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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattattcctgcatattcatttgtggctgtctggtacatggttcactgcattctgattttggtacactattatgttctttttttctattgtagATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCATGACTTCCCTGAGTTCCTTTGCGATTACCACTTCAGTTTCTGTGATGTCA

Basic information

species Oryza sativa
transcript LOC_Os10g40780.3
intron # 42
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|58681156|gb|CK069843.1|CK069843
EST:     TG-TCAAATTCATGGAACCATATTTAAGAAATGCTGAACTGGGACAACCC                         ATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCAT
genomic: TGTTCAAATTCATGGAACCATATTTAAGAAATGCTGAACTGGGACAACCCgtaagtatta ... tctattgtagATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCAT
EST: gi|33679180|gb|CF307419.1|CF307419
EST:     TGTTCAAATTCATGGAACCATATTTAAGAAATGCTGAACTGGGACAACCC                         ATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCAT
genomic: TGTTCAAATTCATGGAACCATATTTAAGAAATGCTGAACTGGGACAACCCgtaagtatta ... tctattgtagATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCAT
EST: gi|163928760|gb|EG711897.1|EG711897
EST:     TGTTCAAATTCATGGAACCATATTTAAGAAATGCTGAACTGGGACAACCC                         ATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCAT
genomic: TGTTCAAATTCATGGAACCATATTTAAGAAATGCTGAACTGGGACAACCCgtaagtatta ... tctattgtagATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCAT
EST: gi|58677103|gb|CK065790.1|CK065790
EST:     TGTTCAAATTCATGGAACCATATTTAAGAAATGCTGAACTGGGACAACCC                         ATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCAT
genomic: TGTTCAAATTCATGGAACCATATTTAAGAAATGCTGAACTGGGACAACCCgtaagtatta ... tctattgtagATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCAT

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), 65 (downstream exon)
Score: 11

GTGCAATGCACAGAAGGGCTGGCCATTCTTCCAGAGGTTGCTTGTCGATTTGTTCAAATTCATGGAACCATATTTAAGAAATGCTGAACTGGGACAACCCgtaagtatta ... tctattgtagATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCATGACTTCCCTGAGTTCCTTTGCGATTACCACTTCAGTTTCTGTGATGTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttcactgcattctgattttggtacactattatgttctttttttctattgtagATACACCTGTTGTACAAAGGAACTTTGAGAGTGTTACTTGTGCTACTGCATGACTTCCCTGAGTTCCTTTGCGATTACCACTTCAGTTTCTGTGATGTCA
            ttctgat  putative branch site (score: 11)
                               ttatgttctttttttc  putative PPT
                             tattatgttctttttt  TA-rich tract