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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttgattttttttcttcatccaccttattgaaccattgataatactgagcataaacaattaaacatgaacttataatggttttactgaaacagATAAGTCACAAGATAAACAAGCTTTCCTTTGGGGTAGAATTCCCTGGTGTTGTCAATCCTCTTGATGG

Basic information

species Oryza sativa
transcript LOC_Os03g20520.1
intron # 7
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|58601079|gb|CK011607.1|CK011607
EST:     CATTCAACTTCCTTCAAGATCTCTTGAACTTCCAACAAGAAAATTACAAT                         ATAAGTCACAAGAATAA-CAAGCTTTCCTTTGGGGTAGAATTCCCTGGTGT
genomic: CATTCAACTTCCTTCAAGATCTCTTGAACTTCCAACAAGAAAATTACAATgcaagttgat ... actgaaacagATAAGTCACAAGA-TAAACAAGCTTTCCTTTGGGGTAGAATTCCCTGGTGT
EST: gi|33796334|gb|CF324034.1|CF324034
EST:     CATTCAACTTCCTTCAAGATCTCTTGAACTTCCAACAAGAAAATTACAAT                         ATAAGTCACAAGATAAACAAGCTTTCCTTTGGGGTAGAATTCCCTGGGTGT
genomic: CATTCAACTTCCTTCAAGATCTCTTGAACTTCCAACAAGAAAATTACAATgcaagttgat ... actgaaacagATAAGTCACAAGATAAACAAGCTTTCCTTTGGGGTAGAATTCCCTGG-TGT
EST: gi|29657637|gb|CB653912.1|CB653912
EST:     CATTCAACTTCCTTCAGGATCTCTTGAACTTCCAACAAGAAAATTACAAT                         ATAAGTCACAAGATAAACAAGCTTTCCTTTGGGGTAGAATTCCCTGGTGTT
genomic: CATTCAACTTCCTTCAAGATCTCTTGAACTTCCAACAAGAAAATTACAATgcaagttgat ... actgaaacagATAAGTCACAAGATAAACAAGCTTTCCTTTGGGGTAGAATTCCCTGGTGTT

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: 69 (upstream exon), 73 (downstream exon)
Score: 48

CAAAGTAGCTGGAAATTTTCACTTTGCCCCTGGGAAAAGCTTGGACCAATCATTCAACTTCCTTCAAGATCTCTTGAACTTCCAACAAGAAAATTACAATgcaagttgat ... actgaaacagATAAGTCACAAGATAAACAAGCTTTCCTTTGGGGTAGAATTCCCTGGTGTTGTCAATCCTCTTGATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatactgagcataaacaattaaacatgaacttataatggttttactgaaacagATAAGTCACAAGATAAACAAGCTTTCCTTTGGGGTAGAATTCCCTGGTGTTGTCAATCCTCTTGATGG
 cattgat  putative branch site (score: 48)
                                         ttttact  putative PPT
            ataaacaattaaacat  TA-rich tract