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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctctttgcttataaacatgtaaaaatgtatgagagatgtaccctgaactaataagatccctgtgtacagAACTGACGGAAATTCTTGGAGTAATGGACCAGCACCACCACCTCCACCGTATTCAGCTCCACCTCCACCAAACCGTCCAAACAGCCCAGGTCAAAACAAT

Basic information

species Oryza sativa
transcript LOC_Os03g08550.2
intron # 8
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|58652520|gb|CK041200.1|CK041200
EST:     CATTTCACTGGCTGGATTCCTAGTCAACTTAAGAAGATAAACAATCTACA                         AACTGACGGAAATTCTTGGAGTAATGGACCAGCACCACCACCTCCACCGTA
genomic: CATTTCACTGGCTGGATTCCTAGTCAACTTAAGAAGATAAACAATCTACAgtgagttctc ... ctgtgtacagAACTGACGGAAATTCTTGGAGTAATGGACCAGCACCACCACCTCCACCGTA
EST: gi|58661405|gb|CK050085.1|CK050085
EST:     CATTTCACTGGCTGGATTCCTAGTCAACTTAAGAAGATAAACAATCTACA                         AACTGACGGAAATTCTTGGAGTAATGGACCAGCACCACCACCTCCACCGTA
genomic: CATTTCACTGGCTGGATTCCTAGTCAACTTAAGAAGATAAACAATCTACAgtgagttctc ... ctgtgtacagAACTGACGGAAATTCTTGGAGTAATGGACCAGCACCACCACCTCCACCGTA
EST: gi|58658124|gb|CK046804.1|CK046804
EST:     CATTTCACTGGCTGGATTCCTAGTCAACTTAAGAAGATAAACAATCTACA                         AACTGACGGAAATTCTTGGAGTAATGGACCAGCACCACCACCTCCACCGTA
genomic: CATTTCACTGGCTGGATTCCTAGTCAACTTAAGAAGATAAACAATCTACAgtgagttctc ... ctgtgtacagAACTGACGGAAATTCTTGGAGTAATGGACCAGCACCACCACCTCCACCGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtaaaaatgtatgagagatgtaccctgaactaataagatccctgtgtacagAACTGACGGAAATTCTTGGAGTAATGGACCAGCACCACCACCTCCACCGTATTCAGCTCCACCTCCACCAAACCGTCCAAACAGCCCAGGTCAAAACAAT
                               aactaat  putative branch site (score: 2)
                                          tccctgt  putative PPT
     taaaaatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctctttgcttataaacatgtaaaaatgtatgagagatgtaccctgaactaataagatccctgtgtacagAACTGACGGAAATTCTTGGAGTAATGGACCAGCACCACCACCTCCACCGTATTCAGCTCCACCTCCACCAAACCGTCCAAACAGCCCAGGTCAAAACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC