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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATTGAAGAAAAAGAATTACGCAATCAAGTTGCAGGAGTTCAATAGTATATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAGgtttgttaaatgatctctccaaactcatgctagaattttttgtggtatgttttttctacatagaatccgtattttagattgtgaacgtttccaccaactt...

Basic information

species Oryza sativa
transcript LOC_Os01g28810.1
intron # 3
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|55440355|gb|CV733487.1|CV733487
EST:     TATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAG                         ATTCAACGCCTTTATGCCCGTGCTACAAACCAGGAGACTGAAGCACAACCT
genomic: TATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAGgtttgttaaa ... ttatgtgcagATTCAACGCCTTTATGCCCGTGCTACAAACCAGGAGACTGAAGCACAACCT
EST: gi|88337448|gb|CI630745.1|CI630745
EST:     TATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAG                         ATTCAACGCCTTTATGCC
genomic: TATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAGgtttgttaaa ... ttatgtgcagATTCAACGCCTTTATGCC
EST: gi|55435717|gb|CV730991.1|CV730991
EST:     TATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAG                         ATTCAACGCCTTTATGCCCGTGCTACAAACCAGGAGACTGAAGCACAACCT
genomic: TATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAGgtttgttaaa ... ttatgtgcagATTCAACGCCTTTATGCCCGTGCTACAAACCAGGAGACTGAAGCACAACCT
EST: gi|88383868|gb|CI631758.1|CI631758
EST:     TATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAG                         ATNT-AACGCCTTTATGCCCGTGCTACAAANCAGGAGAATGAAGCACAACC
genomic: TATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAGgtttgttaaa ... ttatgtgcagAT-TCAACGCCTTTATGCCCGTGCTACAAACCAGGAGACTGAAGCACAACC

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: 70 (upstream exon), 70 (downstream exon)
Score: 4

GAAATTGAAGAAAAAGAATTACGCAATCAAGTTGCAGGAGTTCAATAGTATATGCAGTACTTGTCATATGAGGGCTGAAAATGCTTGCCTTGGAACTGAGgtttgttaaa ... ttatgtgcagATTCAACGCCTTTATGCCCGTGCTACAAACCAGGAGACTGAAGCACAACCTGAAGAAGTGGACCTTCCATTCCCCCCTACAGCTGGGTCTCAGGAAGGAG




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