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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcacaattgattgcatttctgggagatatgttataaacataggagtatctgtgtatttttctacagattctggtatcaaaccgagttgctaagacattgtttattcgtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG

Basic information

species Oryza sativa
transcript LOC_Os06g33710.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G047867_T01 (Zea mays), 3'ss of exon 2
---------------------------------gtacatcacaattgattgcatttctg-ggagatatgttataaacataggagtatctgtgtatttttctacagattctggtatcaaaccgagttgctaagacattgtttattcgtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
                                  ||  | || ||   |||  | | |  ||  | |    ||| | |  |||  || | ||| | ||||  ||| ||||| |||  |      |   ||  |     || ||  |||||||||||||||||||||||||||||||||||||| || || ||||||||||
gtacgttcaggatccagactggtagctaatgggctatgtgaccatcatttgtttgtgtccggcaacaatcaatacatacgggaa-atatatgt-tctttcagcag-ttctgatatatatatatatatatagtatcaaattgat--gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAATAACCCGATGTGGCCTG
















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|29677612|gb|CB673887.1|CB673887
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|29678039|gb|CB674314.1|CB674314
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|29661773|gb|CB658048.1|CB658048
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|29660327|gb|CB656602.1|CB656602
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|29657057|gb|CB653332.1|CB653332
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|29681267|gb|CB677542.1|CB677542
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|88431166|gb|CI574337.1|CI574337
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|29681920|gb|CB678195.1|CB678195
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|29674257|gb|CB670532.1|CB670532
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|29657894|gb|CB654169.1|CB654169
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
EST: gi|29639074|gb|CB644083.1|CB644083
EST:     CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTG                         GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
genomic: CCATGCCACAGTGGTGTCAGGGTGGTTCACGGAACCCCGCTCGCACTCTGgtacatcaca ... gtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagattctggtatcaaaccgagttgctaagacattgtttattcgtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG
                                  attgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatcacaattgattgcatttctgggagatatgttataaacataggagtatctgtgtatttttctacagattctggtatcaaaccgagttgctaagacattgtttattcgtatgtgcagGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG