Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaactggttatcttctgtttcttgtttcaattgttgagcacttgagctactattagataaaactgactcaaaaaatctcacctgttatttctattgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC

Basic information

species Oryza sativa
transcript LOC_Os02g38010.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 5
--gttaactggttatcttctgtttcttgtttcaa--ttgttgagcacttgagctactattagataaaactgactcaaaaaatctcacctgt-tatttctat-tgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC
  | |   | ||    | || ||||| |   |||  |  ||    || ||    |||  ||  ||||| ||  |       | |    ||| | |   | | ||  ||||||||||| || || || |||||||| |  |||||||| |||||| ||||||| || ||| |||||||||  || |||||  | ||| | || |||||  
gtgattgtttgtaccttactttttctagaagcaagttcattcgagacatgtaa-acttgtaagtaaaagtgtattt-----ttttttttgtgtgtgcgtgtgtgtgcagTGGAACTTTCGCATCGGTTTTACTCCTAGGGAAGGTTTGGTTATTTATTCTGTAGCCTATATTGATGGAAGTCGAGGGCGAAGGCCTGTGGCCCACAGAT

upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 5
gttaactggttatcttctgtttcttgtttcaattgttgagcacttgagctactattagataaaactgactcaaaaaatctcacctgttatttctattgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC
  ||  || | |  | || | |  | | |   |  |||   |  ||      |||| |||  |  ||   | |  | |||    | || | ||| || |||||||||| ||||||||||| || || |||||||||||||| |||||  |||||||||||||||||||||| |  | ||| ||  | ||| | ||||| ||||
-gtagatgttaagttactatattgtttatttgtcattggaaatgtgcaaagatatttgattca-ttgtaactactagtcttttttctt-tctctttt-aacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC

upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 5
gttaactggttatcttctgtttcttgtttcaattgttgagcacttgagctactattagataaaactgactcaaaaaatctcacctgttatttctattgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC
               |   ||||  ||   |        | |    ||  | |||  | | || || | |   |||   |  |     ||||   ||  |||||||||||| |||||||| || ||||| |  ||||||||||| || ||||| || |||||||||||||| |  || || ||  | ||| | || |||||||
--------------gtagatttccagtaatagcctacttgaaaccaagtgattat--gcttaagcttatttctaaa--ttggctcaacattttgttt--acagTGGAACTTTCGTATTGGATTCACTCCAAGGGAAGGTTTAGTCATACATTCGGTAGCATATGTTGATGGCAGTCGAGGTCGAAGGCCTGTTGCACACAGGC

upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 5
gttaactggttatcttctgtttcttgtttcaattgttgagcacttgagctactattagataaaactgactcaaaaa--atctcacctgttatttctattgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC
      || ||| ||| |  |       |   ||  ||   | |  |  | | |   | || |  || || |  |   || |    | ||||| ||  |   |||||||| || |||||||| || || |||| ||| ||||| |||||| |||||||||||||| ||||||| |  || || ||  || || | || || ||| 
-----gtgattacctttt--tgggaaagtaggttactggaaaatctaagttcaacctgctata--tggcttatcatctatttttatttttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT

upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 5
gttaactggttatcttctgtttcttgtttcaa-ttgttgagcacttgagctactattagataaaactgactcaaaaaatctcacctgttatttctattg--aacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC
          ||  ||  ||||||||       ||||| |  | |  |  ||   | |||  |  |  ||| || |      |  | |||| | | | |    |||||||| ||||||||||| || ||||||| ||| ||||| ||||| ||||||||||||||||||||||| |  || || ||  ||||| | ||||| ||| 
---------gtacttttggtttcttgagctggcttgttaataaatgtaattaaagtcaga-gatgcatactaaacactatcaatgttttatctttttggttggcagTGGAATTTCCGTATTGGTTTCACTCCCAGAGAGGGTTTGGTTATCCATTCTGTTGCATATGTTGATGGTAGTCGGGGTCGAAGACCTGTAGCTCATAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactattagataaaactgactcaaaaaatctcacctgttatttctattgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC
                                      ttatttct  CT-rich tract
                                      ttatttctattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaactggttatcttctgtttcttgtttcaattgttgagcacttgagctactattagataaaactgactcaaaaaatctcacctgttatttctattgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA