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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttcttcttactagactcatttgaaattcacaggcatccattatctgtaaattttaatttactgcgcccatctgcttataagtaacatttttctatagGTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAATTCAATGTTTACATGGATTGGCAATGCCAGTTCGTATGAACAGCAACAAT

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 14
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|58670584|gb|CK059270.1|CK059270
EST:     GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCG                         GTGTCATCAAACTTGAGTCCCACAGATTGTTTTGTCCTGCAATCTGGAAAT
genomic: GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCGgtaatattta ... ttttctatagGTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAAT
EST: gi|88692350|gb|CI735925.1|CI735925
EST:     GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCG                         GTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATC
genomic: GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCGgtaatattta ... ttttctatagGTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATC
EST: gi|88722817|gb|CI746327.1|CI746327
EST:     GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCG                         GTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAAT
genomic: GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCGgtaatattta ... ttttctatagGTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAAT
EST: gi|12404685|gb|AU166286.1|AU166286
EST:     GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCG                         GTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAAT
genomic: GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCGgtaatattta ... ttttctatagGTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAAT
EST: gi|426363|gb|D22226.1|D22226
EST:     GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCG                         GTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAAT
genomic: GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCGgtaatattta ... ttttctatagGTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAAT
EST: gi|88569524|gb|CI660699.1|CI660699
EST:     GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCG                         GTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAAT
genomic: GAATTTCTGGAACATCAATTCACAACAATAAAGTGCTTCAAGTTGATGCGgtaatattta ... ttttctatagGTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtaaattttaatttactgcgcccatctgcttataagtaacatttttctatagGTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAATTCAATGTTTACATGGATTGGCAATGCCAGTTCGTATGAACAGCAACAAT
                                    aagtaac  putative branch site (score: 2)
                                          catttttct  CT-rich tract
                                ttataagtaacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttcttcttactagactcatttgaaattcacaggcatccattatctgtaaattttaatttactgcgcccatctgcttataagtaacatttttctatagGTGTCATCAAACTTGAGTCCCACGGATTGTTTTGTCCTGCAATCTGGAAATTCAATGTTTACATGGATTGGCAATGCCAGTTCGTATGAACAGCAACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA