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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgctatcagttatcatatattcctgattttcgacctttaaagtagtcttcatgtttatggttatgagatataatcagttttcctttccctatcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAG

Basic information

species Oryza sativa
transcript LOC_Os06g30460.3
intron # 13
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 13
lower sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 15
cgctatcagttatcatatattcctgattttcgacctttaaagtagtcttcatgttta-tggttatgagatataatcagttttcctt--tccctatcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAG
  ||| || || |   |||  || |  || | |  | || |  | |||  || || | ||||| ||||  ||     | || | ||  ||   ||||||  ||||||||||| |||||||||||||| | |||||||||||||| ||||| |||||||| || || ||||||||
-tcta-caattctaccataaaccagccttcctatgtgtagaacaatctctattttcaatggttttgagtcatttatgggttcctttgttcataatcact-cagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG

upper sequence: LOC_Os06g30460.4 (Oryza sativa), 3'ss of exon 13
lower sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 18
-------------------------------------cgctatcagttatcatatattcc-tgattttcgacc---tttaaagtagtcttcatgtttatggttatgagatataatcagttttcctttccctatcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAG
                                      |||||       ||||| ||   | | ||   |||   ||  | ||  | || ||   ||| |||||||  | ||||    | ||   |   | |      |||||||| || ||||  ||||||| ||  |||| |||||||||||| |||| ||||| |||||||| |||||
gtaattttattctctctgaagttaaacgaatatggaaggctatagaggcacatatgtttgatcagttcttaccatattccatgtgttgttgatcgctatagttatgaattttaata---tgtcaaatgatttttggatcagGTTAAGGAGCTGGCACAAAAGGCTCGATCTGGAAAGCTTGCTCCTCATGAGTTTCAAGGAGGGACATTCAG

upper sequence: LOC_Os06g30460.4 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 18
-------cgctatcagtta-tcatatattcctgattttcgacctttaaagtagtcttcatg--tttatggttatgagatataatcagttttcctttccctatcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAG
         || ||| ||| | ||  ||||   |||       |    | || | | | |   || |||| | |    | |||| | ||||  |  | |         |||| ||  | || |||||||||||||| || |||||||||   || ||||||||||| ||||| ||||||||
tccaatatcctttcaattacttatcaattctcaattaattctttggggaataatttcccttgtttcatggatttctagt-taattaatttttgtacctc---------agGTCAAAGAATTAGCTGAAAAGGCACGAGCAGGGAAGCTTAAGCCCAATGAATTTCAAGGAGGAACTTTCAG

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|58692196|gb|CK080883.1|CK080883
EST:     CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAG                         GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
genomic: CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagaga ... atcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
EST: gi|27578288|gb|CB000983.1|CB000983
EST:     TATTATAAGAAATGCAGAATCAAA-GACTATATCAGCAATATCCTCAGAG                         GTTAAGCAGTTGGCTGAAAAAGCACGTGCTGGG
genomic: TATTATAAGAAATGCAGA-TCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagaga ... atcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGG
EST: gi|88849307|gb|CI087829.1|CI087829
EST:     CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAG                         GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
genomic: CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagaga ... atcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
EST: gi|218482631|gb|FG947596.1|FG947596
EST:     CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAG                         GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
genomic: CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagaga ... atcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcatgtttatggttatgagatataatcagttttcctttccctatcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAG
                                ttttcctttccctatc  CT-rich tract
               ttatgagatataat  TA-rich tract