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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaacctcaataaggtttttgtctattctcttaatgttaccttgctaattcaagatcttttgattcgtgtgacttggatatgactttgcttagGTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGACTTGTACTAGTGATGTATTGACCTGGTCAGTGAACCTGTGATGTAATTG

Basic information

species Oryza sativa
transcript LOC_Os01g28989.5
intron # 3
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|29657952|gb|CB654227.1|CB654227
EST:     GCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAG                         GTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGA
genomic: GCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAGgtcaacctca ... ctttgcttagGTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGA
EST: gi|163928204|gb|EG712532.1|EG712532
EST:     TTGTCGTTTGATTGGCCTCAACACTCAG                         GTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGA
genomic: TTGTCGTTTGATTGGCCTCAACACTCAGgtcaacctca ... ctttgcttagGTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGA
EST: gi|29671852|gb|CB668127.1|CB668127
EST:     GCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAG                         GTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGA
genomic: GCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAGgtcaacctca ... ctttgcttagGTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGA
EST: gi|33683397|gb|CF311636.1|CF311636
EST:     GCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAG                         GTCAGTGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGA
genomic: GCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAGgtcaacctca ... ctttgcttagGTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGA

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: 50 (upstream exon), 75 (downstream exon)
Score: 55

TTTGTTGTGCCTAAGTAACACCTCTTTTGCTATGGATAGATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAGgtcaacctca ... ctttgcttagGTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGACTTGTACTAGTGATGTATTGACCTGGTCAGTGAACCTGTGATGTAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttgctaattcaagatcttttgattcgtgtgacttggatatgactttgcttagGTCAATGTGTGAACGACTATTTGGCATTTGGCTGGATTTGGTGGTCAGTGACTTGTACTAGTGATGTATTGACCTGGTCAGTGAACCTGTGATGTAATTG
                                             ctttgctt  CT-rich tract
       taattcaa  TA-rich tract