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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaccaagataggtgtgtgcataggatacgttgccctgttaatgacgaacctattttgagtccttttttagggtgcaaccttttgtgagttttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGTTCTACCTAAATTACCAGGTCGGCTATACTATCTATTTGGAAAACCAATT

Basic information

species Oryza sativa
transcript LOC_Os01g25990.2
intron # 11
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|29668220|gb|CB664495.1|CB664495
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|27547623|gb|CA767376.2|CA767376
EST:     ATATCATGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: ATATCA-GAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29674812|gb|CB671087.1|CB671087
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29672920|gb|CB669195.1|CB669195
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29613579|gb|CB618592.1|CB618592
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29674021|gb|CB670296.1|CB670296
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29679493|gb|CB675768.1|CB675768
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29675942|gb|CB672217.1|CB672217
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29672881|gb|CB669156.1|CB669156
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAG-A-G                         ---TACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|86887382|gb|CI313285.1|CI313285
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCA-GTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29673981|gb|CB670256.1|CB670256
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29613652|gb|CB618665.1|CB618665
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
EST: gi|29673211|gb|CB669486.1|CB669486
EST:     TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAG                         GAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT
genomic: TATATCAGAGAAACAATAGAGTCGTTCAACCAAGATTGTCCAGGAGTAAGgtcagatctc ... tttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaacctattttgagtccttttttagggtgcaaccttttgtgagttttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGTTCTACCTAAATTACCAGGTCGGCTATACTATCTATTTGGAAAACCAATT
                                            ttttgtttc  CT-rich tract
                  tttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaccaagataggtgtgtgcataggatacgttgccctgttaatgacgaacctattttgagtccttttttagggtgcaaccttttgtgagttttgtttcagGAGTACTGTAAAAGGAGAGGAAGGAAATCAGGTCTTACACTTGCCTGCTGTTCTACCTAAATTACCAGGTCGGCTATACTATCTATTTGGAAAACCAATT

- accaaga
- - - - - - - - gtgcata
- - - - - - - - - - - - - - - -tgccctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaacc