Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttacttccatttgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------------------------------atgttccttaagataaacatgt-tgtattgttgttgttggcatgagttacttacttccatttgacctttcaa--ttgacatctgatccctgcacttttc-aaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
                                                                                                ||||   || || |   | ||| ||| |||    ||     || | | |||    ||||||  |     |||  |  ||||||||||  | |||||||| ||||||| ||||||| |||||||| |||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||
gtaagttctaggttaatacataattgaattgcatttctagctttccttttgtagttttgctttactcaattaaatcttgatttattagggatcatcatgtaatttcaggttcccttgtatgttttggatgtgccaatataaat-actg--ctccattaaaatacacaaactaaacatctgatca-tacacttttcgaaagGATGCTATGGCGCGGAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 18
-----------------------------------------------------------------------------------------------atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttacttccatttgacctttcaa-ttgacatctgatccctgcacttttcaaa-gGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
                                                                                               ||||   || || |   | |||  |||| | | ||| | ||  |   |  |  |||||||  |     |||  | |||||||| || | || |||||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||
gtaagttctagattaatacataattgtattgcatttctagctttcttttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgt-atattttggatgt-gccaatataaatatttttccattaaaatacacaaactaacatctga-ccatacatttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
atgttccttaagata--aacatgttgtattgttgttgttggcatgagttacttacttccat-ttgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
 | ||    ||| ||  ||||||    | | ||   ||     |  |  | | |||| |   ||  | |  |||||      || | |    |   | |  ||||||| |||||  | | |||||| ||||| ||||| || || ||||||||||| || ||||| |||||||||||||| |||||| | || || || || |
cttttttagaaggtacaaacatgaaccaat-ttacagtccatctagg--attcactttcggattctcataacaatttctccatgttgcaaaaatcgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
atgttccttaagataaacatgt-tgtattgttgttgttggcatgagttacttacttcca-tttgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
   ||  |||  |   |||    || |    | |      |||     | | |||| |  |||    | ||||||  |  |   |  |   |   |||||||||||| |||||  ||| |||||| ||||| || || || || ||||||||||| || ||||| |||||||||||||| |||||| | || || || ||||
-gcttttttagaaggtacaaacatgaaccaatttacagtccatctagaattcactttcggtttcttatatcaattt-ctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 18
atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttacttccatttgacctttcaat---tgacatctgatccctgca---cttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
         || || || |   |  ||   |   |     ||  |||| |       || ||    || | |   |   || | ||      |   | |  |  |||| || ||||| || ||||||||||||||||| ||||||||  |||||||||| || ||||||||||| |||||||| || ||||| |||||| | || |
-----taacaaaattaaaaaaatacataaataaagaataaatt-gttattcctgaaaatgtggttattgactgtgtattattttattttcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 18
-----atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttacttccatttgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
       ||   |  |     |   |||| ||     ||      || | | | |   ||    |||||| |  | ||   || |  |       |   ||  |||| || ||||| || ||||||||||| ||||| ||||||||  |||||||||| || ||||||||||| |||||||| || ||||| |||||| | || |
tgattgagtcagtctaagctgaggagttgcataacaatta--aaaataaataaatg--ttgttattgaccatgta-ttattatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv03s0038g00540.t01 (Vitis vinifera), 3'ss of exon 3
atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttactt-ccatttgacctttca--attgacatctgat--ccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
        ||   |   |       ||   |  | | |     | ||  | | ||   ||| |  ||||     ||    | ||    || || |  ||| | ||||||| |||||  | ||| || | ||||| |||||||| ||  | |||||||| || ||||| |||||||||||||| |||||| |||| || || || |
-----ttctatactggtcccagaacataaattctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggctgccttgaaaattttatagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 18
atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttactt-ccatttgacctttca--attgacatctgat--ccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
        |    |   |       ||   |  | | |     | ||  | | ||   ||| |  ||||     ||    | || |  || || |  ||| | ||||||| |||||  | |||||||| ||||| |||||||| ||  |||||||||| || ||||| |||||||||||||| |||||| |||| || || || |
-----ttctgtactggccccagaacataaattctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggttgccttgaaaattttatagGATACAATGGCCAGAAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttacttccatt------tgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
      | ||     |   | || ||   || |   |   || ||  | ||| ||||  |      ||     |    |||    |||||         ||   ||||||| ||||  || |||||||| || || |||||||||||| |||||||||| || ||||| ||||| |||||||| || ||||| || |||||||| |
------cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatattatggttccttgtatgattgttgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG

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|325493116|gb|JG457640.1|JG457640
EST:     CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTG                         GGATACTATGGCACGGAGAACTGCTGATCCTGAAGAAGAACTTAGATGGAT
genomic: CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTGgtagtttcta ... cttttcaaagG-ATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGAT
EST: gi|29614012|gb|CB619025.1|CB619025
EST:     CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTG                         GATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTGgtagtttcta ... cttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|29657562|gb|CB653837.1|CB653837
EST:     CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTG                         GATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTGgtagtttcta ... cttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|58652777|gb|CK041457.1|CK041457
EST:     CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTG                         GATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTGgtagtttcta ... cttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|33795777|gb|CF323758.1|CF323758
EST:     CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTG                         GATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTGgtagtttcta ... cttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|25798429|gb|CA754390.1|CA754390
EST:     CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTG                         GATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTGgtagtttcta ... cttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|58679703|gb|CK068390.1|CK068390
EST:     CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTG                         GATACTATGGCACGG
genomic: CAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTGgtagtttcta ... cttttcaaagGATACTATGGCACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttacttccatttgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
                                     tccctgcacttttc  CT-rich tract
                    tttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttacttccatttgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT