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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcactcgcctgtttttcttcaatgttctttgtaattgtttacataaacactgtagctagcaattactaagttgattggactgtttgtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTTGTTATTATCTTTGTCATCACCGTGCTCCTGGCAGCACTTGACTTCTGGG

Basic information

species Oryza sativa
transcript LOC_Os01g22870.1
intron # 2
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|88315643|gb|CI615515.1|CI615515
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|38472061|gb|CF956192.1|CF956192
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|33680657|gb|CF308896.1|CF308896
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|88315649|gb|CI615521.1|CI615521
EST:     GGGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|29678098|gb|CB674373.1|CB674373
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|11544405|gb|BF475223.1|BF475223
EST:     GCGAGAATTATGCAAATCCAAAGACATGCTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCCGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|66913390|gb|CX100238.1|CX100238
EST:     GCGAGAATTATGCAAATCCAAAGACATGCTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCCGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|163925698|gb|EG714534.1|EG714534
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|88692086|gb|CI735661.1|CI735661
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|88417344|gb|CI579005.1|CI579005
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|44679016|gb|CR292450.1|CR292450
EST:     GCGAGAATTATGCAAATCCAAAGACATGCTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCCGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|88400723|gb|CI596144.1|CI596144
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|29678099|gb|CB674374.1|CB674374
EST:     AATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: AATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|25806557|gb|CA762518.1|CA762518
EST:     GCGAGAATTATGCAAATCCAAAGACATGCTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCCGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|27920913|gb|CB096721.1|CB096721
EST:     GCGAGAATTATGCAAATCCAAAGACATGCTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCCGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|88693063|gb|CI736638.1|CI736638
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|86891022|gb|CI305874.1|CI305874
EST:     GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT
EST: gi|218478253|gb|FG951116.1|FG951116
EST:     GCGAGAATTATGCAAATCCAAAGACATGCTTCTTCCATGTCCTCTTCAAG                         GCAGGGGCATTGGCGTTCTACATACTGTCCGCGCTGTTCGTGACCAACTTT
genomic: GCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTT

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: 57 (upstream exon), 70 (downstream exon)
Score: 24

GTGGTCGGCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAGgtactcactc ... gtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTTGTTATTATCTTTGTCATCACCGTGCTCCTGGCAGCACTTGACTTCTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acataaacactgtagctagcaattactaagttgattggactgtttgtatgtgaagGCAGGGGCATTGGCGTTCTACATACTGTCTGCGCTGTTCGTGACCAACTTTGTTATTATCTTTGTCATCACCGTGCTCCTGGCAGCACTTGACTTCTGGG
                            agttgat  putative branch site (score: 24)
                    aattactaa  TA-rich tract