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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctactgagtatttgaagattctttcaattctgtaatgtctgccacatgcttttgtgcatttttgtttcaacctatttaaccacattaagattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCATCAATGCTATGATCTCTAACATCTCATTCACTTACCGGAGCATTTATTC

Basic information

species Oryza sativa
transcript LOC_Os01g13770.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13770.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 6
gtgctactgagtatttgaagattctttcaattctgtaat-gtctgccacatgcttttgtgcatttttgtttcaacctatttaaccacattaagattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCATCAATGCTATGATCTCTAACATCTCATTCACTTACCGGAGCATTTATTC
          |||| | |        ||| |||  | ||  |||   |  |  |  |      | | | |  || | ||   |  | ||||    | |||||||||||||||||||| || ||||| || ||||| |||||||| |||||||||||||| ||||| || |||||||||||||| ||| |||||||||||||
----------gtatgtaa-----tcctcagttcgatcatcatctcataattaatccta-atgctctagct--aagcgatcacatgaaattac--ctgccagGTGTTTCAATGGCATCCCTTACTGAGCTCTCATTCAACTGGACTGGCTTCATCAATGCCATGATATCAAACATCTCATTCACCTACAGGAGCATTTATTC

upper sequence: LOC_Os01g13770.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgctactgagtatttgaagattctttcaattctgtaatgtctgccacatgcttttgtgcatttttgtttcaacctatttaaccacattaagattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCATCAATGCTATGATCTCTAACATCTCATTCACTTACCGGAGCATTTATTC
                    |  |  |||||     ||  |||  | |||| || | ||  |  |   || |      ||||||     ||  || | ||||||| ||||||| ||||| ||||| || ||||| ||||||   || ||||||| ||||||||| || ||||| || ||||||||||| ||||| |  ||
------------------gtaaacactcaatc----aaactctttc-catgtttct-tgtgtcctaagttta-ttggattaacctttaaaatgttgc-agGTGTTGCAATGGCTTCACTAACTGAGCTATCATTCAACTGGCTCGGTTTCATCAGTGCTATGATATCAAACATTTCTTTCACTTACCGAAGCATCTTCTC

upper sequence: LOC_Os01g13770.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 6
-----gtgctactgagtatttgaagattctttcaattctgtaatgtctgccacatgcttttgtgcatttttgtttcaacctatttaaccacattaagattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCATCAATGCTATGATCTCTAACATCTCATTCACTTACCGGAGCATTTATTC
      ||  | |   ||||  ||| |  |||| |        ||  |   ||| |  |||   |  |||  | | |   ||  |   || | ||| ||   ||||||| |||||||||||| ||||||| || ||||| |||||||  |||||||| | ||||||||| ||||| ||||| ||||||||| |||| || |||||
tgaacttgtgaattcttattcaaagctgttttccagaaatacttgattatgaca-gtgtttccaccatttcatgtgattttaact--tcaaaataaaat--gcagGTGTGTCAATGGCATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTC

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|84117005|gb|CD150772.1|CD150772
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|313084102|gb|HO213885.1|HO213885
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29613763|gb|CB618776.1|CB618776
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29671609|gb|CB667884.1|CB667884
EST:     CCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: CCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29643944|gb|CB648951.1|CB648951
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29661884|gb|CB658159.1|CB658159
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|25797136|gb|CA753097.1|CA753097
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatgcttttgtgcatttttgtttcaacctatttaaccacattaagattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCATCAATGCTATGATCTCTAACATCTCATTCACTTACCGGAGCATTTATTC
                               atttaac  putative branch site (score: 3)
               atttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctactgagtatttgaagattctttcaattctgtaatgtctgccacatgcttttgtgcatttttgtttcaacctatttaaccacattaagattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCATCAATGCTATGATCTCTAACATCTCATTCACTTACCGGAGCATTTATTC

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