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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatacatgactgtgatcatcagtagctgtgtgtttatttatcagttaacccgctctcttcagtctttgcattgtaaaccatgaagatatcatatcagactatggtgttagtagtaactcatggtgtgaagatttgtgtgtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGGCTTACATTTGCCAACATACTGACAATGGGAGCATACTCTGTCCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g73910.2
intron # 4
splice site 3'
intron type U2

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|29624825|gb|CB629836.1|CB629836
EST:     TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAG                         GCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
genomic: TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAGgtagatacat ... gtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
EST: gi|58687641|gb|CK076328.1|CK076328
EST:     TAGAAAAGAACTGCAG                         GCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
genomic: TAGAAAAGAACTGCAGgtagatacat ... gtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
EST: gi|29624826|gb|CB629837.1|CB629837
EST:     TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAG                         GCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
genomic: TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAGgtagatacat ... gtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
EST: gi|313079079|gb|HO213970.1|HO213970
EST:     TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAG                         GCTGTGTTGGCTTATGAACTGGGACGCCTCAAGTGTGACCATGGCGTGTGG
genomic: TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAGgtagatacat ... gtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
EST: gi|29689228|gb|CB685503.1|CB685503
EST:     TAGTTGTTCATACAAGCCTCGTGGAGCTGCTCACTAGAAAAGAACTGCAG                         GCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
genomic: TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAGgtagatacat ... gtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
EST: gi|58591227|gb|CF989535.1|CF989535
EST:     TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAG                         GCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGAC
genomic: TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAGgtagatacat ... gtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGAC
EST: gi|29683738|gb|CB680013.1|CB680013
EST:     TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAG                         GCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG
genomic: TAGTTGTTCATACAAGCCTTGTGGAGCTGCTCACTAGAAAAGAACTGCAGgtagatacat ... gtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagactatggtgttagtagtaactcatggtgtgaagatttgtgtgtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGGCTTACATTTGCCAACATACTGACAATGGGAGCATACTCTGTCCCTG
                 tagtaac  putative branch site (score: 1)
                                  aagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatacatgactgtgatcatcagtagctgtgtgtttatttatcagttaacccgctctcttcagtctttgcattgtaaaccatgaagatatcatatcagactatggtgttagtagtaactcatggtgtgaagatttgtgtgtttggctagGCTGTGTTGGCTCATGAACTGGGACACCTCAAGTGTGACCATGGCGTGTGGCTTACATTTGCCAACATACTGACAATGGGAGCATACTCTGTCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA