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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacactcatctattcaaacaacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagcatttatttcatcttaatttggggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC

Basic information

species Oryza sativa
transcript LOC_Os02g21750.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 4
gtacactcatctattcaaacaacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagcatttatttcatcttaat-ttggggcccatgaatcatgatcataagtgataa-ctattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
                                        ||||  |   |  |    | |||   | ||     |||||  |||| | ||    |  |       || ||    | |  |  ||  ||  || |||  |||| || || |||||||  ||  || |||| || || || |||||||| || || |||||||||||||||||||| |||||||||||| |||| || || |
-------------------------------------gtgtttaattccaaaatccaaactctt--accttacgctagcaactattgcttcaggttgctttcttttatcaagttagttagtgtgttttattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC

upper sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
gtacactcatctattcaaacaacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagcatttatttcatcttaatttggggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
                     |   |  ||||| | | |   |       ||  |    || |  | |    | |     |||  || |   | |||||  |   || ||     || ||         || |||  ||||| | || ||||||||||| | |||||| || || || |||||||| || ||||||||||| ||||||||||| |||||||||||| |||| || || |
-------------------gtatgacattcttt-tacacaactgaaccaaaccaa---gttttatgtttctctctcttttttttctttaagattatttgaagttaataaaattgtattatt--------ctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC

upper sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv10s0003g02580.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------gtacactcatctattcaaacaacccctctctttctgcccttttagcttt---gacttatggattctgcgatctctttttagcatttatttcatcttaatttggggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
                                                   || ||   ||| ||  ||  |  ||     |     | ||| | | |    ||| | || | |        || |   | ||   |  |  |  |  | |      ||  | |    |||||  ||| |   | ||| ||||| || || |||||||| ||||| ||||| || ||| ||||||| |||||||| ||||||||||||||||||||||| ||||||||| | || || || |
gtgagcctatgattcattcatattcaggtcacagttgaaagagggttcaaatatacatgtctgttagaatgagtccatgaatcactgcatttcaacctcacagacctttgtaataataagagtcatgcaatcaaacaaattcttctcttcttttcatcagtattttgaatcatg-gtggtg--tgtttacagGGGCTGGACACAATGGTGGGTGAACATGGAACGCAGTTATCTGGAGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAATCCAAGAATCC

upper sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
-----------------gtacactcatctattcaaac--aacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagc-atttatttcatcttaatttg--gggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
                  |     | | ||||       ||  |||   | |    | |  |||     | |||   ||  |    |   |   |||  |   | ||| ||||   ||     | ||   |||  |    ||   ||     | | | ||||| ||||| |||||||| ||||| ||||| || ||||||||||| |||||||| ||||||||||||||||||||||| ||||||||| ||||  | || |
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaa-aagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC

upper sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
-------------------gtacactca----tctattcaaacaacccctctctttctgcccttt-tagc-tttgacttatggattctgcgatctctttttagcatttattt-catcttaatttggggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
                   ||  | |||      ||||||    ||   || ||  | |  || |  ||| ||  |   ||   | | | |    ||  | |    || ||| | | |||||        |||     ||| |  |  |||  |  || || |||||||| || |||||||| ||||||||||| || ||||||||||| |||||||| ||||||||||||||||||||||| ||||||||| |||| || || |
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtg-gtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC

upper sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv10s0003g02550.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtacactcatctatt-caaacaacccctctctttctgcccttttagctttg-acttatggattctgcgatctctttttagcatttatttcatcttaatttggggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
                   |       || |||  |  ||  |  ||   | |||  || ||||  ||| ||| ||  |   ||  | || | | || ||   ||   || ||  ||  |  |   ||| | ||    |    ||    || ||  |||||  | || |||||||| ||||||||||| || ||||| ||||  |||||||| |||||||||||||| ||||| || ||| ||||| |||| || || |
gtgagcccattctttcttttgtgggattccattatatccaggcattcatctactgttctgttagaattgtactaattcaacttgacacctttctctatcaca-atactattttc-ttctgatcttttgagtaattgg-actgttgtggtctgttaacagGGGATTGAAACAATGGTGGGTGAGCATGGAACTCAGCTCTCTGAAGGACAGAAGCAAAGAATTGCAATAGCAAGGGCCATTCTGAAGAACCCAAGAATCC

upper sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0388g00070.t01 (Vitis vinifera), 3'ss of exon 1
gtacactcatctattcaaacaacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagc-atttatttcatcttaatttg--gggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
                                          |||     | |||   ||  |  | |   |   |||  |   | ||| ||||   ||     | ||   |||  |    ||   ||     | | | ||||| || || |||||||| ||||| ||||| || ||||||||||| |||||||| |||||||||                                     
-----------------------------------------ctagaaa-aagttacaaatcttctgtttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT-------------------------------------

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|86826083|gb|CI310971.1|CI310971
EST:     GAGCAATTGTCCTTGCCAATGCTGCGAAGTTCATCGATAAGCTACCAAAT                         GGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAG
genomic: GAGCAATTGTCCTTGCCAATGCTGCGAAGTTCATCGATAAGCTACCAAATgtacactcat ... ctattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatcttaatttggggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
                                       tgataac  putative branch site (score: 2)
                                             ctattttc  CT-rich tract
                                         ataactatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacactcatctattcaaacaacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagcatttatttcatcttaatttggggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG