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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattattgcatatgttctgtactgttcatacttcatactgtaaaatattatcctttgtccacaccagcccattttgattgaattttttgttgtctgcagGTTTTAATTTTGTCTGTACTGGTTTCAGCTGCTCCTAGAG

Basic information

species Oryza sativa
transcript LOC_Os11g10200.1
intron # 3
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|86859175|gb|CI277074.1|CI277074
EST:     CCTCGAGAAAATTAACATCAAACTGACTAGTGAACACTGTCGATCTGAAT                         GTTTTAATTTTGTCTGTACTGGTTTCAGCTGCTCCTAGAG
genomic: CCTCGAGAAAATTAACATCAAACTGACTAGTGAACACTGTCGATCTGAATgtgagctaat ... ttgtctgcagGTTTTAATTTTGTCTGTACTGGTTTCAGCTGCTCCTAGAG
EST: gi|86425226|gb|CI070323.1|CI070323
EST:     CCTCGAGAAAATTAACATCAAACTGACTAGTGAACACTGTCGATCTGAAT                         GTTTTAATTTTGTCTGTACTGGTTTCAGCTGCTCCTAGAG
genomic: CCTCGAGAAAATTAACATCAAACTGACTAGTGAACACTGTCGATCTGAATgtgagctaat ... ttgtctgcagGTTTTAATTTTGTCTGTACTGGTTTCAGCTGCTCCTAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattatcctttgtccacaccagcccattttgattgaattttttgttgtctgcagGTTTTAATTTTGTCTGTACTGGTTTCAGCTGCTCCTAGAG
                           ttttgat  putative branch site (score: 4)
                                      ttttttgtt  putative PPT
                          attttgattgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattattgcatatgttctgtactgttcatacttcatactgtaaaatattatcctttgtccacaccagcccattttgattgaattttttgttgtctgcagGTTTTAATTTTGTCTGTACTGGTTTCAGCTGCTCCTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - ttgcata
- - - - - - - - - tgtactg
- - - - - - - - - - - - - - - - - catactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgattg