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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaaaatcatgtcaaatgtaagttctcattgatttcctgtagtttttattgttgaacatgaacgatacatttttacaagatatttatgtcaggaaatgctaatcgaaactctgctataacctttcattggtactttcatactcatcgtctaccagtttctaaatgtagTGTCATCAAGCTTCCACTTTGTCCAGTGATGGAAGGGTCATACTGTCATGAGTTTTCAAGCAAACATACAGTTTCACCGTTAGCACTCTCAATCAATTGT

Basic information

species Oryza sativa
transcript LOC_Os01g39810.1
intron # 9
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|29628584|gb|CB633595.1|CB633595
EST:     ATGGCAAATCTTTGTGCGGACATACTGAACCTCATAAAATCGTGTCAAAT                         TGTCATCAAGCTTCCACTTTGTCCAGTGATGGAAGGGTCATACTGTCATGA
genomic: ATGGCAAATCTTTGTGCGGACATACTGAACCTCATAAAATCATGTCAAATgtaagttaaa ... ctaaatgtagTGTCATCAAGCTTCCACTTTGTCCAGTGATGGAAGGGTCATACTGTCATGA
EST: gi|29628609|gb|CB633620.1|CB633620
EST:     ATGGCAAATCTTTGTGCGGACATACTGAACCTCATAAAATCGTGTCAAAT                         TGTCATCAAGCTTCCACTTTGTCCAGTGATGGAAGGGTCATACTGTCATGA
genomic: ATGGCAAATCTTTGTGCGGACATACTGAACCTCATAAAATCATGTCAAATgtaagttaaa ... ctaaatgtagTGTCATCAAGCTTCCACTTTGTCCAGTGATGGAAGGGTCATACTGTCATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataacctttcattggtactttcatactcatcgtctaccagtttctaaatgtagTGTCATCAAGCTTCCACTTTGTCCAGTGATGGAAGGGTCATACTGTCATGAGTTTTCAAGCAAACATACAGTTTCACCGTTAGCACTCTCAATCAATTGT
                                           ttctaaa  putative branch site (score: 2)
                                          tttct  CT-rich tract
                                          tttctaaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaaaatcatgtcaaatgtaagttctcattgatttcctgtagtttttattgttgaacatgaacgatacatttttacaagatatttatgtcaggaaatgctaatcgaaactctgctataacctttcattggtactttcatactcatcgtctaccagtttctaaatgtagTGTCATCAAGCTTCCACTTTGTCCAGTGATGGAAGGGTCATACTGTCATGAGTTTTCAAGCAAACATACAGTTTCACCGTTAGCACTCTCAATCAATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA