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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatttagtagtatatgttatactgcatttgcttatgtcatggctcaaaatttctgtttccatcttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g04990.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 2
TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatttagtagtatatgttatactgcatttgcttatg--tcatggctcaaaatttctgtttccatcttgcag-----------------
  || || || |||| ||||||||| ||||| || ||||| ||||||||||| || ||||||||      ||   | | |   | ||  ||  |||    ||   ||| ||  |||| ||     |    | |||                    
AACAAGGGTATAGTGTTGTACTCCCAGAGAAATTACAAACAGGAAAGTGGAACGTTTACAGgtatacctcttc-caatgttcttgatcttgattttttacatcattcaggggccaaatttctgagtatggtattgtttttaattctttctggcag

upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 2
TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggt-----------tatttagtagtatatgttatactgcattt----gcttatgtcatggctcaaa----atttctgtttccatcttgcag
  || || || |||| ||||||||| ||||| || ||||| ||||||||||| || ||||||||              |  ||  |  |   | ||||||  ||||     ||| |  | |||  |   |    |||| |  |||  ||| ||||
AACAAGGGTATAGTGTTGTACTCCCAGAGAAATTACAAACAGGAAAGTGGAACGTTTACAGgtatacctcttccaatgttcttgatcttgatttttatacatcattctggggctaaatttatgagtatgatattatttttaattctttctggcag
















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|88307649|gb|CI644685.1|CI644685
EST:     AGTGCTGTACTCCCTGAGAAGTGGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|58590036|gb|CF988344.1|CF988344
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCGAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88569586|gb|CI660761.1|CI660761
EST:     AGTGCTGTANTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGGTTNCCTGATAACCCACA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|29667939|gb|CB664214.1|CB664214
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88294822|gb|CI604694.1|CI604694
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|87009029|gb|CI304972.1|CI304972
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATANATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88372758|gb|CI612686.1|CI612686
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88288563|gb|CI663352.1|CI663352
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGGTTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|29626657|gb|CB631668.1|CB631668
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCGAAGTCACCTCTTAAGGTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|29627108|gb|CB632119.1|CB632119
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCGAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|29630786|gb|CB635795.1|CB635795
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCGAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|29627343|gb|CB632354.1|CB632354
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCGAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|58605691|gb|CK033724.1|CK033724
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCGAAGTCAGCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|29674287|gb|CB670562.1|CB670562
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88574980|gb|CI666749.1|CI666749
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|33801569|gb|CF326656.1|CF326656
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|117224882|gb|CT845959.1|CT845959
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCGAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88356323|gb|CI652760.1|CI652760
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGGTTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88307728|gb|CI644768.1|CI644768
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatttagtagtatatgttatactgcatttgcttatgtcatggctcaaaatttctgtttccatcttgcag

- - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - -  AGTGGA