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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagagagaacaaactctataaccatgatttcctggttttgttcttatgatttattttacggatgcaaacatgtgaatgaagttcttcatgacattattctggtgatctttataagactaagcatgtggataatggtagcacatttttttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGATGGTAAAACAGAACCAAGTGGTTATTGAATTTCATGATTATTCAGAAGG

Basic information

species Oryza sativa
transcript LOC_Os11g35400.1
intron # 18
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|88320893|gb|CI528045.1|CI528045
EST:     TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAG                         GATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
genomic: TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
EST: gi|58679886|gb|CK068573.1|CK068573
EST:     TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAG                         GATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
genomic: TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
EST: gi|66947112|gb|AU311956.1|AU311956
EST:     TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAG                         GATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
genomic: TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
EST: gi|66947111|gb|AU311955.1|AU311955
EST:     TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAG                         GATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
genomic: TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
EST: gi|66947113|gb|AU311957.1|AU311957
EST:     TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAG                         GATTGCNNNGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
genomic: TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
EST: gi|88476345|gb|CI413616.1|CI413616
EST:     TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAG                         GATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
genomic: TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
EST: gi|86501811|gb|CI144444.1|CI144444
EST:     TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAG                         GATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
genomic: TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
EST: gi|88460370|gb|CI529445.1|CI529445
EST:     NGACTCCAACTTTTAAGCTCAAGAGACCCCANCTGCTCAAATATTACAAG                         GATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
genomic: TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
EST: gi|86501867|gb|CI144500.1|CI144500
EST:     TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAG                         GATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA
genomic: TGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGA

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), 61 (downstream exon)
Score: 12

AAAGGCAATTCACCTAGAGACAACGCCATTCAGCATAGAGAAGGACCTGGTGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagaga ... tttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGATGGTAAAACAGAACCAAGTGGTTATTGAATTTCATGATTATTCAGAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatctttataagactaagcatgtggataatggtagcacatttttttaatgcagGATTGCATTGATCAGCTGTACAAGGATGCCAAGGTGGGAAATAAACAGTGATGGTAAAACAGAACCAAGTGGTTATTGAATTTCATGATTATTCAGAAGG
                                            ttttaat  putative branch site (score: 12)
                                       cattttttt  CT-rich tract
                                      acatttttttaat  TA-rich tract