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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgaaccaactgccttttattttttttgctttgttctatagataaactcctaagaaacatgacttacgaactttgtaagcacctgaattgcattgtctttcatttgtcatatccaatttatctgcttgatggattcaatcgacaacaagtatgataacaaaatctttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g25820.2
intron # 10
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|27577180|gb|CA999874.1|CA999874
EST:     TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAG                         GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
genomic: TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAGgtaattgaac ... tttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
EST: gi|58665614|gb|CK054300.1|CK054300
EST:     TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAG                         GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
genomic: TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAGgtaattgaac ... tttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
EST: gi|29679760|gb|CB676035.1|CB676035
EST:     TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAG                         GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
genomic: TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAGgtaattgaac ... tttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
EST: gi|29686947|gb|CB683222.1|CB683222
EST:     TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAG                         GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
genomic: TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAGgtaattgaac ... tttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
EST: gi|27577154|gb|CA999848.1|CA999848
EST:     TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAG                         GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
genomic: TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAGgtaattgaac ... tttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
EST: gi|58670791|gb|CK059477.1|CK059477
EST:     TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAG                         GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
genomic: TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAGgtaattgaac ... tttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
EST: gi|27554471|gb|CA998371.1|CA998371
EST:     TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAG                         GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
genomic: TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAGgtaattgaac ... tttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
EST: gi|163925582|gb|EG715403.1|EG715403
EST:     TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAG                         GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
genomic: TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAGgtaattgaac ... tttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
EST: gi|27576530|gb|CA999224.1|CA999224
EST:     TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAG                         GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT
genomic: TTCGCACAAGGGGTGATTGGACTTCACGGCTTAGAACTGTTTTCTCTGAGgtaattgaac ... tttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgcttgatggattcaatcgacaacaagtatgataacaaaatctttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAG
                                tgataac  putative branch site (score: 2)
                                           tcttt  putative PPT
                              tatgataacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgaaccaactgccttttattttttttgctttgttctatagataaactcctaagaaacatgacttacgaactttgtaagcacctgaattgcattgtctttcatttgtcatatccaatttatctgcttgatggattcaatcgacaacaagtatgataacaaaatctttgaaccagGCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG