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

...tttttctctctctacctttttcccttgcctgtgtgtttattatatatgcatgttttatatgaacatcatgttcttattatttacctcattatatgtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC

Basic information

species Vitis vinifera
transcript Vv10s0003g04530.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 13
tttttctctctctacctttttcccttgcctgtgtgtttattatatatgcatgttttatatgaacatcatgttcttattatttacctcattatatgtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC
          | || || | | | | |    |   |  || |||| || |  | ||| |     | | ||||  ||  | | | |  ||| |     |||||| ||||||||| || ||||| ||||| || ||||| || ||||||||||| || ||||| || || ||||| ||||| || || || || ||  | ||
---------gtataactctcttcttggaaactaaat--atcatatttgaaactatta-agagttaccttgtttgtaacactgaac--attcttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCTTGGGGTAAACTTCCAGAAAATGTACCTTGTCATCCAAAGCTTGC

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G401874_T01 (Zea mays), 3'ss of exon 7
tttttctctctctacctttttcccttgcctgtgtgtttattatatatgcat-gttttatatgaacatcatgttcttatta---tttacctcattatat--gtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC
                  |          |   | | |||||| | | |||  | ||  ||| | || |   | |  |||    |  | ||||||| |  ||||||||| |   || || |||||||||||||| || ||||| |||||||||||||| || ||||| ||||| |||||||| || || ||||| || ||  | ||
-----------------gtacgtagaatatacatatatattatttcttcattatattgcatggaaattaaactttatttagagctagcttcattatcttggtgcagCAAACAGCGTACATCCAAAGAACTGGTACCCGATTCCTCTCATATTCTGCCGCCCTTGGGGCAAGCTTCCAGAGAACGTCCCGTGCCATCCGAAGCTCGC

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G113276_T01 (Zea mays), 3'ss of exon 7
tttttctctctctacctttttcccttgcctgtgtgtttattatatatgcatgttttatatgaacatcatgttcttattatttacctcattatatgtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC
                          | |||  | | |  | |  |   ||   |||     || | |   | || | | ||   || ||   | |||||||| |||||| || || ||||| ||||| || ||||| || ||||||||||| |||||||| || ||||| || ||||| || || || || ||| | ||
----------------------gtgcggctgactatctgctttgca---attacttaatcatacttaacaattttgtaactttggtcctt---tctgcagCAAACCAAGTCCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCATGGGGCAAACTGCCGGAAAATGTTCCTTGTCATCCAAAACTTGC

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 11
tttttctctctctacctttttcccttgcctgtgtgtttattatatatgcatgttttatatgaacatcatgttcttattatttacctc--attatatgtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC
      |      | |||| |  | |      |    | |||  |   |   | ||  |     |   || |||| | | |||  ||   | || | || |||||||||||||||||| ||||| |||||||| ||||| ||  |||| ||||| || ||||| || |||||||| ||||| ||||| || || ||| | ||
--cacgtagaaggagctttatagcattatgccgcccattttagtttctccattattgcaaatttaggttgctcttgtaacttatttccgttcatttttgtagCAAGCCAAGTGCACCCGAAGAATTGGTATCCAATTCCACTGGTATTTTGCCGACCCTGGGGCAAACTGCCAGAAAATGTTCCCTGTCATCCCAAACTTGC

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 12
-----------------------------------------------------------------tttttctctctctacctttttcccttgcctgtgtgtttattat-atatgcatgttttatatgaacatcatgttcttattatttacctcattatatgtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC
                                                                   || |  | |  |     | || |  |   |  ||| |||||   |||     | ||| | ||  | || |  |      | |  || | | || |||||| |  ||||||||||||||||||||||| || ||||||||  | |||||| | || |||||  |||| || || ||||| || || ||||||||  | ||
gtatgaacctggcatatctaagtcttgttcatgtaacccgttgtctatataatactaaatctctaagttccattatgcagaacctgccatatctaattggttcattattgaatggtccatgtatctaaagctaatctcatgtactgtcatttcttcaaat-tgcagCGAATCAAGTGCACCCAAAGAACTGGTACCCAATTCCCCTTGTCTTCTGCAGACCGTGGGGACAGCTCCCGGAAAATGTTCCATGTCACCCTAAGCTGGC

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S14_51V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------tttttctctctctacctttttcccttgcctgtgtgtttattatatatg-catgtttta-------tatgaacatcatgttcttattat--ttacctcattatatg------tgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC
                    || || | |  |  |  ||     |    |   |  |    | ||| | | |||||       | | ||   |||| |   |  |    ||   ||| | ||       ||||||||  ||||| || ||||| || |||||||||||||| ||||| ||||||  |||||||||||   ||||  |  | | ||| ||||| || ||| | ||
gtgctactacagtgcatgacttgcttttttgaattacttattcagttctttaatacaccccagatggctttttttagggtaactcttaatgccatggtagaaccagaactaatgcataaaatcattcgctgcagCAACTCAAGTACATCCAAAAAATTGGTATCCTATTCCTCTCATCTTCTGCAAGCCATGGGGGATCTTGCCGAATGACGCGCCTTGCCATCCAAAACTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatgttttatatgaacatcatgttcttattatttacctcattatatgtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC
                            ttattatttacctcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctctctctacctttttcccttgcctgtgtgtttattatatatgcatgttttatatgaacatcatgttcttattatttacctcattatatgtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - -ctctctc
- - - - - - - - - - - ccttgcc
- - - - - - - - - - - - - - -tgtgtgt
- - - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctcat