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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcaccaattcccttgaatatttcttgtgcggcatcgatgcatcaatcttggcattttcatctgctggagaacttacattcggtaattatttctacagGTCATGGTTCCGAGATCATGTAGTCTCTATACTGCTTGGAATTTTGCTAGTTGTTTTGCTGACTTTATCGGCCCTTTTAGTACTGATTGTCTGGAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g40260.2
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|33798177|gb|CF324947.1|CF324947
EST:     AGTTATCAGTTACTTGAATGGAATGTGCAGCCTTTATCCAAGAG                         GTCATGGTTCCGAGATCATGTAGTCTCTATACTGCTTGGAATTTTGCTAGT
genomic: AGTTATCAGTTACTTGAATGGAATGTGCAGCCTTTATCCAAGAGgtaagcaaac ... atttctacagGTCATGGTTCCGAGATCATGTAGTCTCTATACTGCTTGGAATTTTGCTAGT
EST: gi|55408880|gb|CV721256.1|CV721256
EST:     CTTGGCAGTTATCAGTTACTTGAATGGAATGTGCAGCCTTTATCCAAGAG                         GTCATGGTTCCGAG
genomic: CTTGGCAGTTATCAGTTACTTGAATGGAATGTGCAGCCTTTATCCAAGAGgtaagcaaac ... atttctacagGTCATGGTTCCGAG
EST: gi|88197947|gb|CI197797.1|CI197797
EST:     CTTGGCAGTTATCAGTTACTTGAATGGAATGTGCAGCCTTTATCCAAGAG                         GTCATGGTTCCGAGATCATGTAGTCTCTATACTGCTTGGAATTTTGCTAGT
genomic: CTTGGCAGTTATCAGTTACTTGAATGGAATGTGCAGCCTTTATCCAAGAGgtaagcaaac ... atttctacagGTCATGGTTCCGAGATCATGTAGTCTCTATACTGCTTGGAATTTTGCTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcttggcattttcatctgctggagaacttacattcggtaattatttctacagGTCATGGTTCCGAGATCATGTAGTCTCTATACTGCTTGGAATTTTGCTAGTTGTTTTGCTGACTTTATCGGCCCTTTTAGTACTGATTGTCTGGAGAAAG
                           aacttac  putative branch site (score: 2)
                                           ttatttct  putative PPT
                                        taattatttctaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcaccaattcccttgaatatttcttgtgcggcatcgatgcatcaatcttggcattttcatctgctggagaacttacattcggtaattatttctacagGTCATGGTTCCGAGATCATGTAGTCTCTATACTGCTTGGAATTTTGCTAGTTGTTTTGCTGACTTTATCGGCCCTTTTAGTACTGATTGTCTGGAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- ttcacca
- - - - - - - cttgaat
- - - - - - - - - - - - - - gtgcggc
- - - - - - - - - - - - - - - - - - - -atgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttacat