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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGTGGGTAGGACCCAAATGAATGAACAATCTTCCCGGAGCCATTTTGTTTTCACACTGAAGATATCTGGATCAAATGAGgtactcgcttcacccatattttagaatattaatcacagtgctgaaactttacaaactggtcacaatattttttttttcattttcatgctaactaaacagaaccactgaaacttgagcaaatgtatgtcactaattttcttttgatcttaatgcag

Basic information

species Oryza sativa
transcript LOC_Os04g53760.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53760.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 13
GTCTGTGGGTAGGACCCAAATGAATGAACAATCTTCCCGGAGCCATTTTGTTTTCACACTGAAGATATCTGGATCAAATGAGgtactcgcttcacccatattttagaatattaatcacagtgctgaaactttacaaactggtcacaatattttttttttcattttca-----tgctaactaaacagaaccactgaaacttgagcaaatgt------atgtcactaattttcttttgatcttaatgcag
||||||||||| ||| || ||||||||||| || ||| | || |||||||| |||||| | |||||||||||||| || ||||||   |  |    ||| ||    | ||| |   ||   | |  | |   | | | |||||   ||  | | |||   | |  |        ||   || ||| |     || |   | |  |  | |      |   ||    |||  ||||    ||  |||||
GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgta---gaatggaacattttcataattatca--taccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag
















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|86855868|gb|CI271087.1|CI271087
EST:     GGATCAAATGAG                         AACACTGGGCAACAAGTCCAAGGTGTCCTTAACGTGATTGATTTAGCTGGC
genomic: GGATCAAATGAGgtactcgctt ... cttaatgcagAACACTGGGCAACAAGTCCAAGGTGTCCTTAACTTGATTGATTTAGCTGGC
EST: gi|29637660|gb|CB642669.1|CB642669
EST:     CTTCCCGGAGCCATTTTGTTTTCACACTGAAGATATCTGGATCAAATGAG                         AACTCTGGGCAACAAGTCCAAGGTGTCCTTAACTTGATTGATTTAGCTGGC
genomic: CTTCCCGGAGCCATTTTGTTTTCACACTGAAGATATCTGGATCAAATGAGgtactcgctt ... cttaatgcagAACACTGGGCAACAAGTCCAAGGTGTCCTTAACTTGATTGATTTAGCTGGC
EST: gi|87021429|gb|CI274036.1|CI274036
EST:     GTTTTCACACTGAAGATATCTGGATCAAATGAG                         AACACTGGGCAACAAGTCCAAGGTGTCCGTAACTTGATTGATTTAGCTGCC
genomic: GTTTTCACACTGAAGATATCTGGATCAAATGAGgtactcgctt ... cttaatgcagAACACTGGGCAACAAGTCCAAGGTGTCCTTAACTTGATTGATTTAGCTGGC
EST: gi|86829533|gb|CI286731.1|CI286731
EST:     CTTCCCGGAGCCATTTTGTTTTCACACTGAAGATATCTGGATCAAATGAG                         AACACTGGGCA
genomic: CTTCCCGGAGCCATTTTGTTTTCACACTGAAGATATCTGGATCAAATGAGgtactcgctt ... cttaatgcagAACACTGGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGTGGGTAGGACCCAAATGAATGAACAATCTTCCCGGAGCCATTTTGTTTTCACACTGAAGATATCTGGATCAAATGAGgtactcgcttcacccatattttagaatattaatcacagtgctgaaactttacaaactggtcacaatattttttttttcattttcatgctaactaaacagaaccactgaaacttgagcaaatgtatgtcactaattttcttttgatcttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA