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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggtgcttctgcgaacacccaagagatgcactgaaacatggcatcaaagataagaaacctcattatagattcacaccacttcatttggttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTGTCCATCATCAAGGACACAGTAAAAGAGCCTGGAATGTGCTCCAAGCGGC

Basic information

species Oryza sativa
transcript LOC_Os01g36080.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36080.4 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv08s0040g00760.t01 (Vitis vinifera), 3'ss of exon 11
tttggtgcttctgcgaacacccaagagatgcactgaaacatggcatcaaagataagaaacctcatt---atagattcacaccacttcatttggttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTGTCCATCATCAAGGACACAGTAAAAGAGCCTGGAATGTGCTCCAAGCGGC
  ||| ||   ||      |        |  |  || | |||      |  | |  | |  ||  |   | | |   | |  | ||    || |    |  |||| |||||||| |||||  | ||||| ||  ||||||| |  || ||  ||  ||| |||| |||||| || |||||||||||||||||||||||| | |
--tgg-gcagttggatttcctaccttcttttaaggacagatgattgtgagaacatcacatttcccttggaaaaacagagagtaattatactgttgtttttcagGTAATGGCAAGCGATGGGCTCTGGGATGTTGTGAGCAATGCAGAGGTTGTGAGCATAATCAGGGACACTGTTAAAGAGCCTGGAATGTGCTCCAAGAGAC
















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|88506325|gb|CI433831.1|CI433831
EST:     ACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTG                         GTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
genomic: ACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTGgtatgtccat ... ttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
EST: gi|29625169|gb|CB630180.1|CB630180
EST:     CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTG                         GTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
genomic: CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTGgtatgtccat ... ttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
EST: gi|29676790|gb|CB673065.1|CB673065
EST:     CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTG                         GTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
genomic: CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTGgtatgtccat ... ttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
EST: gi|29663423|gb|CB659698.1|CB659698
EST:     CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTG                         GTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
genomic: CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTGgtatgtccat ... ttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
EST: gi|86500133|gb|CI142766.1|CI142766
EST:     CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTG                         GTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
genomic: CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTGgtatgtccat ... ttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
EST: gi|88219801|gb|CI219361.1|CI219361
EST:     CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTG                         GTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG
genomic: CACAACCTGAGGTTATAGAAACCATTTTATCACCTGATGATGAGTTCCTGgtatgtccat ... ttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaagataagaaacctcattatagattcacaccacttcatttggttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTGTCCATCATCAAGGACACAGTAAAAGAGCCTGGAATGTGCTCCAAGCGGC
                  attatagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggtgcttctgcgaacacccaagagatgcactgaaacatggcatcaaagataagaaacctcattatagattcacaccacttcatttggttacctgtagGTGATGGCAAGTGATGGATTGTGGGACGTGATGAGCAACGAGGATGTCCTGTCCATCATCAAGGACACAGTAAAAGAGCCTGGAATGTGCTCCAAGCGGC

- - -tgcttct
- - - - - - - - - - - - - gatgcac
- - - - - - - - - - - - - - - - - gaaacat
- - - - - - - - - - - - - - - - - - - - - -catcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcacac