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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcccaaattaaaccgatcagatcatgcacgctcaacacaaaactgaatcaaggctagcgaaaggaacttaacacggttgtgtgcgcgtgatcgagcatggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGGTGTCGCTGATCAGGGCGGTGCTGTACATCATCGCGCAGTGCCTGGGCGC

Basic information

species Oryza sativa
transcript LOC_Os02g41860.4
intron # 1
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|88402055|gb|CI593767.1|CI593767
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATCAACC
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACC
EST: gi|33665208|gb|CF296175.1|CF296175
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
EST: gi|33661591|gb|CF292558.1|CF292558
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAG
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAG
EST: gi|88456051|gb|CI567767.1|CI567767
EST:     TTCGGCGGCATGATCTT-AGTCCTCGTCTACTGCACCGACGGCATCTCAG                         GTGGGCACATCAACCCGGCGGTGACGTTCGGGATGTTCCTGGCGAGGAAGG
genomic: TTCGGCGGCATGATCTTCA-TCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
EST: gi|33662304|gb|CF293271.1|CF293271
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
EST: gi|29686713|gb|CB682988.1|CB682988
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
EST: gi|86888563|gb|CI305631.1|CI305631
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGACGGCATCTCAG                         GTGGGCACATCAACCCG
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCG
EST: gi|58655264|gb|CK043944.1|CK043944
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
EST: gi|33666008|gb|CF296975.1|CF296975
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
EST: gi|33663061|gb|CF294028.1|CF294028
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAG
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAG
EST: gi|88349128|gb|CI678098.1|CI678098
EST:     CTTCGGCGGNATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATTAAACCGGCGGTGA
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGA
EST: gi|9884532|gb|BE607365.1|BE607365
EST:     CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAG                         GTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG
genomic: CTTCGGCGGCATGATCTTCATCCTCGTCTACTGCACCGCCGGCATCTCAGgtcccaaatt ... catggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggctagcgaaaggaacttaacacggttgtgtgcgcgtgatcgagcatggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGGTGTCGCTGATCAGGGCGGTGCTGTACATCATCGCGCAGTGCCTGGGCGC
               acttaac  putative branch site (score: 3)
              aacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcccaaattaaaccgatcagatcatgcacgctcaacacaaaactgaatcaaggctagcgaaaggaacttaacacggttgtgtgcgcgtgatcgagcatggtgcagGTGGGCACATCAACCCGGCGGTGACGTTCGGGCTGTTCCTGGCGAGGAAGGTGTCGCTGATCAGGGCGGTGCTGTACATCATCGCGCAGTGCCTGGGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT