956121.1|CF956121
EST:     GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
genomic: GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
EST: gi|8858037|gb|AU095355.1|AU095355
EST:     GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGNGACTTGCGTGTGCACTTCAAG
genomic: GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGG-GACTTGCGTGTGCACTTCAAG
EST: gi|27577501|gb|CB000196.1|CB000196
EST:     AAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
genomic: AAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
EST: gi|55411166|gb|CV723542.1|CV723542
EST:     GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
genomic: GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
EST: gi|286646|gb|D15453.1|D15453
EST:     GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGT                         CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG
genomic: GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG

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: 71 (upstream exon), 74 (downstream exon)
Score: 402

GTGAAGTACTCGAGGGAGGCGAACAACCCCACCAAGTgtaagcttcc ... ttcgctgcagCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG




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