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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaagcttcatgtttcctctacacaaaacaaaacagagaaggaactgtaccttgaattatgttgtgagctgaatcacatctgtatgtacacatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG

Basic information

species Oryza sativa
transcript LOC_Os05g24550.4
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|29688861|gb|CB685136.1|CB685136
EST:     ATCCTCGTCGCTGCTGGCCCCCAG                         GCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
genomic: ATCCTCGTCGCTGCTGGCCCCCAGgtccttttct ... acatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
EST: gi|33798896|gb|CF325305.1|CF325305
EST:     ATCCTCGTCGCTGCTGGCCCCCAG                         GCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
genomic: ATCCTCGTCGCTGCTGGCCCCCAGgtccttttct ... acatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
EST: gi|88400733|gb|CI596154.1|CI596154
EST:     GCATGCCTCTGCTGCTGCTGCTGGTGATCCTCGTCGCTGCTGGCCCCCAG                         GCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
genomic: GCATGCCTCTGCTGCTGCTGCTGCTGATCCTCGTCGCTGCTGGCCCCCAGgtccttttct ... acatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
EST: gi|58593972|gb|CF992280.1|CF992280
EST:     GCATGCCTCTGCTGCTGCTGCTGGGGATCCTCGTCGCTGCTGGCCCCCAG                         GCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
genomic: GCATGCCTCTGCTGCTGCTGCTGCTGATCCTCGTCGCTGCTGGCCCCCAGgtccttttct ... acatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
EST: gi|88693705|gb|CI737280.1|CI737280
EST:     GCATGCCTCTGTTGCTGCTGCTGCTGATCCTCGTCGCTGCTGGCCCCCAG                         GCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
genomic: GCATGCCTCTGCTGCTGCTGCTGCTGATCCTCGTCGCTGCTGGCCCCCAGgtccttttct ... acatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
EST: gi|88351318|gb|CI627334.1|CI627334
EST:     GCATGCCTCTGCTGGTGCTGTTGCTGATCCTCGTCGCTGCTGGCCCCCAG                         GCAGGCAGAGCTGGAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
genomic: GCATGCCTCTGCTGCTGCTGCTGCTGATCCTCGTCGCTGCTGGCCCCCAGgtccttttct ... acatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG
EST: gi|58593525|gb|CF991833.1|CF991833
EST:     GCATGCCTCGGCTGCTGCTGCTGCTGATCCTCGTCGCTACTGGCCCCCAG                         GCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTTATGACCAAGGAG
genomic: GCATGCCTCTGCTGCTGCTGCTGCTGATCCTCGTCGCTGCTGGCCCCCAGgtccttttct ... acatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtaccttgaattatgttgtgagctgaatcacatctgtatgtacacatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG
       ttgaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaagcttcatgtttcctctacacaaaacaaaacagagaaggaactgtaccttgaattatgttgtgagctgaatcacatctgtatgtacacatgcacagGCAGGCAGAGCTGCAAAGCCAATCCCAAATCTCCAGCTCATGACCAAGGAGGGCGGCAGTTCAAGAATCATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG