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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgtactcttcttataacaatttgcatttttgtatctgtgaagtctgttttgagttttgttttatgcagaaaagctgttttagatgctttctggcatttggt...

Basic information

species Oryza sativa
transcript LOC_Os09g32680.4
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32680.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G408242_T03 (Zea mays), 5'ss of exon 7
GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgta----ctcttcttat-aacaatttgcatttttgt-atctgtgaagtctgttttgagttttgttttatgcagaaaagctgttttagatgctttctggcatttggt-
||| ||||||||||||||||||||||| ||||||||||||||||||||    ||  | |||  ||||  ||   |   | | | | || ||| |      ||  ||| | || |||  |  |    ||| ||   |  ||||   |||||  
GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactgcttttacgaacagcttaattcagtatcaacagttaaggcgaaaaggaacttt-tattctgcttaggac---tttcag---ccctctgtgttttgggt
















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|24468776|gb|CA305725.1|CA305725
EST:     GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
EST: gi|86493556|gb|CI136189.1|CI136189
EST:     GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
EST: gi|29660228|gb|CB656503.1|CB656503
EST:     GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
EST: gi|88833089|gb|CI369979.1|CI369979
EST:     ATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: ATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
EST: gi|88258947|gb|CI363240.1|CI363240
EST:     CATAACAGATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: CATAACAGATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgtactcttcttataacaatttgcatttttgtatctgtgaagtctgttttgagttttgttttatgcagaaaagctgttttagatgctttctggcatttggt

- - - - AGGATG
- - - - -  ATGCTG