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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgagtatacaaatatgttgcatagaattttgttttggtatcatcttcaatccatcagtccatctaaactgctattctctcccctttgtgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTG

Basic information

species Oryza sativa
transcript LOC_Os05g43540.1
intron # 6
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|88466361|gb|CI529770.1|CI529770
EST:     TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATG                         GTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
genomic: TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATGgtaactgagt ... tgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
EST: gi|88839208|gb|CI378132.1|CI378132
EST:     CATGAGTTTTCATCTCCAGAGACTACTACACCTGGAATCAACCTAAGATG                         GTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
genomic: CATGAG-TCTCATCT-CAGAGACTACTACACCTGGAATCAACCTAAGATGgtaactgagt ... tgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
EST: gi|33691827|gb|CF320066.1|CF320066
EST:     TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATG                         GTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
genomic: TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATGgtaactgagt ... tgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
EST: gi|88296681|gb|CI537648.1|CI537648
EST:     TACTACACCTGGAATCAACCTAAGATG                         GTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
genomic: TACTACACCTGGAATCAACCTAAGATGgtaactgagt ... tgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
EST: gi|29666719|gb|CB662994.1|CB662994
EST:     TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATG                         GTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
genomic: TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATGgtaactgagt ... tgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
EST: gi|11544398|gb|BF475216.1|BF475216
EST:     TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATG                         GTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAG
genomic: TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATGgtaactgagt ... tgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAG
EST: gi|29666720|gb|CB662995.1|CB662995
EST:     TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATG                         GTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG
genomic: TACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATGgtaactgagt ... tgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGG

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), 75 (downstream exon)
Score: 51

TTACTGCTGTAACGTATACTATGCTTTCTGGGGAAGGACAGTTATACACATACATGAGTCTCATCTCAGAGACTACTACACCTGGAATCAACCTAAGATGgtaactgagt ... tgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcaatccatcagtccatctaaactgctattctctcccctttgtgttatcaagGTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTG
                  atctaaa  putative branch site (score: 51)
                         ctgctattctctcccc  CT-rich tract
                  atctaaa  TA-rich tract