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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaatttttattcctttccattgcactacaattccacctattctgcccagatatattatcttctcatgttttggtcttcttag

Basic information

species Oryza sativa
transcript LOC_Os02g42520.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42520.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G149272_T02 (Zea mays), 5'ss of exon 8
GTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaatttttattc---ctttccattgcactacaattccacctattctgcccagatatattatcttc--tcatgttttggtcttcttag
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GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttcttgtcatgccttttgtttccatacatgcatacttcacatatcctattcccttctattcatttgcatttccaacttgctag
















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|86500952|gb|CI143585.1|CI143585
EST:     GGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGAT                         GGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
genomic: GGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaattttta ... gtcttcttagGGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
EST: gi|29643822|gb|CB648829.1|CB648829
EST:     GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGAT                         GGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
genomic: GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaattttta ... gtcttcttagGGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
EST: gi|29618347|gb|CB623359.1|CB623359
EST:     GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGAT                         GGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
genomic: GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaattttta ... gtcttcttagGGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
EST: gi|117244917|gb|CT849641.1|CT849641
EST:     GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGAT                         GGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
genomic: GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaattttta ... gtcttcttagGGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
EST: gi|32948088|gb|BP184660.1|BP184660
EST:     GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGAT                         GGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
genomic: GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaattttta ... gtcttcttagGGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
EST: gi|88965373|gb|CI011624.1|CI011624
EST:     TACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGAT                         GGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
genomic: TACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaattttta ... gtcttcttagGGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
EST: gi|58684609|gb|CK073296.1|CK073296
EST:     GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGAT                         GGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT
genomic: GCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaattttta ... gtcttcttagGGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTT

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), 51 (downstream exon)
Score: 5

GTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATgtaattttta ... gtcttcttagGGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTTTCTGCTCATTATGCACTACTTCTGTCTGGAAGAACATTGAAGGGGTCTT




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