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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatgcctttctatttcaattcgttcttctcaccttattgtattttcttatttactcatgacatatcattcaatggtattttgttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT

Basic information

species Oryza sativa
transcript LOC_Os05g24550.4
intron # 3
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|29688861|gb|CB685136.1|CB685136
EST:     CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
EST: gi|27578059|gb|CB000754.1|CB000754
EST:     CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
EST: gi|29686789|gb|CB683064.1|CB683064
EST:     CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
EST: gi|33798896|gb|CF325305.1|CF325305
EST:     CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
EST: gi|88400733|gb|CI596154.1|CI596154
EST:     CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATAATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
EST: gi|58593972|gb|CF992280.1|CF992280
EST:     CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
EST: gi|29640250|gb|CB645259.1|CB645259
EST:     CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
EST: gi|88693705|gb|CI737280.1|CI737280
EST:     CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACA
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACA
EST: gi|88351318|gb|CI627334.1|CI627334
EST:     CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACAAGCATCCCAATGGTGGCTGGACGGCT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
EST: gi|29656220|gb|CB652495.1|CB652495
EST:     CAAATCTCCAGCTCATGCCCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT
EST: gi|58593525|gb|CF991833.1|CF991833
EST:     CAAATCTCCAGCTTATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG                         GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGAT
genomic: CAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAGgttatgcctt ... gttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtattttcttatttactcatgacatatcattcaatggtattttgttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT
                                         ttttgtt  CT-rich tract
     ttttcttatttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatgcctttctatttcaattcgttcttctcaccttattgtattttcttatttactcatgacatatcattcaatggtattttgttgtcacagGACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA