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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgaccctatgcatatttgattttttattacctttgctgtttggacattaagttctaatattcttgctactttgccagGTCAAATAAAGAATTTGATGACCTAGTGAAGCATGTCATTGATTATGATATTGTTCTAGAAACTGATGTTAGTTTTGCCAAGCTGCTAGTCTTCCCTTCT

Basic information

species Oryza sativa
transcript LOC_Os11g06130.2
intron # 2
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|33678420|gb|CF306659.1|CF306659
EST:     GTACCTAGTGCTGAGAGTATTGGCTTATTTTTCTTTTCACAGAATACGAG                         GTCAAATAAAGAATTTGATGACCTAGTGAAGCATGTCATTGATTATGATAT
genomic: GTACCTAGTGCTGAGAGTATTGGCTTATTTTTCTTTTCACAGAATACGAGgtttgttgac ... actttgccagGTCAAATAAAGAATTTGATGACCTAGTGAAGCATGTCATTGATTATGATAT
EST: gi|33795027|gb|CF323389.1|CF323389
EST:     GTACCTAGTGCTGAGAGTATTGGCTTATTTTTCTTTT-ACAGAATACGAG                         GTCAAATAAAGAATTTGATGACCTAGTGAAGCATGTCATTGATTATGATAT
genomic: GTACCTAGTGCTGAGAGTATTGGCTTATTTTTCTTTTCACAGAATACGAGgtttgttgac ... actttgccagGTCAAATAAAGAATTTGATGACCTAGTGAAGCATGTCATTGATTATGATAT
EST: gi|33796490|gb|CF324112.1|CF324112
EST:     GTACCTAGTGCTGAGAGTATTGGCTTATTTTTCTTTTCACAGA-TACGAG                         GTCAAATAAAGAATTTGATGACCTAGTGAAGCATGTCATTGATTATG
genomic: GTACCTAGTGCTGAGAGTATTGGCTTATTTTTCTTTTCACAGAATACGAGgtttgttgac ... actttgccagGTCAAATAAAGAATTTGATGACCTAGTGAAGCATGTCATTGATTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattacctttgctgtttggacattaagttctaatattcttgctactttgccagGTCAAATAAAGAATTTGATGACCTAGTGAAGCATGTCATTGATTATGATATTGTTCTAGAAACTGATGTTAGTTTTGCCAAGCTGCTAGTCTTCCCTTCT
                             ttctaat  putative branch site (score: 2)
                                           ctacttt  putative PPT
                       attaagttctaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgaccctatgcatatttgattttttattacctttgctgtttggacattaagttctaatattcttgctactttgccagGTCAAATAAAGAATTTGATGACCTAGTGAAGCATGTCATTGATTATGATATTGTTCTAGAAACTGATGTTAGTTTTGCCAAGCTGCTAGTCTTCCCTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT