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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGCTATGGTGGAATGGATGTTGGTGGTGGTACTATGGTACTTGGTGGGATGCCTGCTCCTCCTGACATGGTTTTCTCTCATTCAAACCCTGTCCGCAGgtattatacatttttgttttttccacaccagactgaagattcttttagtagcctgctggaggaaggttttctaatgttctgtatatttaatacatttccttattaattttggattgtcaacag

Basic information

species Oryza sativa
transcript LOC_Os07g40260.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g40260.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G39800.1 (Glycine max), 5'ss of exon 6
TGTGCTATGGTGGAATGGATGTTGGTGGTGGTACTATGGTACTTGGTGGGATGCCTGCTCCTCCTGACATGGTTTTCTCTCATTCAAACCCTGTCCGCAGgtattatacatttttgttttttccacaccagactgaagattcttttagtagcctgctggaggaaggttttctaatgttctgtatatttaatacatttccttattaattttggattgtcaacag
|||||||||||||||||| ||||||||||||| ||||||| |||||||| ||  || | ||  |||||||||| ||  | | |||| | ||||| || |||| |    ||  ||| || ||||      |||    |||   | | |      | ||  |  || |  ||  | |         || | | |||||| ||   || ||| ||  || | ||||
TGTGCTATGGTGGAATGGGTGTTGGTGGTGGTGCTATGGTTCTTGGTGGCATATCTCCCCCAGCTGACATGGTCTTTACACGTTCAGATCCTGTTCGAAGgtgtgtgccaaatttcttatttca----tagatatgaga---tgtcatgcattttcttaacaaatgcatttgatta--------atctcacacatttact--ctagtttcgggatggcgacag

upper sequence: LOC_Os07g40260.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G05490.1 (Glycine max), 5'ss of exon 3
TGTGCTATGGTGGAATGGATGTTGGTGGTGGTACTATGGTACTTGGTGGGATGCCTGCTCCTCCTGACATGGTTTTCTCTCATTCAAACCCTGTCCGCAGgtattatacatttttgttttttccacaccagactgaagattcttttagtagcctgctggaggaaggttttctaatgttctgtatatttaatacatttccttattaattttggattgtcaacag
|||||||||||||||||| ||||||||| ||| ||||||| |||||||| ||  || | ||  |||||||||| ||  | |||||| | ||||| || |||| |    ||  ||| || |||       |||    |||   | | |      | ||  |  || |  ||  | |         || | | |||||| ||   || ||||||  || | ||||
TGTGCTATGGTGGAATGGGTGTTGGTGGGGGTGCTATGGTTCTTGGTGGCATATCTCCCCCAGCTGACATGGTCTTTACACATTCAGATCCTGTTCGAAGgtgtgtgtcaaatttcttatttta----tagatatgaga---tgtcatgcattttcttaacaaatgcatttgatta--------atctcacacatttact--ctagttttgggatggcgacag

upper sequence: LOC_Os07g40260.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G21800.1 (Glycine max), 5'ss of exon 3
TGTGCTATGGTGGAATGGATGTTGGTGGTGGTACTATGGTACTTGGTGGGATGCCTGCTCCTCCTGACATGGTTTTCTCTCATTCAAACCCTGTCCGCAGgtattatacatttttgttttttccacaccagactgaagattcttttagtagcctgctggaggaaggttttctaatgttctgtatatttaatacatttccttattaattttggattgtcaacag
| |||||||||||||||||||||||||| ||| | ||||| || ||||| ||  || ||||  | ||||||  |||  |  ||||| | ||||  ||||||| |  | ||   || || | | |     |||    |||   | | |      | ||  |  || |  || || |         || | | |||||| ||   || ||| ||  || ||||||
TATGCTATGGTGGAATGGATGTTGGTGGGGGTGCAATGGTTCTCGGTGGCATATCTCCTCCATCAGACATGACTTTTGCATATTCAGATCCTGATCGCAGgtgtgtttcaaaattcttatcttc----tagatatgaga---tgtaatgcattttcttaacaaatgcattttatta--------atctcacacatttact--ctagtttcggggtggcaacag

upper sequence: LOC_Os07g40260.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA17G17990.1 (Glycine max), 5'ss of exon 3
TGTGCTATGGTGGAATGGATGTTGGTGGTGGTACTATGGTACTTGGTGGGATGCCTGCTCCTCCTGACATGGTTTTCTCTCATTCAAACCCTGTCCGCAGgtattataca---tttttgttttttccacaccagactgaagattcttttagtagcctgctggaggaaggttttctaatgttctgtatatttaatacatttccttattaattttggattgtcaacag
| |||||||||||||||||||||||||| ||| | ||||| || ||||| ||  || | ||  | ||||||| |||  |  ||||| | ||||| || |||| |  | ||    |||| | || |  | |  |||   ||     |||          ||  |  || |  || || |         || | | |||||| ||   || ||| ||  || | ||||
TATGCTATGGTGGAATGGATGTTGGTGGGGGTGCAATGGTTCTCGGTGGCATATCTCCCCCATCAGACATGGCTTTTGCATATTCAGATCCTGTTCGTAGgtgtgtttcaaaacttttatcttctagatatgagatgtaatgcatttt----------cttaacaaatgcattttatta--------atctcacacatttact--ctagtttcggggtggcgacag

upper sequence: LOC_Os07g40260.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G43100.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTGCTATGGTGGAATGGATGTTGGTGGTGGTACTATGGTACTTGGTGGGATGCCTGCTCCTCCTGACATGGTTTTCTCTCATTCAAACCCTGTCCGCAGgtattatacatttttgttttttccacaccagactgaagattcttttagtagcctgctggaggaaggttttctaatgtt-ctgtatatttaatacatttccttattaattttggattgtcaacag
|||| ||||| |||||||| |||||||||||| ||||||| ||||||   ||  || |||| ||||  ||||| || ||||||||  | ||| ||||||||||   ||  ||  |   |||| ||    | | ||||   | ||  |||||  | |     ||   | ||  ||  |  |||||  |||      ||| |                        
TGTGTTATGGAGGAATGGAAGTTGGTGGTGGTGCTATGGTTCTTGGTAAAATATCTCCTCCACCTGGAATGGTGTTTTCTCATTCTGATCCTTTCCGCAGgtagagtaacttcatagattttgcagtttata-tgaattattttagagtagatttc-----gagcttcttacaacatcactgta-gtttcgggtgtttgcag----------------------

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|33801360|gb|CF326551.1|CF326551
EST:     GGTTTTCTCTCATTCAAACCCTGTCCGCAG                         CCCGTATTACAACATTGAGTTAAAGGAAATACATGTTGCCGGAAAGGCATT
genomic: GGTTTTCTCTCATTCAAACCCTGTCCGCAGgtattataca ... ttgtcaacagCCCGTATTACAACATTGAGTTAAAGGAAATACATGTTGCCGGAAAGGCATT
EST: gi|58611100|gb|CK038812.1|CK038812
EST:     ATGCCTGCTCCTCCTGACATGGTTTTCTCTCATTCAAAGCCTGTCCGCAG                         CCCGTATTACAACATTGAGTTAAAGGAAATACATGTTGCCGGAAAGGCATT
genomic: ATGCCTGCTCCTCCTGACATGGTTTTCTCTCATTCAAACCCTGTCCGCAGgtattataca ... ttgtcaacagCCCGTATTACAACATTGAGTTAAAGGAAATACATGTTGCCGGAAAGGCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGCTATGGTGGAATGGATGTTGGTGGTGGTACTATGGTACTTGGTGGGATGCCTGCTCCTCCTGACATGGTTTTCTCTCATTCAAACCCTGTCCGCAGgtattatacatttttgttttttccacaccagactgaagattcttttagtagcctgctggaggaaggttttctaatgttctgtatatttaatacatttccttattaattttggattgtcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC