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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCATGGAACCACCATTTGGCTGTGCCTTCTTGTGTAATGCCAAATATACACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcgagtattaccaaaattttttttctttaagttagaactgttgtatacatagttctgtttatcgattgacacacaccccttgaattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g29409.1
intron # 8
splice site 5'
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|86871960|gb|CI332132.1|CI332132
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|88846613|gb|CI373381.1|CI373381
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|88517790|gb|CI445444.1|CI445444
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|86260139|gb|CI066012.1|CI066012
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|88199516|gb|CI199366.1|CI199366
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|29617638|gb|CB622650.1|CB622650
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|29618956|gb|CB623968.1|CB623968
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|88485196|gb|CI422467.1|CI422467
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|86882808|gb|CI327409.1|CI327409
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACCCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|86890133|gb|CI321310.1|CI321310
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|86482719|gb|CI125352.1|CI125352
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|29689147|gb|CB685422.1|CB685422
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
EST: gi|88544195|gb|CI474269.1|CI474269
EST:     ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAG                         AGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA
genomic: ACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGA

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: 56 (upstream exon), 72 (downstream exon)
Score: 11

CTCATGGAACCACCATTTGGCTGTGCCTTCTTGTGTAATGCCAAATATACACGTGTATGGATTCTCCAAAGCAGAAGATCCTGAATATGACTTCCATGAGgtaagcagcg ... tgaattgcagAGGATAAATTTGACGCTGGGTGAGAACGTGTCCGATGTTGAAATGCATAGAGTGCGGCTCGTTGCTCCTGGAAAATGGATGCTTTGTGCATCATTTACCC




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