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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgatcattaggattatctttctttctaatataattggcagttgttccctatttaatcttatctccaactaacaacaaatttcccctacaatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT

Basic information

species Oryza sativa
transcript LOC_Os02g32610.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 11
tatgatcattaggattatctttctttctaatataattggcagttg--ttccctatttaatcttatctccaactaacaacaaatttcccctaca---atgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT
    | ||   |||| |  |  |  | || | |  ||  || | |  |||  |    |   || |  |    |||   ||  | | | || |    || |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||
----aacaaagggataaagtg-cagtgtagtttgtttaccattagaattcaatgaccatctttctacctgtgtaatgtcatgtcttcacttctcttattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT
















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|29680443|gb|CB676718.1|CB676718
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29660723|gb|CB656998.1|CB656998
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29639477|gb|CB644486.1|CB644486
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29625152|gb|CB630163.1|CB630163
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTGCACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29678550|gb|CB674825.1|CB674825
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|88585426|gb|CI703056.1|CI703056
EST:     GGGATCTAAAGTCACCAAATCTGTCGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATCTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29662085|gb|CB658360.1|CB658360
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29680716|gb|CB676991.1|CB676991
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29665413|gb|CB661688.1|CB661688
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29664340|gb|CB660615.1|CB660615
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|33675051|gb|CF303290.1|CF303290
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29630303|gb|CB635312.1|CB635312
EST:     TGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: TGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29664339|gb|CB660614.1|CB660614
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCT
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCT
EST: gi|29675290|gb|CB671565.1|CB671565
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29672353|gb|CB668628.1|CB668628
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|29628356|gb|CB633367.1|CB633367
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
EST: gi|58595275|gb|CF993583.1|CF993583
EST:     GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC
genomic: GGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatcctt ... aatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccctatttaatcttatctccaactaacaacaaatttcccctacaatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT
                      aactaac  putative branch site (score: 1)
     tatttaatcttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgatcattaggattatctttctttctaatataattggcagttgttccctatttaatcttatctccaactaacaacaaatttcccctacaatgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG