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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTCGTCTGCTAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaaacacacattttttatatgttatattctcttccaattttcag

Basic information

species Oryza sativa
transcript LOC_Os06g49430.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G306028_T02 (Zea mays), 5'ss of exon 6
CCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTCGTCTGCTAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaaacacacattttttatatgttatattctcttccaattttcag
 |||||  |||| || || || ||| | || || ||||||||||||||  ||||||||||||| ||||||||||||||||||||| || | || ||||| || | ||||      | |||| ||  |||||    |||      ||| |    ||||      | |  || |  |||| | |  |     ||||  | |  | | ||  |        
GCCCTTTACTCATAAATTTCGAAATGCCGATCCTTTGGCTCTTCGTCTTTTAGAGCGTTTACTTGCATTTGATCCTAAAGATCGGCCTACTGCAGAAGAGgtgaactca------atcataacacactttcttttcctttgt--tagatccgcttta------agagtttccgtaaaaaagatgtcacacatataatttgattttttatacccc----

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G135904_T01 (Zea mays), 5'ss of exon 6
CCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTCGTCTGCTAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaa-acacacattttttatatgttat-attctcttccaat-tttcag
 |||||  |||| || || ||  || |||| || |||||||||||||| ||||||||||| || ||||||||||||||||| ||| ||   || ||||| || | |||||   |||  ||    || ||| |   | | | |  | | |||   | |||| |    ||    | | | | |  ||||||| | ||  ||| ||| ||||    |  |||||
GCCCTTTACTCATAAATTTCGACATGCTGATCCTTTGGCTCTTCGTCTTCTAGAGCGTTTGCTTGCATTTGATCCTAAAGACCGGCCTAGTGCAGAAGAGgtgaactcaatt-aaaatatgttttctttttctttcattagatct-gctttccataaaaagatgtcacacgtatatatatatgcatttttgacattatattattatcttatcgtacttcag
















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|33684106|gb|CF312345.1|CF312345
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|88406114|gb|CI593894.1|CI593894
EST:     TAAAGATCGGTCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|33381883|gb|CF197226.1|CF197226
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|58693904|gb|CK082591.1|CK082591
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|58663177|gb|CK051863.1|CK051863
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|218481672|gb|FG962985.1|FG962985
EST:     CATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: CATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|218490968|gb|FG950249.1|FG950249
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|58589575|gb|CF987883.1|CF987883
EST:     TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGCCTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCC
EST: gi|58661035|gb|CK049715.1|CK049715
EST:     TAGAGCGTTTACTGGCATTTGATCCTCAAGATCGGACTTCAGCTGAAGAA                         GCTTTGGCTGATCCGTACTTCG
genomic: TAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaa ... caattttcagGCTTTGGCTGATCCGTACTTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTCGTCTGCTAGAGCGTTTACTGGCATTTGATCCTAAAGATCGGTCTTCAGCTGAAGAAgtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaaacacacattttttatatgttatattctcttccaattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA