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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcatttatattataattctatttcaaagtatggcttactgttgtttatacattgtactattgctaatggagtaatggtattcccggttcattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA

Basic information

species Oryza sativa
transcript LOC_Os03g62640.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G118014_T02 (Zea mays), 3'ss of exon 8
----tatcatttatattataattctatttcaaagtatggcttactgttgtttatacattgtactattgctaatggagtaatggt-attcccggttcattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA
     |  |||| | ||| |  | |  ||||   |||    |     | || || |||  | | || ||||      || || | ||||   ||| | ||||||||| ||||| |||||||| |||||||| ||||||||||||||||| ||||| || |||||
ttggcactattt-tgttacagattt--ttcatcttattatctgtgtctattcat-catgatgcaat-gctagatacatactgatgattctttgtttaatttgtagACCGATCAAAAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAA

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 8
tatcattta-tatta-taattctatttcaaagtatggc-ttactgttgtttatacattgtactattgctaatggagtaatggtattcccggttcattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA
 ||   | | | | | |  || ||||  | |  |     ||||||   || | |          |   |||| |  |||||  ||||   ||| ||||| ||||||||||| || || || |||||||||||||||||||||||||| ||||| || |||||
catatctcactgtcactggttatattgtatatgacattattactgcaattcacaagcaagtgcctacataattgc-taatg--attctttgtttattttatagACTGATCAAAAATTACGCCTCTGTGACATATGTGGAGCATTTCTGAGTGTATATGACAA

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G03340.1 (Arabidopsis thaliana), 3'ss of exon 8
tatcatttatattataattctatt-tcaaagtatggcttact-gttgtttatacattgtactattgctaatggagtaatggtattcccggttcattttgt-agACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA
    ||||  |  | || | ||   ||   | ||  | |  |   ||| | ||||   |  | |         |       ||||     |  || || | |||| || || ||||||||||| ||||||||||||||||||||  | || ||||| |||| 
---tatttggaccaaaagtataacatcttcgcatcccctgtttaatgtatctacacattggtttcatcttctaacctcacttattgttcctatatcttctcagACAGACCAAAAGTTGCGTCTATGTGACATATGTGGAGCATTCTTGAGCGTCTATGACAG

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|29665629|gb|CB661904.1|CB661904
EST:     GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT                         ACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
genomic: GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATTgtgagtttaa ... cattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
EST: gi|86502553|gb|CI145186.1|CI145186
EST:     TATACTGCTGCTGATGTTCGAATT                         ACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
genomic: TATACTGCTGCTGATGTTCGAATTgtgagtttaa ... cattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
EST: gi|29630312|gb|CB635321.1|CB635321
EST:     GGGAACCNACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT                         ACTGATCAGAAGTTGCGTCTCTG
genomic: GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATTgtgagtttaa ... cattttgtagACTGATCAGAAGTTGCGTCTCTG
EST: gi|84117476|gb|CD151243.1|CD151243
EST:     GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT                         ACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
genomic: GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATTgtgagtttaa ... cattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
EST: gi|454535|gb|D28304.1|D28304
EST:     GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT                         ACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
genomic: GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATTgtgagtttaa ... cattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
EST: gi|29664073|gb|CB660348.1|CB660348
EST:     GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT                         ACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
genomic: GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATTgtgagtttaa ... cattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
EST: gi|29661288|gb|CB657563.1|CB657563
EST:     GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT                         ACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
genomic: GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATTgtgagtttaa ... cattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
EST: gi|29674744|gb|CB671019.1|CB671019
EST:     GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT                         ACTGATCACAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC
genomic: GGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATTgtgagtttaa ... cattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatacattgtactattgctaatggagtaatggtattcccggttcattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA
                 tgctaat  putative branch site (score: 2)
                                           ttcatttt  putative PPT
                                           ttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcatttatattataattctatttcaaagtatggcttactgttgtttatacattgtactattgctaatggagtaatggtattcccggttcattttgtagACTGATCAGAAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA