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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgatctttttattatttttgtacatcagaaataccatctcaaggggtgtgggatttattgtttgctattcacag

Basic information

species Oryza sativa
transcript LOC_Os01g16414.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16414.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G088487_T03 (Zea mays), 5'ss of exon 3
AATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgatctttttattatttttgtacatcagaaa----taccatctcaaggggtgtggg-atttattgtttgctattcacag------------------------------------
 || ||| ||||||| |||||||| || |||||  |||||||||||||||||||||||| | | ||||  ||| | | |||  | |      ||   | ||| | | ||     | || || |||| | |     |                                    
CATCATCTTGACAGGTGGAAGCACACTGTTCCCCAGATTCACCGAAAGATTgtaagttg-tttctttagcattatag-acagtatatgcctttattttgtcatgagttggatacacttgttatttggtttcttttgaggtagtcactgagattgcataaactgcattgacag
















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|87024681|gb|CI259396.1|CI259396
EST:     ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATT                         GGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
genomic: ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgat ... ctattcacagGGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
EST: gi|86426261|gb|CI071358.1|CI071358
EST:     ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATT                         GGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
genomic: ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgat ... ctattcacagGGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
EST: gi|86487394|gb|CI130027.1|CI130027
EST:     ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATT                         GGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
genomic: ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgat ... ctattcacagGGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
EST: gi|86496996|gb|CI139629.1|CI139629
EST:     ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATT                         GGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
genomic: ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgat ... ctattcacagGGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
EST: gi|86427550|gb|CI072647.1|CI072647
EST:     ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATT                         GGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
genomic: ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgat ... ctattcacagGGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
EST: gi|58669740|gb|CK058426.1|CK058426
EST:     ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATT                         GGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
genomic: ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgat ... ctattcacagGGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
EST: gi|86433723|gb|CI094066.1|CI094066
EST:     ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATT                         GGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT
genomic: ATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgat ... ctattcacagGGAAAAGGAACTTCGTCCTCTTGTGCCTGATGACTACCAAGTAAAGATAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTATCCTGACAGGAGGAAGCACGCTATTCCCTCGATTCACCGAAAGATTgtaagttgatctttttattatttttgtacatcagaaataccatctcaaggggtgtgggatttattgtttgctattcacag

- - - - - -  GGAGGA