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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttttccttccagagttcatgatatttggttggaattgtatttctttatatattctatgaactgctcaagtgcatccttttctaaaaagggtttaggtatattgttttatagcttgttagatgcaaggtttttcttaattgttgtttgtttatgaattgtagTTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGTTGTCACGCTCTGTATAACCATGGTGCTACCAGACTATCTGTAATTCCAA

Basic information

species Oryza sativa
transcript LOC_Os06g43630.1
intron # 11
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|58684428|gb|CK073115.1|CK073115
EST:     AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCAT                         TTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
genomic: AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCATgtaagccttt ... tgaattgtagTTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
EST: gi|27576514|gb|CA999208.1|CA999208
EST:     AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCAT                         TTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
genomic: AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCATgtaagccttt ... tgaattgtagTTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
EST: gi|163928456|gb|EG715436.1|EG715436
EST:     AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCAT                         TTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
genomic: AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCATgtaagccttt ... tgaattgtagTTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
EST: gi|88314082|gb|CI600084.1|CI600084
EST:     AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCAT                         TTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
genomic: AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCATgtaagccttt ... tgaattgtagTTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
EST: gi|29630588|gb|CB635597.1|CB635597
EST:     AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCAT                         TTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
genomic: AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCATgtaagccttt ... tgaattgtagTTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
EST: gi|29636933|gb|CB641942.1|CB641942
EST:     AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCAT                         TTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT
genomic: AGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCATgtaagccttt ... tgaattgtagTTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGT

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: 65 (upstream exon), 47 (downstream exon)
Score: 14

GGTAGAAAGAAGAGGGAGGATTGAAAAACAAGTTATCTTCGAAGATCCAGAGCACTCTTCAACATACTGTCTTGCATTTAAAGTGGTCAATCCAAATCATgtaagccttt ... tgaattgtagTTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGTTGTCACGCTCTGTATAACCATGGTGCTACCAGACTATCTGTAATTCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagcttgttagatgcaaggtttttcttaattgttgtttgtttatgaattgtagTTACCTCCTTTAAAGGAGCTGCAAAAGTTGATGAGAATTCAGTCACTCCGTTGTCACGCTCTGTATAACCATGGTGCTACCAGACTATCTGTAATTCCAA
                         tcttaat  putative branch site (score: 14)
                     tttttcttaattgtt  TA-rich tract