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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTCCAGAGATGGAAATGAATCAACAGCATAATGAGGGCAACGAATCTTTCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctcccaaaatttcatagttcttctcttgagaattttgtgcttgtgttccgaaagaattgggatagaagaatgatttttcacaaaatgtgagca...

Basic information

species Oryza sativa
transcript LOC_Os01g57890.1
intron # 1
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|88728990|gb|CI752500.1|CI752500
EST:     TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCG                         AATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
genomic: TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctc ... ttttaatcagAATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
EST: gi|88726288|gb|CI749943.1|CI749943
EST:     TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCG                         AATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
genomic: TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctc ... ttttaatcagAATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
EST: gi|88721836|gb|CI743348.1|CI743348
EST:     TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCG                         AATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
genomic: TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctc ... ttttaatcagAATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
EST: gi|88720267|gb|CI743566.1|CI743566
EST:     TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCG                         AATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
genomic: TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctc ... ttttaatcagAATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
EST: gi|88729603|gb|CI751406.1|CI751406
EST:     TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCG                         AATGATGGGGAGCAGAGAGTGAGTATTCCAGCAAGAGAATTATTTGCAGCA
genomic: TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctc ... ttttaatcagAATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
EST: gi|88730931|gb|CI754544.1|CI754544
EST:     TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCG                         AATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
genomic: TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctc ... ttttaatcagAATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
EST: gi|88728831|gb|CI752341.1|CI752341
EST:     TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCG                         AATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
genomic: TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctc ... ttttaatcagAATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
EST: gi|88719773|gb|CI743283.1|CI743283
EST:     TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCG                         AATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA
genomic: TCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctc ... ttttaatcagAATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCA

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: 73 (upstream exon), 63 (downstream exon)
Score: 6

ATCTCCAGAGATGGAAATGAATCAACAGCATAATGAGGGCAACGAATCTTTCGTGGCCTTGATGAACGGTTTTGCTGGTGACGGGACGGCAACACTACCGgtattttctc ... ttttaatcagAATGATGGGGAGCAGAGAATGAGTATTCCAGCAAGAGAATTATTTGCAGCAATTGAGGCCGACTCAGGCTTGTTGCCTGTGAACAGTAGCAACACTAATG




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