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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaagactatgattgcttattggttcattacaaaagaaagtgggtcgttctttcttttcttgctgcaggcataaaagggaaaccattccattat...

Basic information

species Oryza sativa
transcript LOC_Os02g04710.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G065494_T01 (Zea mays), 5'ss of exon 7
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaagactatgattgcttattggttcattacaaaagaaagtg-ggtcgt---tctttcttttcttgctgcaggcataaaagggaaaccattccattat
||| |  |||||||||||||||||| |||| || | |||||| ||| |||| ||||| ||||||||||| || || |||||||||||||| ||||||||||||| |||| | |||| |||| ||  ||     ||||  ||| |  || |||| |   |  | || || ||||||||  ||| | | ||  |  || | |    
TGGCAGTAAATTGAGGGAGAAAGCTCTGGAGACAGCCATGCAACATGTTCACTATGAGGATGAGAACACTCGGTACATTTGCATTGGTCCTGTAAACAAGgtaaattgagggctattattgattgctgaacttttacttaaggagatgtggtcttatgttgtcctatttttgctgcaaacatcacaaggccat-atgctag---

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 5
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaagactatgattgcttattggttcattacaaaagaaagtg-ggtcgttcttt---cttttcttgctgcaggcataaaagggaaaccattccattat
||| | ||||||||||||||||||| |||| || |||||||| ||| |||||||||||||||||||||| || ||||||||||||||||| ||||||||||||| || | | |||| ||||||  |||   | ||||||||| | ||| |||| |  |||   || ||||||||||| ||||   | ||  |  || | | |  
TGGCAGCAAATTGAGGGAGAAAGCTCTGGAAACAGTCATGCAACATGTTCATTATGAAGATGAGAACACTCGTTATATTTGCATTGGTCCTGTAAACAAGgtaaattaaggcctatcattgctcgttgaacc-ttacaaaaggaggtgtggtcttattttatcctattcttgctgcaagcatctcaaggccat-atgctact--

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA01G00430.2 (Glycine max), 5'ss of exon 8
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatt--tgaagactat--gattgcttattggttcattacaaaagaaagtgggtcgttctttc-ttttcttgctgcaggcataaaagggaaaccattccattat
||| || | ||||||||| || ||| |     |||   || ||||||| ||||| ||||||||||| || |||||||||||||| ||||| ||||| |||||||||  ||||     |  |    || |  || || || ||||     ||   | |||||||   ||||  ||||  |   ||  || |  |  || | |  | 
TGGAAAAAGATTGAGGGAAAAGGCTATTATTTCTGCATTGGAGCATATACATTACGAAGATGAGAATACTCGATATATTTGCATAGGTCCTGTAAATAAGgtaattgttgaaaggggtcaggcatctaaggggctcctttcaaa---ttgttcattgttcttttactttccagctgttga-gtaggagcgtgagaatactaaca-

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv09s0018g00630.t01 (Vitis vinifera), 5'ss of exon 7
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgta-atttgaagactatgattgcttattggttcattacaaaagaaagtgggtcgttctttcttttcttgctgcaggcataaaagggaaaccattccattat
 || ||||| ||||||||||| |||||   |||||| ||||||||| | || |||||||||||||| || || ||||| ||||| || || || ||||||||| || |||||  || ||  |||  || |  |   |  ||| | | ||  |  |   |||  |   ||        |  |      ||  ||   |  | 
CGGAAACAAGTTGAGGGAGAAGGCTTTATGCACTGTAATGCAGCATGTACACTATGAAGATGAGAATACACGGTATATATGCATAGGGCCTGTGAACAAGgtacatgtgaagtata-gaaagctcctttgaactgcaataaatatactgattactaagttcaataaatgtacggattactattaattaagaataaaaccag

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv09s0054g01110.t01 (Vitis vinifera), 5'ss of exon 9
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgta-atttgaagactatgattgcttattggttcattacaaaagaaagtgggtcgttctttcttttcttgctgcaggcataaaagggaaaccattccattat
 || ||||| ||||||||||| |||||   |||||| ||||||||| | || |||||||||||||| || || ||||| ||||| || || || ||||||||| || |||||  ||  |  |    |||       | ||| |    ||  |  |   |||| |   ||   |    |  |      ||  | |  |  | 
CGGAAACAAGTTGAGGGAGAAGGCTTTATGCACTGTAATGCAGCATGTACACTATGAAGATGAGAATACACGGTATATATGCATAGGGCCTGTGAACAAGgtacatgtgaagtatagaaaggtcctttgaactgcaataaatgtgc-tgattactaagttctataaatgtaccgattactattaattaagaactaaaccag

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv09s0054g01090.t01 (Vitis vinifera), 5'ss of exon 8
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgta-atttgaagactatgattgcttattggttcattacaaaagaaagtgggtcgttctttcttttcttgctgcaggcataaaagggaaaccattccattat
||| ||||| ||||| ||||| |||||   |||||| ||||||||| | || |||||||||||||| || || ||||| ||||| || || || ||||||||| || |||||  ||  |  |    |||       | ||| | | |||  |  |   |||  |   ||        |  |      ||  | |  |  | 
TGGAAACAAGTTGAGAGAGAAGGCTTTATGCACTGTAATGCAGCATGTACACTATGAAGATGAGAATACACGGTATATATGCATAGGGCCTGTGAACAAGgtacatgtgaagtatagaaaggtcctttgaactgcaataaatgta-gtgattactaagttcaataaatgtactgattactattaattaagaactaaaccag

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv09s0054g01120.t01 (Vitis vinifera), 5'ss of exon 6
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgta-atttgaagactatgattgcttattggttcattacaaaagaaagtgggtcgttctttcttttcttgctgcaggcataaaagggaaaccattccattat
 || ||||| ||||||||||| |||||   |||||| ||||||||| | || |||||||||||||| || || ||||| ||||| || || || ||||||||| || |||||  ||  |  |    |||       | ||| | | |||  |  |    ||  |   ||   |    |  |      ||  | |  |  | 
CGGAAACAAGTTGAGGGAGAAGGCTTTATGCACTGTAATGCAGCATGTACACTATGAAGATGAGAATACACGGTATATATGCATAGGGCCTGTGAACAAGgtacatgtgaagtatagaaaggtcctttgaactgcaataaatgta-gtgattactaaggtcaataaatgtaccgattactattaattaagaactaaaccag

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv09s0054g01250.t01 (Vitis vinifera), 5'ss of exon 4
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgta-atttgaagactatgattgcttattggttcattacaaa---agaaagtgggtcgttctttc--ttttcttgctgcaggca--taaaagggaaaccattccattat--------------------------------------------------------------------------------------
 || ||||| ||||| ||||| |||||   |||||| ||||||||| | || |||||||||||||| || || ||||| ||||| || || || ||||||||| || |||||  ||  |  |    |||       | |||   ||  | |     ||||  |   | | |    | |    |  ||| |   |||||| |    |                                                                                        
CGGAAACAAGTTGAGAGAGAAGGCTTTATGCACTGTAATGCAGCATGTACACTATGAAGATGAGAATACACGGTATATATGCATAGGGCCTGTGAACAAGgtacatgtgaagtatagaaaggtcctttgaactgcaataaatgtagtgattactaagttcaataaatgtaccgattactattaattaagaactaaaccagttagcttctttagttctaccactctactcaggtgctcttgatctaattgtctgttccatgaaggtcttgatttcctgttatctaatttgtacag

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv09s0054g01180.t01 (Vitis vinifera), 5'ss of exon 6
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgta-atttgaagactatgattgcttattggttcattacaaaagaaagtgggtcgttctttcttttcttgctgcaggcataaaagggaaaccattccattat----------------------------------------------------------------------------------
 || ||||| ||||||||||| |||||   |||||| ||||||||| | || |||||||||||||| || || ||||| ||||| || || || ||||||||| || |||||  ||  |  |    |||       | ||| |||    | |   | ||  ||        | |  ||   |       | |||| |  |                                                                                   
CGGAAACAAGTTGAGGGAGAAGGCTTTATGCACTGTGATGCAGCATGTACACTATGAAGATGAGAATACACGGTATATATGCATAGGGCCTGTGAACAAGgtacatgtgaagtatagaaaggtcctttgaactgcaataaatgaa--ctgattactattaattaag--aacgaaaccagttagcttcttcaattcgaccactctactcaggttcacttgatctaattgtctgttcttttctgttccatgaagctcttgatttcctgttatctgatttgtacag

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 8
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaagactatgattgcttattggttcattacaaaagaaagtgggtcgttctttcttttcttgctgcaggcataaaagggaaaccattccattat-----
|||||| || ||||| ||||| ||| |   ||||||| || ||||| | || || ||||| |||||||| || ||||| ||||| ||||| ||||||||||||  |     | ||||  | || | | ||   ||||    |  |  |   |  | | |   ||      ||  | ||      |    || |  | ||      
TGGGAAAAAGTTGAGAGAGAAGGCTCTTCGCACTGTCTTGGAGCATGTACACTACGAAGACGAGAACACTCGCTATATATGCATAGGTCCTGTAAACAAGgtatat-----attatgggttctcaattgtgttttacctctgttaaggttcctctttgttcattgggagggctagaatgttgttgtgtgcaattgagtaggaggt

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|2310417|gb|C26572.1|C26572
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|33675594|gb|CF303833.1|CF303833
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|58690263|gb|CK078950.1|CK078950
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|29646295|gb|CB651302.1|CB651302
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|29676836|gb|CB673111.1|CB673111
EST:     ATTATGACGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|33675264|gb|CF303503.1|CF303503
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTC
EST: gi|29617095|gb|CB622107.1|CB622107
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGAACAAATTGAGGGAGAAAGCTTTGGACACTGTCATGCAGCATATTCATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaagactatgattgcttattggttcattacaaaagaaagtgggtcgttctttcttttcttgctgcaggcataaaagggaaaccattccattat

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG