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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttctgaatgttcaaatatgtggtcacattttttcacacttacacattcacaatctatatgttctatgtattaattttctctaataaatgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA

Basic information

species Oryza sativa
transcript LOC_Os09g32260.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G008374_T02 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------aggttctgaatgttca-aatatgtggtcacattttttcacactta-cacattcacaatctatatgttctatgtattaattttctctaataaatgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
                                                                                                     |||   | ||   || |||    |     | |    || || ||  |||  |   | |    | ||| ||| | |  ||  | ||| |||    |||||||| || ||  | ||||| || || ||||| ||||| ||||||||||| || ||||||||||| |||||||| || ||||| || ||||| ||||||||
gtaatcatcatcggagaaaccaactgttaattaacctgttcatgtgtatatacacgcacatgtacatgcatgcatatgtagtaatcttttctcctctcttctctccttatttggaacatgcatgcgggagtgtcagaacgtaacaatttcttatattttccagtatatatataagtgatcgattatatatgcatgccagAGAAAGCGAAGCTCGGAGAAAAAGAGTGGTATTTCTTCAGCCTAAGGGACCGGAAGTACCCAACAGGCGTGCGAACGAACCGCGCCACTAACGCTGGTTA

upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G386163_T02 (Zea mays), 3'ss of exon 1
aggttctgaatgttcaaatatgtggtcacattttttcacacttaca--cattcaca-atctatatgttctatgtattaattttctctaataaatgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
    | |  ||   |   ||    || |  |||    | | || |   |||| |   |   |||     |     ||   ||| | |  | |||     |||||||| || ||  ||||||| || || ||||| ||||| ||||| ||||| || ||||||||||| || ||||| |||||||| || ||||| ||||||||
--aatgtatataaccggtta-aaagttagctttgaaaaaagttgcgttcatttatgcacacataaaaaatgaaacttggatttatttgttgaattgttgccagAGAAAGCGAAGCTGGGAGAAAAAGAGTGGTATTTCTTCAGCCTGAGGGACCGCAAGTACCCAACGGGTGTGCGAACAAACCGTGCCACTAACGCTGGTTA

upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G20340.1 (Glycine max), 3'ss of exon 1
aggttctgaatgttcaaatatgtg-gtcacattttttcacacttacacattcacaatctatatgttctatgtattaattttctctaa----taaatgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
        |||  | ||| ||     ||  |||| |||  ||| |   |    || |  || |  |||||  ||  |||||   |||    |   ||||    ||||||||| ||||||||| | || |||||||||||||| || ||||| ||||| ||||||||||| || ||  | || |||||||| || ||  | || ||
----atgaaattattaaacattcctatctaatttattctgactaat-tagcatcagttaatttcctctattaatatatttttattaaattgtttctgtgaaatagAGAAGGCGAAAATGGGACAAAAAGAATGGTACTTCTTCAGTCTAAGAGATCGTAAGTACCCAACGGGTGTTAGAACCAACCGAGCCACGAACACAGGGTA

upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G08440.1 (Glycine max), 3'ss of exon 1
aggttctgaatgttcaaatatgtggtcacattttttcacact-tacacattcac---aatctatatgttct-atgtattaatt-ttctctaataaat--gtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
          | ||   |||| |||  | || | | |   || || | | | |    ||| ||||| |||| ||  || |||| |||| ||||   |   ||    || ||||||||| |||||||| || |||||||||||||| || || || || || || |||||||| || ||| | ||||| ||||||||||| || || ||
-------ctttcttgtgatatatggata-atatatacgtgctatatataataatttgaatgtatatattctcatcaataaattattctataattttttcatgaaatagGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA

upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G24430.1 (Arabidopsis thaliana), 3'ss of exon 2
-aggtt--ctgaatgttcaaatatgtggtcacattttttcacacttacacattcacaatctatatgttctatgtattaattttctctaataaatgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
   |||   |   || | |||| | |||  | ||||  | | |   |      |  ||||   | ||| |    |    || |   | ||||   || |  ||||||||| ||||||||||  || ||||||||||| ||||||||  |||| || |||||||| || || ||| | || ||  | || || ||| | || ||
attgttagttacgtgctaaaattt-tggaaatatttgataaaaaaaaagtcagctaaatcgccaagttattcacaaagtttctgatttataatgttgat--agAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACCGGAAGTACCCGACGGGAGTGAGGACGAATAGGGCGACGAATACAGGATA

upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g02710.t01 (Vitis vinifera), 3'ss of exon 1
aggttctgaatgttcaaatatgtggtcacattttttcacacttacacattcacaatcta-tatgttctatgtattaattttctctaataaatgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
|  ||||     |  ||    |      | |  |||  ||   | || |  | ||| |  ||| |  | ||   || ||     |  |      | |  || |||||| ||||||||||| ||||| ||||| ||||| ||||| ||||| || || ||||||||||| ||  | ||||||||||| || ||  |||||||
aatttcttgtgatgaaagagagcatattcttcattttccaaacaaacttggaaaatttcctatatcttctgatctagttaatctttgttctctcgatt-agGGAAGGCGAAAATGGGAGAAAAGGAGTGGTATTTCTTCAGCCTCAGGGACCGGAAATACCCAACTGGAGTAAGAACAAACCGAGCCACAAACACTGGTTA

upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ22540 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------aggttctgaatgttcaaatatgtggtcacattttttcac---acttacacattcacaatctatat---gttctatgtattaattttctctaataaa------tgtgctc---------------cagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
                                                                      ||   ||||| | |     ||   |||     || ||    ||||  | ||  |  |  |   |   |||   || |  || || |||||| ||       | || ||               ||||||| ||||| |||||||||||||||||||||||||||||| | ||||| || |||||||| || ||  |||| || || || |||||  | || || ||
gtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttgga-atcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGGAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ11746 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------aggttctgaatgttcaaatatgtggtcacattttttcac---acttacacattcacaatctatat---gttctatgtattaattttctctaataaa------tgtgctc---------------cagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
                                                                      ||   ||||| | |     ||   |||     || ||    ||||  | ||  |  |  |   |   |||   || |  || || |||||| ||       | || ||               ||||||| ||||| |||||||||||||||||||||||||||||| | ||||| || |||||||| || ||  |||| || || || |||||  | || || ||
gtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttgga-atcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGTAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ32111 (Selaginella moellendorffii), 3'ss of exon 1
aggttctgaatgttcaaatatgtggtcacattttttcacacttacacattcacaatctatatgttctatgtattaattttctctaataaatgtgctcca----gAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
   ||||     |         |  ||     |     |  |       |   | ||  |  |  |||  ||  | |||  | |        |||||||    || ||||| || ||||| |||||||||||||||||||| |  ||  |||| |||||||| || || ||  |||||||||||||||| ||  | || || ||
---ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactac-taacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGTGAGAAGGAATGGTACTTCTTCACGCTGCGGGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA

upper sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
aggttctgaatgttcaaatatgtggtcacattttttcacacttacacattcacaatctatatgttctatgtattaattttctctaataaatgtgctcca----gAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
   ||||     |         |  ||     |     |  |       |   | ||  |  |  |||  ||  | |||  | |        |||||||    || ||||| || |||||||||||||||||||||||||| |  ||  | || |||||||| || || ||  |||||||||||||||| ||  | || || ||
---ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactac-taacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA

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|88356937|gb|CI620825.1|CI620825
EST:     GGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAG                         AGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTACCCTAAGGGATC
genomic: GGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAGgtaattaatt ... tgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattcacaatctatatgttctatgtattaattttctctaataaatgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA
            tatatgttctatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttctgaatgttcaaatatgtggtcacattttttcacacttacacattcacaatctatatgttctatgtattaattttctctaataaatgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
-ggttctg
- - - - - - - - - - - - - - - - - ttcacac
- - - - - - - - - - - - - - - - - - - - - - - cattcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtat