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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA

Basic information

species Oryza sativa
transcript LOC_Os06g36770.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtt----tttttgatg-aactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
 ||  | ||  || ||   ||   |  |||||||   | ||| |   ||||| | | | || |||  | |  ||   |||    ||||| ||| || | || |||||||| |||||||||||||||||||||||||| |||||||||| ||||| |||||||||||||||||| ||| | ||||||||| |||||||||||||||
-tgctgtatgccagtaccatgtgctattcttgtt---tcctttcaaaaattaatggtagattgaagtt-atgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 3
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactca-catctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
             | ||  |  | || ||  ||  ||||    |    ||    ||  |  | | | |||  || |||  | | | ||| |  ||||  ||||||| || || || ||||||||||| || ||||| |||||||| ||||| |||||||| | ||| |||  | | |||| |||||| |||||||||||||
------------gtaatcatcatttggtca-gtaatgttgc-accaacatcctatgggtcagaagagtcaatatttataatgtat-gatca-ttgtttcagTTTGACTATCTTAAGAGTTTGGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 3
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactca-catctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
             | ||  |  | || ||  ||  ||||    |    ||    ||  |  | | | |||  || |||   | | |||| |  ||||  ||||||| || || || |||||||| || || ||||| |||||||| ||||| |||||||| ||||| |||  | | || | |||||| |||||||||||||
------------gtaatcatcatttggtca-gtaatgttgc-accaacatcctatgggtcagaagagtcaatatttataaatgtatgatca-ttgtttcagTTTGACTATCTTAAGAGTTTGGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 3
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcata-tggaaac--tcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
                |  |  |  |    || ||  | || || |||| | ||||   |   ||||   | |||| ||||   | |   ||   ||||  ||||||| || || || |||||||||||||| ||||| || ||||| ||||  |||||||| |||||||||  | |  | | |||||| || ||||||||||
---------------gtaattttcagtcactggttaatgct-gcctgaaatgcttgtggagcagaaatgttaacatttatgacatgtgattg--ttgtttcagTTTGACTATCTTAAGAGTTTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 3
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
         |||||||      |||   |   |||   |   |  | ||||   | | |   |  |||||    || | ||  ||    | |||||  ||||||| || ||||| |||||||| ||||||||||| |||||||| ||||| ||||| ||| |||| |||  | || | |  || || |||||||| ||||
--------gtacattaaaac-ttatcaccagatttcacttacgagt-aattgtgttccttgagctactcaa---taagcttgcttttcaatctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgtt-----ctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
              |||| || | | |||| ||||| ||||| ||  |  || |||  |||   | ||   |||| | ||||  || |  |   ||     | |||||||||||||||| |||||||| ||||||||||| || ||||| || || ||||| || ||||| |||    | || |  || || || || |||||||
-------------gtatt-tgatttactct-gttttcttcttactc-agctatttggctat---accttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacat--ctatgtttttttgatgaactg--ttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
     | |||  | | || ||   ||||     | |  || |   |   || |  | || || |   |    |  |||  | |     ||    |   ||| |||||||||| ||||| |||||||||||||||||||| ||||| ||||| || ||||| || ||||| || ||| || | |  ||||| || || ||||| |
-----gtatt-tacttttctgtgttgctaacactctaatcat-tgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 3
----------------------atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaa--ttacttgcatatggaaactcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
                       ||      |  || |||    ||| || || | ||||   |  |  |   ||||| |  | |||||  | |  |||   |||  |  |||      |  ||||||| || ||||| || |||||||| |||||||| ||||||||||| || ||||| |||||||| || |   |||| |  ||||| || || |||||||
gtgtcctttaagaatttcgtttctgggttgctg-atgattaccatatccttttatcttgtctgtcttccatccttactggactctggaa-tttaattctgcatttaat--atgtttgaattcagTTTGACTATCTCAAGAGCTTGGAAATTGAGGAGAAAATCAACAAGATTAGATGGTGTCAGACAGCTAACAGCGCACTGTTTCTTCTCTCCACTAATGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
----atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaa-actcacatctatgtttttttgatgaa---ctgttct-agTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
     |    ||| |  |  |  |||       ||||||    |   |||   | ||| |  | || ||   |   ||  |||     ||| | |    |||| || ||||||| || || || || ||||||||||||||||| ||||| |||||||| |||||||||||||| |||  | | || |  ||||| ||||| |||||||
gtatttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctcactaggctctgaaatgttttaattgatgccacattgcttattctctgtgctcagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 3
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcac--atctatgtttttttga---tgaactgttct--agTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
     | |||    |  || | ||   | | |  ||| | ||| |  | ||  || |   |   | || ||  ||   || ||||||||   ||    ||| |  ||||||||||  | || |||||||||||||||||||||||||| || || |||||||||||||| || |||  | | |  | ||| || ||||||||||| |
----gggattg---ttctgagatacagtatggcgttgattttgttgcacttcgtttccagttctatcttactgatgcctgcttttttgaatatgtttggttatgcagTTTGATTATTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGGTGGTGCCAGACTGCTAATGCTGCTCAGTTCCTACTTTCTACAAATGACA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------------atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgttct----agTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
                                                                                      || ||||| || |   |    |  || | |||  |   |     | |||  |  ||         |   |     ||    |  || | |  | |    ||||||||||| | || |||||||||||||||||||||||||| || || || ||||| ||||| |||||     | |  | | |  | ||||| ||||| |
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------------------------------atgaagcattacattat-tgtgctatgc----tcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgt-tctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
                                                                       | || ||| |  || | ||||| | |       || |||| |  ||  ||| |  | |  ||  |   |  ||         ||| |||| |    | | |  ||||||||||| | |||||||||||||| |||||||||||||| || ||||| |||||| | ||  | |||  | | |  |  || || || ||||||||||
gtacgttcttgcacttctcttgagcgttagatttccatgtttcactttatttttggtttctacgtgtcacctcaatcataagtttctatgtgccaggtggagcatttttttctgatttgttgtagcattgacaagtttgatgtcttgaactgttttgtttggtactttttgtgcagTTTGATTACTTGAAAAGTTTGGAAATTGAGGAGAAGATCAATAAAATCAGATGGTGCGACACTACTAATGGTGCCCGATTGCTGCTCTCCACAAATGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
-atgaagcattacattattgtgcta-tgctcttgttttgttcttgcttga-attacttgcatatggaaactcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
  || ||   |||  | |   | || | |  |||  ||   |||| | |  | | ||    || | | ||   | | | ||  | | |  ||   |  |  |||| |||||||| || ||||||||||||||||||||||||||||| || || |||||||||||  |||||  | | |  |  || || ||||||||||| |
tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttg---ttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcac--atctatgtttttttgatgaactgttct-------agTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
        |||  || ||||| | |  |  | |||||       ||| | || ||  |  | |||  ||||  |||  | |   |||  |  |   ||||       ||||||||||| | || |||||||||||||||||||||||||| || || || ||||||||||| ||||||    | |  |  || || ||||| |||||||
--------ttat-ttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 3
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
                        ||| |||| | | |  |||    ||      || | | ||  || ||||   | || |||||     ||   | ||||||| |||||||| ||  |||| |||||||| ||||||||||| ||||| ||||| || || || ||     | |  |   || | || || ||||| |
-----------------------gtgcgcttgctctatcgttg----aa------gcgtgttgatgct-acattacttttgttttgg----cttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
                        ||| |||| | | |  |||    ||      || | | ||  || ||||   | |||||||  |   ||   | ||||||| |||||||| ||  |||| |||||||| ||||||||||| ||||| ||||| || || || ||     | |  |   || | || || ||||| |
-----------------------gtgcgcttgctctatcgttg----aa------gcgtgttgatgct-acattacttttttttt--ttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

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|66912787|gb|CX099635.1|CX099635
EST:     GACACCCAGAGTTTCGCTACAAAAGTGAATTTCAGAGTCATGAACCTGAG                         TTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATC
genomic: GACACCCAGAGTTTCGCTACAAAAGTGAATTTCAGAGTCATGAACCTGAGgtatgttgat ... actgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattacttgcatatggaaactcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
                                              ctgttct  CT-rich tract
                          atctatgttttttt  TA-rich tract