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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaattatttataaacactttgaattccattatctaaaaaataaacactttgaatagtgtccccgctttttcttttttcttactattgtatatccttgttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG

Basic information

species Oryza sativa
transcript LOC_Os05g39230.2
intron # 14
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|8856718|gb|AU094036.1|AU094036
EST:     CCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAG                         GGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
genomic: -CATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAGgtgcaattat ... gttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
EST: gi|88245697|gb|CI245546.1|CI245546
EST:     TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAG                         GGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
genomic: TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAGgtgcaattat ... gttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
EST: gi|27547089|gb|CA765265.2|CA765265
EST:     TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAG                         GGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
genomic: TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAGgtgcaattat ... gttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
EST: gi|29623422|gb|CB628433.1|CB628433
EST:     TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAG                         GGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
genomic: TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAGgtgcaattat ... gttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
EST: gi|86250775|gb|CI007638.1|CI007638
EST:     TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAG                         GGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
genomic: TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAGgtgcaattat ... gttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
EST: gi|58607689|gb|CK035722.1|CK035722
EST:     TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAG                         GGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
genomic: TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAGgtgcaattat ... gttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
EST: gi|88828339|gb|CI000448.1|CI000448
EST:     TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAG                         GGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGTGCATTGTTCAA
genomic: TCATTCTTCATGAAAATGCCGAATTTGAGGCAAAAGATGTTGTCCTTAAGgtgcaattat ... gttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
EST: gi|86840134|gb|CI332756.1|CI332756
EST:     AAGATGTTGTCCTTAAG                         GGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA
genomic: AAGATGTTGTCCTTAAGgtgcaattat ... gttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagtgtccccgctttttcttttttcttactattgtatatccttgttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG
                        ttcttac  putative branch site (score: 2)
                                        tccttgttct  putative PPT
              tttttcttttttctta  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaattatttataaacactttgaattccattatctaaaaaataaacactttgaatagtgtccccgctttttcttttttcttactattgtatatccttgttctaccagGGTAACCATATCTTTGAAGTTCCCACTGGTCATAGAATGCGCATTGTTCAAGATGGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA