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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacacatatattagtaaacagcaagatttcaatcatataaaatataaaaattgatttggaattatcaaaccaacttaactaaccagagcaatgtatgcagGTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGCTTTAACAATTGCGCTATCTTATGTCATTGGTGGACTGGTCCCTCTCCTT

Basic information

species Oryza sativa
transcript LOC_Os04g38940.1
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|29684383|gb|CB680658.1|CB680658
EST:     GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAG                         GTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
genomic: GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAGgtaatatgac ... atgtatgcagGTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
EST: gi|88244031|gb|CI243153.1|CI243153
EST:     AATCCTCAAGCTTGGCTCGACTTCATGATGAG                         GTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
genomic: AATCCTCAAGCTTGGCTCGACTTCATGATGAGgtaatatgac ... atgtatgcagGTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
EST: gi|38474591|gb|CF958724.1|CF958724
EST:     GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAG                         GTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
genomic: GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAGgtaatatgac ... atgtatgcagGTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
EST: gi|88830374|gb|CI010574.1|CI010574
EST:     GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAG                         GTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
genomic: GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAGgtaatatgac ... atgtatgcagGTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
EST: gi|58031144|gb|CX728687.1|CX728687
EST:     GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAG                         GTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
genomic: GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAGgtaatatgac ... atgtatgcagGTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
EST: gi|55436676|gb|CV731474.1|CV731474
EST:     GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAG                         GTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC
genomic: GTGGACGGGCTCCGTAGGAATCCTCAAGCTTGGCTCGACTTCATGATGAGgtaatatgac ... atgtatgcagGTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaattgatttggaattatcaaaccaacttaactaaccagagcaatgtatgcagGTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGCTTTAACAATTGCGCTATCTTATGTCATTGGTGGACTGGTCCCTCTCCTT
                               aactaac  putative branch site (score: 1)
              aattatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacacatatattagtaaacagcaagatttcaatcatataaaatataaaaattgatttggaattatcaaaccaacttaactaaccagagcaatgtatgcagGTTTGAGCTGGGATTGGAGAAACCAGACCCTAAAAGAGCTATACAGAGCGCTTTAACAATTGCGCTATCTTATGTCATTGGTGGACTGGTCCCTCTCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
-acacata
- - - - - - - - aacagca
- - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaac