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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggactaactgaatattcaatttacacatagtggtttaagtcaacttctttgtttggtctaatggatagctcatcattattcttttctcatgaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATATATCTATCGCAGTTGCTACAGAGAAG

Basic information

species Oryza sativa
transcript LOC_Os06g30460.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g30460.4 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 13
ggactaactgaatattcaatttacacatagtggtttaagtcaactt----ctttgtttggtctaatggatagctcatcattattcttttctcatgaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATATATCTATCGCAGTTGCTACAGAGAAG
  |  |||      |||  | | |   |  | |||||   ||   |    || | ||  ||||      | |   ||  ||||   |||  |||  ||| ||||| |||||||||||||| |||||| || | || ||||| | |||||||||||||||||| || |||||||||||||||
--aagaacgctggtttctgtatgc-tttgtttgtttagaccagtatgtagctctcttcagtctccacttttgaagatt-ttatgtattttgcatctattgccagCTTACTGGAACAATGATAAGGAAGAAACTCAAAAGTGCGATTCAGTTGATATATCTATTGCTGTTGCTACAGAGAAG
















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|218488261|gb|FG947096.1|FG947096
EST:     TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATG                         CATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
genomic: TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATGgtaattctta ... gaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
EST: gi|218481815|gb|FG945396.1|FG945396
EST:     TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATG                         CATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGAT
genomic: TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATGgtaattctta ... gaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGAT
EST: gi|58692196|gb|CK080883.1|CK080883
EST:     TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATG                         CATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
genomic: TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATGgtaattctta ... gaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
EST: gi|27578288|gb|CB000983.1|CB000983
EST:     TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATG                         CATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
genomic: TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATGgtaattctta ... gaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
EST: gi|27578255|gb|CB000950.1|CB000950
EST:     TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATG                         CATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
genomic: TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATGgtaattctta ... gaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
EST: gi|58678110|gb|CK066797.1|CK066797
EST:     TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATG                         CATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
genomic: TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATGgtaattctta ... gaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
EST: gi|218482631|gb|FG947596.1|FG947596
EST:     TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATG                         CATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA
genomic: TGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATGgtaattctta ... gaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgtttggtctaatggatagctcatcattattcttttctcatgaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATATATCTATCGCAGTTGCTACAGAGAAG
          gtctaat  putative branch site (score: 3)
                                                tttcc  putative PPT
                          atcattattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggactaactgaatattcaatttacacatagtggtttaagtcaacttctttgtttggtctaatggatagctcatcattattcttttctcatgaatttccagCATACTGGAACAATGACAAGGAACAAGCCCAGAAGTGTGTTTCAGTTGATATATCTATCGCAGTTGCTACAGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT