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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaagttaaaaagtgaatagctagtatccaacgacagattaataatgaaatgcatatagattaatattcatctataataatggtgtgttgggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCGGCGCAAATTTTGCGCAAGCAGTGATGGACAAGCTTCGCCTCAAAGACCC

Basic information

species Oryza sativa
transcript LOC_Os10g42780.1
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|8858775|gb|AU096093.1|AU096093
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88905858|gb|CI002196.1|CI002196
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88669920|gb|CI724036.1|CI724036
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88665559|gb|CI715715.1|CI715715
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88503616|gb|CI431122.1|CI431122
EST:     CTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88676201|gb|CI730314.1|CI730314
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88674712|gb|CI728825.1|CI728825
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88674598|gb|CI728711.1|CI728711
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88668108|gb|CI722847.1|CI722847
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88674693|gb|CI728806.1|CI728806
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|89171620|gb|CI720679.1|CI720679
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88671121|gb|CI725237.1|CI725237
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88673791|gb|CI727904.1|CI727904
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|86878387|gb|CI319620.1|CI319620
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGC-GTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88670306|gb|CI724422.1|CI724422
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88671301|gb|CI724347.1|CI724347
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88908739|gb|CI714881.1|CI714881
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCACTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|29676079|gb|CB672354.1|CB672354
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88669371|gb|CI723289.1|CI723289
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|29626168|gb|CB631179.1|CB631179
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88595273|gb|CI714094.1|CI714094
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88905613|gb|CI712912.1|CI712912
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|86871131|gb|CI328333.1|CI328333
EST:     ACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: ACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88675191|gb|CI729304.1|CI729304
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|88673702|gb|CI727815.1|CI727815
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
EST: gi|29626167|gb|CB631178.1|CB631178
EST:     CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAG                         GTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG
genomic: CAGGTGTATAACCGTGGCATTAGCTTTGAGGGTAGTTTCTCTCTTTGAAGgtttgtccct ... gggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaatgcatatagattaatattcatctataataatggtgtgttgggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCGGCGCAAATTTTGCGCAAGCAGTGATGGACAAGCTTCGCCTCAAAGACCC
              gattaat  putative branch site (score: 3)
         atatagattaatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaagttaaaaagtgaatagctagtatccaacgacagattaataatgaaatgcatatagattaatattcatctataataatggtgtgttgggtgggcagGTGTAAATACTTCAGTAACCGCAGCGGTGGTTGTCCTCACGGGGCTGATCGGCGCAAATTTTGCGCAAGCAGTGATGGACAAGCTTCGCCTCAAAGACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT