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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcttgtccttgttggtccaaactgccagtacttaaacacgcactgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA

Basic information

species Oryza sativa
transcript LOC_Os01g64650.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 4
-tcttcttgtccttgttggtccaaactgccagtacttaa-acacgcactgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
 |  | | ||   | ||||   |  |    | | ||| | || |   |||| || |  |  |   | |||  |  |   |   |   ||||| ||  ||||||| ||||| || |||||||| ||||||||||| |||||||||||||||||||||||||||||||||
gttatgtggttgatattggattatgcctgtattcctttacactctatctgcctcataaagaagcatattcacactactcatgatatgttcatcat--tgtagGATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 3
tcttcttgtccttgttggtccaaactgccagtacttaa-acacgcactgcatcctgcatgaatgttttcttatgagataa----cttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
     | |    |  |||   |  |    |  |||| | || |   |||| || | |   |   |  ||   | |   |     | |||| |  | ||||||||||||||||| || ||||||||  |||||||||| ||||||||||||||||||||||||||||| || 
-----tggctgatactggattatgcctgtatcactttacaccctatctgcctcatacggaagcatactcacgttactcatgggtcatgatatgttcattttgtagGACCCTGCGGAAGCTGACAAACTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATTCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
-------------tcttcttgtccttgttggtccaa--actgccag-tacttaaacacgcactgcatcctgcatgaatgttttcttatgag-ataacttgatttcattattttgt---------------agGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
              ||| || |  |   |||   ||  | ||   | |  |  ||   |   | ||| ||||   ||  ||||   |  || || |||  |   | ||  | |||               |||| ||||||||||| |||||||| |||||||||||||| || ||||||||||| ||||| ||||| 
gcatataaatacccctttttatgttgtctggcaaaacaattgtttgattttctaaattgtgttacattctgct--aacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 3
---------------------------------------------tcttcttgtccttgttggtccaaactgc-cagtacttaaacacgcactgcatcctgcatgaatgttttc----ttatgagataacttgatttcattattttgt---------------agGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
                                               |  |  |  ||||| |   ||| ||  || || |  ||   |   | ||| ||||     | ||| |    |||||  || |||  |   | ||  | |||               |||| |||||||||||||||||||| |||||||| ||||| || ||||||||||||||||| ||||| 
gcatgtaaatacctcttttatgttgtatgagcttcagttagaggagttgttgatttttgtttgaaaaaattgttcaatattctaaattgtgttacattctgctaacctttttacacaattatgt-atgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 3
tcttcttgtccttgttggtccaaactgccagtacttaaaca-cgcactgcatcctgcatgaatgttttcttatg--agataacttgatttcattat------tttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
       || || |  |  | ||  |    |||  ||   | |    |  |  ||  | |||   |||  | ||  |  ||   | | ||  || |      | |  ||||||| ||||| ||||| ||| |  |||||||||||||||| |||||||| || || |||||||| 
-------gttctagaagcactaacttttttgtatctatgaatcttgtttaagactttaggaactatttgctgtgtcaattattcttacttttttttggaatatcttcagGACCCGGCAGAAGCTGATAAGCTGTTGAAAATCCAGAGGGAATTGGATGAGACCAAGATTATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 4
-------tcttcttgtccttgttggtccaaactgccagtacttaaacacgcactgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
       | |  | | ||   ||| |  |   || |  |  ||  |     | ||  |    | | |||   |  || || |||       | |   || | |  ||||||| ||||||||||| ||| |  |||||||||||||||| |||||||| ||||| |||||||| 
aattaattttagtagcccccattgtttta---tgaccatg-ttggattttgagtgatttgatcttaaat---tgattttgggattgtcccgtatttgtaatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0060g00090.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------tcttcttgtccttgttggtccaaactgccagtacttaaacacg-cactgcatcctgcatgaatgttttcttatgagataacttgatttca-----ttattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
                                    ||||| |  |  ||  |  ||| |     ||||      ||  |     |   || | ||| | ||      | || |  || || ||     || || |  ||||||||||||||||||| |||||  ||||||| |||||||| |||||||| || ||||||||||| 
gtacttttctgtcttgttaagaaatttttattcagtttcttctgttgctttctttaaaatattc-tactgggtgtcgataagattttaagcttcaatatcttggctaaatatgatctgtttgcacaaatttcttcttcagGACCCTGCAGAGGCTGATAAGTTGCTGAAAATTCAGAGGGATTTGGATGAGACCAAAATTATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------tcttcttgtccttgttggtccaaact--gccagtacttaaacacgcactgcatcctgc-atgaatgttt-tcttatgagataacttg-atttcattattttg--------tagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
                                                                   | ||    || |      |   || |      || | |     |  | ||  ||  || |||    ||| |      | |||  ||  |||   || | ||          |||| ||||| |||||||| |||||  ||||||| ||||| || ||||||||||| |||||||| || 
gtatttctccacatttttctcattttgtttgttgcgtcataaggctgcatataggtacaattaattttttttgcatcataaactatttcaattttatttgttcctttcttcttaatggttcaagctatggtcatttataacccaaaatactttttattctgttctctttgaaatcttcagGATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT

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|218482998|gb|FG956126.1|FG956126
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|86531269|gb|CI171475.1|CI171475
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAAGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
                                       tttcatt  CT-rich tract
                              ataacttgatttcatt  TA-rich tract