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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaagatgggtatttttagtcccggattcgtactcccggttgtataaccgggactataggggggtttctaaccgggagtaaagcccctttctctaccagTGCGAGGTCCTCATGGAGATTTTTATCAGGCTGCCGGCGAAAACTCTTGCTCGTTTCAAGTCTGTCTGCAAGGCATGGCACACCATCATCTCTGAACCAT

Basic information

species Oryza sativa
transcript LOC_Os01g45020.2
intron # 1
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|25797715|gb|CA753676.1|CA753676
EST:     CTCAAAACATACAAGAGGAGAAGAGTGAACAGGGCTACCATCCCTCAGTTGT                        
genomic: CTCAAAACATACAAGAGGAGAAGAGTGAACAGGGCTTCCATCCCTCAG-T-Tgttagacgac ... tctctacca
EST: gi|58659343|gb|CK048023.1|CK048023
EST:     CTCAAAACATACAAGAGGAGAAGAGTGAACAGGGCTTCCATCCCTCAGTTGT                        
genomic: CTCAAAACATACAAGAGGAGAAGAGTGAACAGGGCTTCCATCCCTCAG-T-Tgttagacgac ... tctctacca
EST: gi|58654783|gb|CK043463.1|CK043463
EST:     CTCAAAACATACAAGAGGAGAAGAGTGAACAGGGCTTCCATCCCTCAGTTGT                        
genomic: CTCAAAACATACAAGAGGAGAAGAGTGAACAGGGCTTCCATCCCTCAG-T-Tgttagacgac ... tctctacca


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaccgggactataggggggtttctaaccgggagtaaagcccctttctctaccagTGCGAGGTCCTCATGGAGATTTTTATCAGGCTGCCGGCGAAAACTCTTGCTCGTTTCAAGTCTGTCTGCAAGGCATGGCACACCATCATCTCTGAACCAT
                     ttctaac  putative branch site (score: 1)
                                       cccctttctctacc  putative PPT
                    tttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaagatgggtatttttagtcccggattcgtactcccggttgtataaccgggactataggggggtttctaaccgggagtaaagcccctttctctaccagTGCGAGGTCCTCATGGAGATTTTTATCAGGCTGCCGGCGAAAACTCTTGCTCGTTTCAAGTCTGTCTGCAAGGCATGGCACACCATCATCTCTGAACCAT

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