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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatcatctcttctgtaatgcagcgaattatgcatatttgggcgtcctttcagttcaatttgtttgatcagGTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT

Basic information

species Oryza sativa
transcript LOC_Os02g43594.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G171406_T03 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------------------------gtaatatcatctcttc-----tgtaatgcagcgaattatgcatatttgggcgtcctttcagttcaatttgtttgatcagGTGTG-GCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT------------------------------------
                                                                                                                       || ||  | || || |     | |||||||||    ||| ||| ||  |||    ||    |||  ||| |||||||||||| | |||||||| ||  ||||||||||||||||  | ||||||||||| ||||| ||| | |                                    
gtttctctctttcctcctcccctcccgacttctccaaatcgccgccttttgttgatttatctattttgcttgcaattagtttttggaaagcaaggttcggaatccgttccaaacagaacgtcatcacttccctccccccttttaatgcagcagtatattcatcttctggc----ttctgtttctgtttctttgatcagGTGGGTGCAATGGGAGGTAGCGGAACGCTGATCTCGGTTTACCCCGAGGAGCTCACCTTCTTGTGTAAGCTGTGTGGATTTATTGATATATTCGTTCGCA

upper sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G171406_T02 (Zea mays), 3'ss of exon 1
-------------------------gtaatatcatctcttc-----tgtaatgcagcgaattatgcatatttgggcgtcctttcagttcaatttgtttgatcagGTGTG-GCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT
                         || ||  | || || |     | |||||||||    ||| ||| ||  |||    ||    |||  ||| |||||||||||| | |||||||| ||  ||||||||||||||||  | ||||||||||| ||||| ||| | |
gttcggaatccgttccaaacagaacgtcatcacttccctccccccttttaatgcagcagtatattcatcttctggc----ttctgtttctgtttctttgatcagGTGGGTGCAATGGGAGGTAGCGGAACGCTGATCTCGGTTTACCCCGAGGAGCTCACCTTCTTGT

upper sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G171406_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------------------------gtaatatcatctcttc-----tgtaatgcagcgaattatgcatatttgggcgtcctttcagttcaatttgtttgatcagGTGTG-GCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT
                                                                                                                       || ||  | || || |     | |||||||||    ||| ||| ||  |||    ||    |||  ||| |||||||||||| | |||||||| ||  ||||||||||||||||  | ||||||||||| ||||| ||| | |
gtttctctctttcctcctcccctcccgacttctccaaatcgccgccttttgttgatttatctattttgcttgcaattagtttttggaaagcaaggttcggaatccgttccaaacagaacgtcatcacttccctccccccttttaatgcagcagtatattcatcttctggc----ttctgtttctgtttctttgatcagGTGGGTGCAATGGGAGGTAGCGGAACGCTGATCTCGGTTTACCCCGAGGAGCTCACCTTCTTGT

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|88728659|gb|CI752169.1|CI752169
EST:     CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAG                         GTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACC
genomic: CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAGgtaatatcat ... gtttgatcagGTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACC
EST: gi|88401755|gb|CI591082.1|CI591082
EST:     CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAG                         GTGTGGCAATGGGTGGCGGGGGAACGCTGATCTCCATCTACCCCGAGGACC
genomic: CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAGgtaatatcat ... gtttgatcagGTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACC
EST: gi|88389102|gb|CI595336.1|CI595336
EST:     CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAG                         GTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACC
genomic: CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAGgtaatatcat ... gtttgatcagGTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACC
EST: gi|88405086|gb|CI685534.1|CI685534
EST:     CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAG                         GTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACC
genomic: CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAGgtaatatcat ... gtttgatcagGTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACC
EST: gi|88581198|gb|CI698173.1|CI698173
EST:     CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAG                         GTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACC
genomic: CTGGAAAGAAAGGCCGGATTTTACTCTGAACGAAGACAACGAAGGGAAAGgtaatatcat ... gtttgatcagGTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcagcgaattatgcatatttgggcgtcctttcagttcaatttgtttgatcagGTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT
                                          tttgttt  CT-rich tract
         aattatgcatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatcatctcttctgtaatgcagcgaattatgcatatttgggcgtcctttcagttcaatttgtttgatcagGTGTGGCAATGGGTGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT