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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT

Basic information

species Oryza sativa
transcript LOC_Os03g22420.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
gtatttt---actaaatga-ttgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
||| ||    | |  |  |    || ||  |     |||  || | |||||| | | ||||| ||      |   | |||  | |||||| ||||||||||||| || || ||||||||||| |||||||||||||| ||||||||||||||||| ||||| ||||| |||                
gtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatag-catctaaa------taacctattttc-cagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G438355_T01 (Zea mays), 3'ss of exon 1
gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccat-taccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
      |||| |  ||||   || || |  |  ||||      ||| |     |||   |     |   || | | |     ||||| ||||||||||| | ||  ||||||||||||| ||||||||| |||| |||| |||||||||||| ||||| ||||| |||                
-----gtacttatcgattag-atgagcctctatttttag----gcagtacatacattatatcatctaaataacctattttctagTGGCTTGGTGAAGGAAAAAA--TTGTGAAAGCTGTGTTTTCACTGACAAG-AAAAATGCTCCAAGTGTAATTTTTGTGGACGAG----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 5
-------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
        |  || |||   |   |  || | |||  || | |   ||     ||      |||||     || |      || |  |||||||||||||| || || |||| ||| |||||||| ||||| ||||| || ||||||||||| || || || || || || ||                 
gttaaatttgcttcactgggtttattttaat-gtctctgctatcagttagttgttcattttatctgtgttcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAGTATGTCAAAGCTGTTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 17
---gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
     | | |  ||||| | |  | ||  |   |  ||   | | ||| |      ||    |||||| || |    ||    ||||||||||||||||||||||| | ||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || || |||                
gtatcaatattgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgt-ttgttgcagTGGTTTGGTGAAGGAGAGAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 18
gtatt--ttactaaat-gattgctattagtcca---tggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
|||||  || | || |  |    | ||  || |   ||  |||  |||      |  |  |   || | ||  |||    ||    |||||||||||||||||||| || | ||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || ||||||                
gtattagttgcaaatttaaacagttttgctctactttgtatttcctttcattcataagtgacaggatagatattgtttttttgttgcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 21
---gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccatt-accacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
    || | |  ||| | | |  | || ||   ||  |||  || |    ||  |  |   |||| ||   ||    ||     ||||||||||||||||||||||||| ||| |||||||| ||||| || || |||||||||||||||||||||||||| || || |||                
gtattaatgttgtaagttacttttttttgtg-gtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
-------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
        |  || |||   |   |  || | |||  || | |   ||     ||      | ||| |   || |      || |  |||||||||||||| || || || |  ||||||||||| ||||| |||||||| ||||||||||| || || || || || || ||                 
gttagatatgcttcactgggtttattttaat-gtctctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 18
gtattt-tactaaatgattgctattagtccatggttttgtttttgcattttgggcatc---tga-aacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
|||||  |   ||||     || ||  | |     | ||| ||| | |||    |||    ||| |  ||  |||    ||    |||||||||||||||||||| || | ||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || ||||||                
gtattagttgcaaatttaaactgttt-tgctctactctgtattttcctttcattcattaagtgacaggatattgtttttttgttgcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 20
---------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaaca-ttgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
         || | |  |||| ||  |  |  |  | ||   || |   |||||  |     || || |     |||  |    || |  |||||||||||||| || ||||| | |||||||||||| || || ||||| || |||||| | || |||||||| || || ||||||                
gttaaatttgtctctctctaagtgtatattgat--ttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcagTGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 21
gta--ttttactaaatgat-tgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccat-taccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
|||  | | |  || |||| || | |   |  ||| |||  |||    |||    | |  |||    ||       ||      |||||||||||||| ||||||||||  || |||||||| || ||  | || ||||| ||||| |||||||| ||||| || ||||||                
gtaactctcataaagtgatatgatttccttttatgctttcttttaatgatt----gtacttgaccatttacactaaatgctttgcagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAG----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 21
------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
       | |    | ||||| |  ||||    |  |  |||     |    |||||   || |   ||||  || |   |     ||||||||||| ||||||||||| | ||| |||||||| || || || || || |||||||| || |||||| |||| || || |||                
gtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctg-atattgcttgcagTGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAG----------------

upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 22
-----------------------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
                        | || ||     ||||  |||| |||   | ||| | |||||   | |  |    |||     |  | |  | ||    ||||||||||| || || ||||||| |||||| || || || ||||| || || ||||||||||| |||||| | || ||||||||                 
gttatcattgataagtagcttcttttttctatcccttgatctctat-agtgggttgttatttttttttttctcag----ctggtttctcatctttc-ttgttgcagTGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGTAAAATTGCTCCTAGTGTTGTATTTGTGGATGAA----------------

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|58688470|gb|CK077157.1|CK077157
EST:     AGGCTGGTGCGAATTTCATAAATATATCAATGTCGAGCATCTCTTCAAAG                         TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGC
genomic: AGGCTGGTGCGAATTTCATAAATATATCAATGTCGAGCATCTCTTCAAAGgtattttact ... attaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT
     ttttgttttt  TA-rich tract