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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcactcttggtgctactacctgtctgaactttctgaagccgtcgatactgaatgtctgaaaaatgactcgtgaatttctctgacaagtagtccaatggtagGTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTTCTCGCTGTGCGAATG

Basic information

species Oryza sativa
transcript LOC_Os10g35070.1
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|25801869|gb|CA757830.1|CA757830
EST:     TACCTCAAGTATGATAACTGCAACAATGGCGACCTGAAGCCACTGGAGAG                         GTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTT
genomic: TACCTCAAGTATGATAACTGCAACAATGGCGACCTGAAGCCACTGGAGAGgtgatcactc ... ccaatggtagGTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTT
EST: gi|58588710|gb|CF987018.1|CF987018
EST:     TACCTCAAGTATGATAACTGCAACAATGGCGACCTGAAGCCACTGGAGAG                         GTACCCGGAGATGAGCAAGGCTCTGATGATTGCCGGCCGGCCGATCTACTT
genomic: TACCTCAAGTATGATAACTGCAACAATGGCGACCTGAAGCCACTGGAGAGgtgatcactc ... ccaatggtagGTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTT
EST: gi|218491995|gb|FG964383.1|FG964383
EST:     TACCTCAAGTATGATAACTGCAACAATGGCGACCTGAAGCCACTGGAGAG                         GTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTT
genomic: TACCTCAAGTATGATAACTGCAACAATGGCGACCTGAAGCCACTGGAGAGgtgatcactc ... ccaatggtagGTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTT
EST: gi|112785532|gb|EE590887.1|EE590887
EST:     TACCTCAAGTATGATAACTGCAACAATGGCGACCTGAAGCCACTGGAGAG                         GTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTT
genomic: TACCTCAAGTATGATAACTGCAACAATGGCGACCTGAAGCCACTGGAGAGgtgatcactc ... ccaatggtagGTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTT

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: 59 (upstream exon), 46 (downstream exon)
Score: 12

GGAGTGGACTACCTCAAGTATGATAACTGCAACAATGGCGACCTGAAGCCACTGGAGAGgtgatcactc ... ccaatggtagGTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTTCTCGCTGTGCGAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgaatgtctgaaaaatgactcgtgaatttctctgacaagtagtccaatggtagGTACCCGGAGATGAGCAAGGCTCTGATGATGGCCGGCCGGCCGATCTACTTCTCGCTGTGCGAATG
                               ctctgac  putative branch site (score: 12)
          tgaaaaat  TA-rich tract