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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaaacacacattttttatatgttatattctcttccaattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCCTCAAGACATCCAATCTCAAAACTTGAGTTTGAATTCGAGAGACGGAAGC

Basic information

species Oryza sativa
transcript LOC_Os06g49430.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 6
gtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaa-acacacattttttatatgttat-attctcttccaat-tttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCCTCAAGACATCCAATCTCAAAACTTGAGTTTGAATTCGAGAGACGGAAGC
|| | |||||   |||  ||    || ||| |   | | | |  | | |||   | |||| |    ||    | | | | |  ||||||| | ||  ||| ||| ||||    |  |||||||| | |||||||| ||||| |||   ||||||||||||||||||||||| |||||||| || || || ||||||||||||||||| || |||  |||||
gtgaactcaatt-aaaatatgttttctttttctttcattagatct-gctttccataaaaagatgtcacacgtatatatatatgcatttttgacattatattattatcttatcgtacttcagGCTCTAGCTGATCCATACTTTGCATCCCTTGCTAATGTGGAACGTGAGCCATCAAGACACCCGATTTCTAAACTTGAGTTTGAATTTGAAAGAAAGAAGC

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G306028_T02 (Zea mays), 3'ss of exon 6
gtaagctcaagagaaagcatagcatcctttccaaacctcaaaagtagtttttttttaaaaaaaaaaactttcagaaaacacacattttttatatgttatattctcttccaattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCCTCAAGACATCCAATCTCAAAACTTGAGTTTGAATTCGAGAGACGGAAGC
         | |  ||  | || |    ||  |    ||||    |    |        |||| ||| |||        |   |     ||||   |||| | |   |  |||| |||||| | |||||||| ||||| |||   ||||||||||||||||||||||| |||||||| ||||| || ||||||||||||||||| || ||| ||||||
---------aaaataaatacagtaattattgtatgaatcaactaaaaaggt--------aaaacaaattttattttggtatggagggggtataatatataattttaacttattt-cagGCTCTAGCTGATCCATACTTTGCATCCCTTGCTAATGTGGAACGTGAGCCATCAAGACACCCAATTTCTAAACTTGAGTTTGAATTTGAAAGAAGGAAGC
















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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaactttcagaaaacacacattttttatatgttatattctcttccaattttcagGCTTTGGCTGATCCGTACTTCGCAAGTCTTGCTAATGTGGAACGTGAGCCCTCAAGACATCCAATCTCAAAACTTGAGTTTGAATTCGAGAGACGGAAGC
                                     ttctcttccaattttc  CT-rich tract
           aaaacacacatttttt  TA-rich tract