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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTGAATTTGTGAATGAGTTGAGTTGCAGCGGGAACAAGTTCCAGTCATGCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctcttatcttgtttggcatagttcagttattttgtgagtgcatttgattaatagtgtacgtttgtttatttatgtcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g42260.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42260.1 (Oryza sativa), 5'ss of exon 17
lower sequence: PP1S371_17V6.1 (Physcomitrella patens), 5'ss of exon 9
CGGTGAATTTGTGAATGAGTTGAGTTGCAGCGGGAACAAGTTCCAGTCATGCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctcttatcttgtttggcatagttcagttattttgt--gagtgcatttgattaatagtgtacgtttgttt-atttatgtcgtgcag---------------------------------------------------------------------------------------------
 || || |  ||| | |||||||| |||| ||||||||||||||| |||||||| || || ||    || || |  ||||| || || ||||| ||  ||| ||            | |        |   | ||    |   | ||||| | |  ||   |||   |  ||  | |  | ||  ||   |                                                                                             
-GGCGAGTGCGTGCACGAGTTGAGCTGCAACGGGAACAAGTTCCATTCATGCGTGTTCCATCCGAACTATCCGTCGTTGCTGGTGATCGGATGTTATCAGgtaaaggggcgggggagatgaatgcgttgatgataaggaggtggggtgcagtgggatag-ggtgggagcgtgcatgaggtgtgatgtttggaagttgaggggggcgtggttggttgggtagtgtatgaatgggcgtgcgtggatgagatgtggtaatggatggtgcatgtggattgaggtgcag

upper sequence: LOC_Os01g42260.1 (Oryza sativa), 5'ss of exon 17
lower sequence: PP1S371_10V6.1 (Physcomitrella patens), 5'ss of exon 4
CGGTGAATTTGTGAATGAGTTGAGTTGCAGCGGGAACAAGTTCCAGTCATGCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctcttatcttgtttggcatagttcagttattttgt--gagtgcatttgattaatagtgtacgtttgttt-atttatgtcgtgcag---------------------------------------------------------------------------------------------
 || || |  ||| | |||||||| |||| ||||||||||||||| |||||||| || || ||    || || |  ||||| || || ||||| ||  ||| ||            | |        |   | ||    |   | ||||| | |  ||   |||   |  ||  | |  | ||  ||   |                                                                                             
GGGCGAGTGCGTGCACGAGTTGAGCTGCAACGGGAACAAGTTCCATTCATGCGTGTTCCATCCGAACTATCCGTCGTTGCTGGTGATCGGATGTTATCAGgtaaaggggcgggggagatgaatgcgttgatgataaggaggtggggtgcagtgggatag-ggtgggagcgtgcatgaggtgtgatgtttggaagttgaggggggcgtggttggttgggtagtgtatgaatgggcgtgcgtggatgagatgtggtaatggatggtgcatgtggattgaggtgcag
















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|88221810|gb|CI221766.1|CI221766
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|16576984|gb|BI804280.1|BI804280
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|29681692|gb|CB677967.1|CB677967
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCCCAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|86430973|gb|CI083396.1|CI083396
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|86431296|gb|CI083719.1|CI083719
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|33690022|gb|CF318261.1|CF318261
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|86260005|gb|CI065878.1|CI065878
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|33690021|gb|CF318260.1|CF318260
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACA
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACA
EST: gi|88842163|gb|CI081419.1|CI081419
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|3107062|gb|D42797.1|D42797
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|8404601|gb|AU091955.1|AU091955
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTNGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACNGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|16575961|gb|BI803257.1|BI803257
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|29673281|gb|CB669556.1|CB669556
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|29638960|gb|CB643969.1|CB643969
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|86601890|gb|CI258566.1|CI258566
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|38478243|gb|CF962376.1|CF962376
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAG
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAG

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: 58 (upstream exon), 52 (downstream exon)
Score: 24

CGGTGAATTTGTGAATGAGTTGAGTTGCAGCGGGAACAAGTTCCAGTCATGCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGTGCTCATGATGGTTTAGTTGCAGCGCTAGCAGCATCGAGCGCAACAGGCA




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