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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgggtttacaggaagaaaaaaccattgactattttttacagcaaacttatgatgatattcccagttgtattttacctgtgattatttgctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG

Basic information

species Oryza sativa
transcript LOC_Os01g55540.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G094712_T02 (Zea mays), 3'ss of exon 3
---gatgggtttacaggaagaaaaaaccattgactattttttacagcaaacttatgatgatattcccagttgtattttacctgtgattatttgctt-tgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG
     || || |||| |      |  | |   |    ||  |   | ||  ||||||   || |   || |||||||||       || | | ||| |  ||||||||||||| ||||||||  | || ||||| || ||||| || |||||||||||||| ||||||||||| ||||| ||||||||
tctcgtgtgtgtacaagccactgatgcgaaaaaactgttggtgtgg-aagtttatga---tacttgaagctgtattttagacacatttttcttcttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAG

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 3
---gatgggtttacaggaagaaaaaaccattgactattttttacagcaaacttatgatgatattcccagttgtattttacctgtgattatttgctt-tgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG----------------
     || || |||| |      |  | |   |    ||  |   | ||  ||||||   || |   || |||||||||       || | | ||| |  ||||||||||||| ||||||||  | || ||||| || ||||| || |||||||||||||| ||||||||||| ||||| ||||||||                
tctcgtgtgtgtacaagccactgatgcgaaaaaactgttggtgtgg-aagtttatga---tacttgaagctgtattttagacacatttttcttcttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAGGTATTCTCTGTTTGAC

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G08670.2 (Glycine max), 3'ss of exon 3
gatgggtttacaggaagaaaaaaccattgactattttttacagcaaacttatgatgatattcccagttgtattttacctgtgattatttgctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG
| | |     ||  |  || | ||  |    |  || | |   |     |   || ||  ||  |  | | | | |  |    || |    | |    ||||||||    ||||| ||| | ||||||  ||| || || ||||| |||||  |||||||||||||||||||||| ||||||||
gttagtacctcactataaatatactttc--tttcttctcatttccgg--tgacattatgctctgaactttttatgatgttctgttctgcattattttcagGTCACGCAACAAGGAATATATTCCGATCGTTGGGCTTGCTGATTTTAATAAATTGAGTGCTAAGCTTATTTTTGGGGCTGACAG

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0016g03720.t01 (Vitis vinifera), 3'ss of exon 3
gatgggtttacaggaagaaaaaaccattgactattttttacagcaaacttatgatgatattcccagttgtattttacctgtgattatttgctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG
           | |      ||||   ||    ||| ||   | |   |||  |||||      ||| ||  || | |  || || | ||| |    |||||| || || || |||||  | || ||   ||||||||| || ||||||||  |||| ||||| || |||||||||||||||||
---------gtaagctattcaaaca--tgggagtttctttttgtacgtttac-atgatg-----agtagttgttgatcactgctt-tgtgcatcttttagGTCCCGGGTCAAAGAGTACCTTCCCATTGTTGGACTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG

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|32948428|gb|BP185000.1|BP185000
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|33685641|gb|CF313880.1|CF313880
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|44667509|gb|CR280943.1|CR280943
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|33678230|gb|CF306469.1|CF306469
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|33794428|gb|CF323098.1|CF323098
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|58591056|gb|CF989364.1|CF989364
EST:     CTGGTGCTGAATGTGGGCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCACTAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|29639571|gb|CB644580.1|CB644580
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|32948311|gb|BP184883.1|BP184883
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|218483959|gb|FG947666.1|FG947666
EST:     TGGNTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: TGG-TGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|33794958|gb|CF323359.1|CF323359
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|58656014|gb|CK044694.1|CK044694
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|29679665|gb|CB675940.1|CB675940
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|29660055|gb|CB656330.1|CB656330
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|32948296|gb|BP184868.1|BP184868
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|218478855|gb|FG949686.1|FG949686
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|29658837|gb|CB655112.1|CB655112
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|33678676|gb|CF306915.1|CF306915
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|58694708|gb|CK083395.1|CK083395
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|33793380|gb|CF322571.1|CF322571
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|10794714|gb|AU108680.1|AU108680
EST:     CTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTNCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|33795088|gb|CF323417.1|CF323417
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
EST: gi|58669037|gb|CK057723.1|CK057723
EST:     CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC                         GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA
genomic: CTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCCgtaagtctga ... ctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttatgatgatattcccagttgtattttacctgtgattatttgctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG
                                         tttgcttt  CT-rich tract
                     ttgtatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgggtttacaggaagaaaaaaccattgactattttttacagcaaacttatgatgatattcccagttgtattttacctgtgattatttgctttgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA