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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttactatcccactaaggaacatcgctgacacaactgaaattgaaataaccggccaggaaattctctcttgcagGTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGACTAGAGAATGGCATTCAGGAATTCGGGTCCATAAAGACGGTGCTTACAT

Basic information

species Oryza sativa
transcript LOC_Os03g20420.1
intron # 16
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|86437525|gb|CI119247.1|CI119247
EST:     CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAG                         GTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGA
genomic: CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAGgtatttttac ... tctcttgcagGTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGA
EST: gi|29680538|gb|CB676813.1|CB676813
EST:     CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAG                         GTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGA
genomic: CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAGgtatttttac ... tctcttgcagGTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGA
EST: gi|38477359|gb|CF961492.1|CF961492
EST:     CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAG                         GTTGTCAATTTTGGTAACAAAGCTGTGAATCTTA
genomic: CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAGgtatttttac ... tctcttgcagGTTGTCAATTTTGGTAACAAAGCTGTGAATCTTA
EST: gi|29645169|gb|CB650176.1|CB650176
EST:     CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAG                         GTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGA
genomic: CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAGgtatttttac ... tctcttgcagGTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGA
EST: gi|29676177|gb|CB672452.1|CB672452
EST:     CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAG                         GTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGA
genomic: CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAGgtatttttac ... tctcttgcagGTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGA
EST: gi|27554516|gb|CA998416.1|CA998416
EST:     CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAG                         GTTGTNCA-TTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGG
genomic: CTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAGgtatttttac ... tctcttgcagGTTGT-CAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGG

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: 55 (upstream exon), 75 (downstream exon)
Score: 34

TCATCCCTTGACAATTCAGGTGTCAAACTATGATCAATTGGCCGCATCTGCTCTCACTTGGCAGAATTCTAACGATGGAAACACTTACTTGAAAATAAAGgtatttttac ... tctcttgcagGTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGACTAGAGAATGGCATTCAGGAATTCGGGTCCATAAAGACGGTGCTTACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcgctgacacaactgaaattgaaataaccggccaggaaattctctcttgcagGTTGTCAATTTTGGTAACAAAGCTGTGAATCTTAATATAGCTGTAGCTGGACTAGAGAATGGCATTCAGGAATTCGGGTCCATAAAGACGGTGCTTACAT
                        aaataac  putative branch site (score: 34)
                                          ttctctcttgc  putative PPT
                tgaaattgaaataa  TA-rich tract