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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGCAACCTCAAAAAGAAATTCCGTGCTAAAACACAGCAAACTGAAAATGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattacatgctcatttcagtttcttttgttaattaattccgtttgaatttgtgtgtagtcctatcacatgttcttggtaaattatttttgtagagg...

Basic information

species Oryza sativa
transcript LOC_Os09g12800.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12800.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AC185415.3_FGT005 (Zea mays), 5'ss of exon 8
TTTGGCAACCTCAAAAAGAAATTCCGTGCTAAAACACAGCAAACTGAAAATGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtatta--catgctcatttcagtttcttttgttaattaattccgttt--gaatttgt-gtgtagtcctatcacatgttcttggtaaattatttttgtagagg--
   |||||||| ||||||||||| ||  ||||| | | ||| |||| || ||| |  || ||||||||||||||||| ||||||||||| |||||||| |||||||||   |   | ||||  | ||    |   | ||| |  | ||||  | |||| | || ||||    |      || ||||| | |    |||| | |    
---GGCAACCTGAAAAAGAAATTTCGCTCTAAAGCTCTGCATACTGGAAGTGCGCAGACACTTCCTGGGTCTGGACGTGCTGGATGGGAAGTTGAGCATCGTGgtatttgtctgacacattggatttgaactccatgatttagactgttttgggatttatcgtctagt----ttctgcctttttggtgattgccatttgaacatctg

upper sequence: LOC_Os09g12800.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AC233865.1_FGT006 (Zea mays), 5'ss of exon 7
TTTGGCAACCTCAAAAAGAAATTCCGTGCTAAAACACAGCAAACTGAAAATGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattacatgctcatttcagtttc---ttttgttaattaattccgtttgaatttgtgtgtagtcctatcacatgttcttggtaaattatttttgtagagg-------------------------------------------------------------------------------------------
   |||||||| ||||||||||| ||  ||||| | | ||| ||||||  |||||   | ||||||||||||||||| ||||||||||| |||||||| ||||||||||       |     | ||     | |     |||      ||||    | | | | |||   |  |  ||| || |   ||  |  ||   ||                                                                                             
---GGCAACCTGAAAAAGAAATTTCGCTCTAAAGCTCTGCATACTGAAGGTGCACAGGCACTTCCTGGGTCTGGACGTGCTGGATGGGAAGTTGAGCATCGTGgtattattctgaaacactggatttaaactctacattttagactgttttgggactatttattgtcaagtttctggttttttggtgatggtcatttgggactctacatttgaacatctgttgcatttggggaaggtgttatgaatttactttgacagtgctgaacatgacctggtgttaattcgctgctgtag
















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|86260178|gb|CI066051.1|CI066051
EST:     GACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: GACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|86260178|gb|CI066051.1|CI066051
EST:     GACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: GACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|86260178|gb|CI066051.1|CI066051
EST:     GACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: GACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|86260178|gb|CI066051.1|CI066051
EST:     GACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: GACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|88249569|gb|CI249418.1|CI249418
EST:     GGATGGGAGGTTGAGCAAC                         GTTCAACTAGAAGAGAAAGCAGGGAAAGGAGCAGAGATCGAGGCAGAGACC
genomic: GGATGGGAGGTTGAGCAACgtggtattac ... atcattatagGTTCAACTAGAAGAGAAAGCAGGGAAAGGAGCAGAGATCGAGGCAGAGACC
EST: gi|87029644|gb|CI257439.1|CI257439
EST:     TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|87029644|gb|CI257439.1|CI257439
EST:     TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|87029644|gb|CI257439.1|CI257439
EST:     TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|87029644|gb|CI257439.1|CI257439
EST:     TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|58601891|gb|CK012419.1|CK012419
EST:     TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAAC                         GTGGTTCAACTAGAAGAGAAAGCAGGGAAAGGAGCAGAGATCGAGGCAGAG
genomic: TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatagGT--T-CAACTAGAAGAGAAAGCAGGGAAAGGAGCAGAGATCGAGGCAGAG
EST: gi|29684967|gb|CB681242.1|CB681242
EST:     TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|29684967|gb|CB681242.1|CB681242
EST:     TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|29684967|gb|CB681242.1|CB681242
EST:     TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-
EST: gi|29684967|gb|CB681242.1|CB681242
EST:     TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAAC                         G
genomic: TGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattac ... atcattatag-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGCAACCTCAAAAAGAAATTCCGTGCTAAAACACAGCAAACTGAAAATGCACCAACCCTTCCTGGGTCTGGACGGGCTGGATGGGAGGTTGAGCAACgtggtattacatgctcatttcagtttcttttgttaattaattccgtttgaatttgtgtgtagtcctatcacatgttcttggtaaattatttttgtagagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA