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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatttaaactcaattgaaggcaaacttttccgttgatagtgttcgttgcaattgacaatttttatgtgactaaaatcatcttttgggttgaattttcagGGGTTTAGGCTCAAACAGGTTTAATGGCTCCCTTCCTTCAGAACTGGGGAACCTGGACAAGCTTCAGGAATT

Basic information

species Oryza sativa
transcript LOC_Os04g52600.1
intron # 5
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|88574965|gb|CI666734.1|CI666734
EST:     TATTCCAAAGGAGCTCGGTAACCTTACGAATCTTGTATCACT                         GGGTTTAGGCTCAAACAGGTTTAATGGCTCCCTTCCTTCACAACTGGGGAA
genomic: TATTCCAAAGGAGCTCGGTAACCTTACGAATCTTGTATCACTgtaagaacta ... gaattttcagGGGTTTAGGCTCAAACAGGTTTAATGGCTCCCTTCCTTCAGAACTGGGGAA
EST: gi|88302417|gb|CI668263.1|CI668263
EST:     TATTCCAAAGGAGCTCGGTAACCTTACGAATCTTGTATCACT                         GGGTTTAGGCTCAAACAGGTTTAATGGCTCCCTTCCTTCAGAACTGGGGAA
genomic: TATTCCAAAGGAGCTCGGTAACCTTACGAATCTTGTATCACTgtaagaacta ... gaattttcagGGGTTTAGGCTCAAACAGGTTTAATGGCTCCCTTCCTTCAGAACTGGGGAA
EST: gi|88570904|gb|CI662277.1|CI662277
EST:     TATTCCAAAGGAGCTCGGTAACCTTACGAATCTTGTATCACT                         GGGTTTAGGCTCAAACAGGTTTAATGGCTCCCTTCCTTCAGAACTGGGGAA
genomic: TATTCCAAAGGAGCTCGGTAACCTTACGAATCTTGTATCACTgtaagaacta ... gaattttcagGGGTTTAGGCTCAAACAGGTTTAATGGCTCCCTTCCTTCAGAACTGGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcaattgacaatttttatgtgactaaaatcatcttttgggttgaattttcagGGGTTTAGGCTCAAACAGGTTTAATGGCTCCCTTCCTTCAGAACTGGGGAACCTGGACAAGCTTCAGGAATT
                       gactaaa  putative branch site (score: 2)
                                                ttttc  putative PPT
     aattgacaatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatttaaactcaattgaaggcaaacttttccgttgatagtgttcgttgcaattgacaatttttatgtgactaaaatcatcttttgggttgaattttcagGGGTTTAGGCTCAAACAGGTTTAATGGCTCCCTTCCTTCAGAACTGGGGAACCTGGACAAGCTTCAGGAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - -tgaaggc
- - - - - - - - - - - - - - - - - - - - - - - - gcaattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaaa