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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattatttcctattcagcatttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG

Basic information

species Oryza sativa
transcript LOC_Os02g08120.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 6
------------gtaagattatttcctattcagcatttttcttcttt--ttttcttttgtttgagttc-taac-atatatg---ttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
            ||  |  | ||    | | |  ||| || | ||||  ||||  | ||||| ||||  | || ||  |||   ||||||   |||| ||||||||||||||||| || || |||||||||   ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||| || |
gtaagttcgtatgtgggtgtgttattaacttactattattatactttcatttttatgtgtttcagtttatgactattaatgctcttctgtgatagATACTTGGAAGTGGTATGTCCAACAAAATGTGGGATGCCCTTGTGGAACATGCAAAGACTTGTGTCTTAAGTGGGAAATATTACATATACTATTCTGATG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G018837_T01 (Zea mays), 3'ss of exon 6
gtaagattatttcc-------tattcagcatttttcttctttttttcttttgtttgagtt-ctaac-atatatg---ttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
||||| || | |         |||| |    || |     |  |||| | |||||  ||| || |  ||| |||   ||||||   |||| ||||||||||||||||| || || |||||||| |  ||||| || |||||||||||||||  |||||||||||||||||||||||| ||||| || |
gtaagtttgtgtgtgcagtgttattaacttattcttactatactttcatgtgttttggttgctgattataaatgctattctgtgatagATACTTGGAAGTGGTATGTCCAACAAAATGTGGGAAACCCTTGTGGAGCATGCAAAGACTTGTACCTTAAGTGGAAAATATTACATATACTATTCTGATG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
------------------------------gtaagattatt---tcctattcagcatttt--tcttctttttttcttttgtttgagttctaacatata---tgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
                              | |||| | |    |   |||   | |  |  | |   ||||||   |      | || | ||  ||    | | ||     |||| ||||| ||||| ||||| || || ||||||||| |||| || || |||||||||||||||||  | |||||||||   ||  |||| ||| | || |
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 7
gtaagattatttcctattcagcatttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
||||| |||  |  |       | | ||    ||   |  |||       ||| |   ||||   |||      |||||||||| ||||||||||| || |||||||||||   |||| | || |||||||| || |||||  ||||||| ||    ||  | |||||| |||| |
gtaagtttaggttttgcgtcttaatcttgaagttaggtcttttcccagttgttttcttatat-cattcaactgtagATCCTTGGGAGTGGTATGTCAAACAAGATGTGGGAGGCTCTTTTAGACCATGCAAAAACATGTGTTCTAAGTGGGAAGCTCTATGTTTATTATCCAGAAG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
-------------------------------------gtaagattatttcctattcagcatttttcttctttttttc-------ttttgtttgagt-tctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
                                     || |  | || |  |  |||     |||    || | ||        |  | | | | | | | |   |||  |  | |   |||| ||||| ||||| ||||| ||||||||||||||||||||||| || || ||||||||||||||  | |||||||||  |||| |||| ||| | || |
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------gtaagattatttcctattcagcatttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
                                                                       |||     |||    ||  |  ||| || |   | |       | | |  | |  |  |||  |    | |   |||| ||||| || || ||||| ||||||||||||||||||||||| || |||||||||||||||||  | |||||||||  |||  |||| ||| | || |
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatac-ttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 6
gtaagattatttcctattcagcatttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
||||| |||  |  |       | | ||    ||      ||||      ||| |   ||||   |||      |||||||||| ||||||||||| || |||||||||||   |||| | || |||||||| || |||||  ||||||| ||    ||  | |||||| |||| |
gtaagtttaggttttgcatcttaatcttgaagttaggcctttttccagttgttttcttatat-cattcaactgtagATCCTTGGGAGTGGTATGTCAAACAAGATGTGGGAGGCTCTTTTAGACCATGCAAAAACATGTGTTCTAAGTGGGAAGCTCTATGTTTATTATCCAGAAG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------gtaagattatttcctattcagcatttttcttcttttttt-cttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
                  || |   |  ||  | ||           ||| ||   | ||  ||  | | |   |  || |    | ||||  |||| ||||||||||| ||||| ||||||||||||||| | || || || |||||||| || |||||| |||| || ||   ||| || || ||| | || |
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtct-agATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
gtaagattatttcctattcagcatttttcttctttttttcttttgt-ttgagttctaacatatatgttctgtccc---agATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
|||||   | |   || |       ||     |    |  | |  | |||  | || | |||| | |   ||  |   ||||||| |||||||| ||||| ||||||||||||||   |||| | || ||||||||||||||   | | |||||||| |  ||  | |||||||| || |
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 7
gtaagattatttcctat-tcagcatttttcttctttttttcttttgtttgagttctaacatatatgttc-----tgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
|||||| | |    | | |   |||||      ||   | | | | ||  | || | |  ||| |||       |||   |||| ||||||||||| ||||| ||||||||||||||| ||||||| || |||||||| ||||||||  ||||||| |||  |||  | || ||| | || |
gtaagaatgtacattttgttgtcatttcagaatttgaatccgtctattgtaatttttatttatttgtctccaattgttgtagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATGTTCTTGTGGAGCATGCAAAAACTTGTGTTCTAAGTGGGAAACTTTATGTTTACTATCCTGATG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
gtaagattatttcctattcagcatttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
          |   || | |   ||  | || | ||| ||| |  | ||    || |  ||  || |||| | ||||| ||||||||||| ||||| ||||||||||||||       || || ||||| || || || ||| | || |||||    ||  | |||||| | ||||
---------gtaagtaatgaaagttagttttttctttctctctc-tctgtcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ05811 (Selaginella moellendorffii), 3'ss of exon 5
gtaagattatttcctattcagcatttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
||||| | ||    | ||     | | |||  || | |   ||| ||| || ||  |  ||  || |||| | ||||| ||||||||||| ||||| ||||||||||||||       || || ||||| || || || ||| | || |||||    ||  | |||||| | ||||
gtaag-taatgagtttttt----tctctctctttctctctctttctttcagctc--atgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG

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|29668781|gb|CB665056.1|CB665056
EST:     TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGT                         ATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
genomic: TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGTgtaagattat ... tctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
EST: gi|51946147|gb|CV152488.1|CV152488
EST:     TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGT                         ATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
genomic: TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGTgtaagattat ... tctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
EST: gi|58689965|gb|CK078652.1|CK078652
EST:     TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGT                         ATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
genomic: TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGTgtaagattat ... tctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
EST: gi|218478168|gb|FG952613.1|FG952613
EST:     TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGT                         ATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
genomic: TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGTgtaagattat ... tctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
EST: gi|569278|gb|D40127.1|D40127
EST:     TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGT                         ATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
genomic: TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGTgtaagattat ... tctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
EST: gi|117244367|gb|CT849708.1|CT849708
EST:     TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGT                         ATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT
genomic: TTGAAGACTTCCTTAGGCTTGTGGTTCGAGATCCTCAGAAGTTGCGCAGTgtaagattat ... tctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
                              ttctaac  putative branch site (score: 1)
                                            ttctgtccc  putative PPT
           tttttttcttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattatttcctattcagcatttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA