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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacgaattagtaattttggcctacttattgacattcaacattggtcgtctcaattgtctttatctaattatgcaaacatttgttaaatggaggagacagGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAACGTGGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTAT

Basic information

species Oryza sativa
transcript LOC_Os02g01710.3
intron # 6
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|88845414|gb|CI084339.1|CI084339
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGACAG                      
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCT----Ggtgcgtacaa ... gaggaga
EST: gi|86497902|gb|CI140535.1|CI140535
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGACAG                      
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCT----Ggtgcgtacaa ... gaggaga
EST: gi|86504655|gb|CI147288.1|CI147288
EST:     GGAGCACCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTG                         GGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAAC
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGgtgcgtacaa ... gaggagacagGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAA-
EST: gi|88831540|gb|CI083934.1|CI083934
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGACAG                      
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCT----Ggtgcgtacaa ... gaggaga
EST: gi|86498521|gb|CI141154.1|CI141154
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTG                         GGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAAC
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGgtgcgtacaa ... gaggagacagGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAAC
EST: gi|88841179|gb|CI080633.1|CI080633
EST:     GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTG                         GGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAAC
genomic: GGAGCAGCTGAAAACTATTGATAGTATCCTGGTCAGGTTCTAGAATGCTGgtgcgtacaa ... gaggagacagGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtctcaattgtctttatctaattatgcaaacatttgttaaatggaggagacagGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAACGTGGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTAT
                 atctaat  putative branch site (score: 3)
            tctttatctaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacgaattagtaattttggcctacttattgacattcaacattggtcgtctcaattgtctttatctaattatgcaaacatttgttaaatggaggagacagGGGAATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAACGTGGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTAT

- - - - - - - - - -gcctact
- - - - - - - - - - - - - - - - cattcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatttg