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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAGACTCTAGATTGCGACCAGATCAGCGATGCCTAGAGAATGGTGAGTATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgttacacctttcgcattatatattctggtaaagcatgcattagttaaaagcaactgaatccagaaacaaacgtttgcatcagctgcatttca...

Basic information

species Oryza sativa
transcript LOC_Os03g49770.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49770.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G147332_T01 (Zea mays), 5'ss of exon 9
AACAGACTCTAGATTGCGACCAGATCAGCGATGCCTAGAGAATGGTGAGTATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgttacacc----tttcgcattatatattctggtaaagcatgcattagttaaaagcaactgaatccagaaacaaacgtttgcatcagctgcatttca--
 |||||||| ||||| |||||||| ||| |||| || ||||| ||||| |||||||| |||||||||||||| ||||||||||||||||||||||| ||||| | ||| | || ||    |||| ||   | | ||    |  | | ||    | || |       |   |  ||  | |   |||| |||    | ||| | |  
TACAGACTCAAGATTACGACCAGACCAGAGATGTCTGGAGAACGGTGAATATGAAAGGGCAAATGCTGAGAAATTGAGGCTTGAACAGAGACAACGGCAGgtcattctatgactccccactttcacagcttctgtttctattgaac-tgtggaattttaggatcttttgtttgagttata---gtttacatt--ttacatgtgaaa
















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|27920528|gb|CB096336.1|CB096336
EST:     AGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: AGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|218479373|gb|FG952379.1|FG952379
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|86481119|gb|CI123752.1|CI123752
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|88998022|gb|CI037907.1|CI037907
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|29633377|gb|CB638386.1|CB638386
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|25806343|gb|CA762304.1|CA762304
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|11233415|gb|AU164827.1|AU164827
EST:     ATGAAAGAGCAAAT-CTGAGAAGTTGAGGCTTGAACAGANACAACGACAG                         A
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcag-
EST: gi|11233415|gb|AU164827.1|AU164827
EST:     ATGAAAGAGCAAAT-CTGAGAAGTTGAGGCTTGAACAGANACAACGACAG                         A
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcag-
EST: gi|29634234|gb|CB639243.1|CB639243
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|8858176|gb|AU095494.1|AU095494
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|66923661|gb|CX110509.1|CX110509
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|88837400|gb|CI078760.1|CI078760
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|29682318|gb|CB678593.1|CB678593
EST:     ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: ATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
EST: gi|38479341|gb|CF963472.1|CF963472
EST:     TGAGGGGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAG                         GCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT
genomic: TGA-AAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgt ... gctgctgcagGCACGGAAGATGCAGGAGAGCGGGTGGAAACCTCGGTGGTTTGCAAAAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAGACTCTAGATTGCGACCAGATCAGCGATGCCTAGAGAATGGTGAGTATGAAAGAGCAAATGCTGAGAAGTTGAGGCTTGAACAGAGACAACGACAGgttagtctgttacacctttcgcattatatattctggtaaagcatgcattagttaaaagcaactgaatccagaaacaaacgtttgcatcagctgcatttca

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT