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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAACATAAAGACATTGAATGACCAAAGAGAACGAAATGTCAAGGCACTTCAAGAAAAGATGAAAATGAATAAAAAGGAGGTTCAACGTTTCAATCCAgtgagtaggcatgccttttacttcatatgtgtttagtttgtcaaccaagaaataggtgttacatgaacattttctcgcctttag

Basic information

species Oryza sativa
transcript LOC_Os06g48770.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48770.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 12
GAGAACATAAAGACATTGAATGACCAAAGAGAACGAAATGTCAAGGCACTTCAAGAAAAGATGAAAATGAATAAAAAGGAGGTTCAACGTTTCAATCCAgtgagtaggcatgccttttacttcatatgtgtttagtttgtcaaccaagaaatagg-tgttacatgaacattttctcgcctttag
||||||||||| ||| | ||||||||||||||  |||||||||| || |||||||||||||||||| |||| || |||||||||||||| || ||||| |||||| || ||| ||    |||  ||  | |    ||   || ||||   || || ||| ||||| ||||||||  || |||||
GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttggaatgtcta--gcttgctacttttcagtttccacagccaattgatggggtgtcacatggacattttcatgcttttag
















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|58606319|gb|CK034352.1|CK034352
EST:     GGAGGTTCAACGTTTCAATCCA                         GTTGATGCTTTCCCTGGTGATGCAATTATATTCAGGGGGGTTTTGAATCTT
genomic: GGAGGTTCAACGTTTCAATCCAgtgagtaggc ... tcgcctttagGTTGATGCTTTCCCTGGTGATGCAATTATATTCATGAGGGTTTTGAATCTT
EST: gi|29679895|gb|CB676170.1|CB676170
EST:     TTCAAGAAAAGATGAAAATGAATAAAAAGGAGGTTCAACGTTTCAATCCA                         GTTGATGCTTTCCCTGGTGATGCAATTATATTCATGAGGGTTTTGAATCTT
genomic: TTCAAGAAAAGATGAAAATGAATAAAAAGGAGGTTCAACGTTTCAATCCAgtgagtaggc ... tcgcctttagGTTGATGCTTTCCCTGGTGATGCAATTATATTCATGAGGGTTTTGAATCTT
EST: gi|87005733|gb|CI316152.1|CI316152
EST:     TCAACGTTTCAATCCA                         GTTGATGCTTTCCCTGGTGATGCAATTATATTCATGA-GGTTTTGAATCTT
genomic: TCAACGTTTCAATCCAgtgagtaggc ... tcgcctttagGTTGATGCTTTCCCTGGTGATGCAATTATATTCATGAGGGTTTTGAATCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAACATAAAGACATTGAATGACCAAAGAGAACGAAATGTCAAGGCACTTCAAGAAAAGATGAAAATGAATAAAAAGGAGGTTCAACGTTTCAATCCAgtgagtaggcatgccttttacttcatatgtgtttagtttgtcaaccaagaaataggtgttacatgaacattttctcgcctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG