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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaataagtccaaaaccatagtttcagataagaatttgaggatttaaagttcattttgcaagtatgaacagtgatcacttacattgggctgctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGACGGCGGCGGCTGCAGCTACACCTCCAAGTCGCTGTCCTGCGCTCCCTCCA

Basic information

species Oryza sativa
transcript LOC_Os01g65100.1
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|29658133|gb|CB654408.1|CB654408
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|88452998|gb|CI574545.1|CI574545
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGGGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|29617558|gb|CB622570.1|CB622570
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCTTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|29660045|gb|CB656320.1|CB656320
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|88326976|gb|CI676089.1|CI676089
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGT
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGT
EST: gi|29677445|gb|CB673720.1|CB673720
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|88576350|gb|CI670495.1|CI670495
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTT
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTT
EST: gi|88410323|gb|CI575921.1|CI575921
EST:     GGCTCGGCCGCTAC-GCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTAGTCGGCGCTCC-GGCGTTCC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCC
EST: gi|29681953|gb|CB678228.1|CB678228
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|58691668|gb|CK080355.1|CK080355
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCTTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|29657453|gb|CB653728.1|CB653728
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|29633992|gb|CB639001.1|CB639001
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|12623245|gb|AU173458.1|AU173458
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|58587513|gb|CF985821.1|CF985821
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|29674560|gb|CB670835.1|CB670835
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|88388197|gb|CI627736.1|CI627736
EST:     GGCTCGGCCGCTAC-GCAC-ATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGG
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGG
EST: gi|29657215|gb|CB653490.1|CB653490
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
EST: gi|88354398|gb|CI624788.1|CI624788
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTC
EST: gi|29681781|gb|CB678056.1|CB678056
EST:     GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTG                         AGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC
genomic: GGCTCGGCCGCTACCGCACCATCGTGCTCGCCTCCCTCCTCTTCGTCGTGgtcagttccc ... gctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagttcattttgcaagtatgaacagtgatcacttacattgggctgctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGACGGCGGCGGCTGCAGCTACACCTCCAAGTCGCTGTCCTGCGCTCCCTCCA
                              cacttac  putative branch site (score: 2)
     tcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaataagtccaaaaccatagtttcagataagaatttgaggatttaaagttcattttgcaagtatgaacagtgatcacttacattgggctgctgctgcagAGCATGGGGATGTTAACCCTCTCGTCGGCGCTCCCGGCGTTCCACGGCGACGGCGGCGGCTGCAGCTACACCTCCAAGTCGCTGTCCTGCGCTCCCTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT