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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttgcttgcttttttttatttttttatttttatacataccattgctggaaaaactttcatcataataatcactgtatattttacatctgatttctagGATTTGCTGGCTATTTTGATGCAACTCTTTACAAAGATGTACATCTTGGTATTGAACCATCGACGGCAACTCCAAACATGTTCAGCTG

Basic information

species Vitis vinifera
transcript Vv04s0008g03120.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03120.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT4G31120.2 (Arabidopsis thaliana), 3'ss of exon 20
ttatttgcttgctttttttta-tttttttatttttatacataccattgctggaaaaactttcatcataataatc----actgtatattttacatctgatttctagGATTTGCTGGCTATTTTGATGCAACTCTTTACAAAGATGTACATCTTGGTATTGAACCATCGACGGCAACTCCAAACATGTTCAGCTG------------
     | | ||||||||| ||    |||| | ||| |  ||  || |  |    | |  | |||     |||||    |||| || |  | |       |  ||||||| ||||||||||||||| |    ||||| |||||||| |||||||| || || ||  | || ||||| |||||||||||||||||            
----gtacctgcttttttctagcccttttttgtttgttaatgtcaatttt----acatctccatttccgtaatctgaaactgaatctactgcgatca--taatagGATTCGCTGGCTATTTTGATTCCGTCCTTTATAAAGATGTTCATCTTGGGATCGAGCCTACAACAGCAACACCAAACATGTTCAGCTGGTAATGGATTAA

upper sequence: Vv04s0008g03120.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT4G31120.1 (Arabidopsis thaliana), 3'ss of exon 20
ttatttgcttgctttttttta-tttttttatttttatacataccattgctggaaaaactttcatcataataatc----actgtatattttacatctgatttctagGATTTGCTGGCTATTTTGATGCAACTCTTTACAAAGATGTACATCTTGGTATTGAACCATCGACGGCAACTCCAAACATGTTCAGCTG
     | | ||||||||| ||    |||| | ||| |  ||  || |  |    | |  | |||     |||||    |||| || |  | |       |  ||||||| ||||||||||||||| |    ||||| |||||||| |||||||| || || ||  | || ||||| |||||||||||||||||
----gtacctgcttttttctagcccttttttgtttgttaatgtcaatttt----acatctccatttccgtaatctgaaactgaatctactgcgatca--taatagGATTCGCTGGCTATTTTGATTCCGTCCTTTATAAAGATGTTCATCTTGGGATCGAGCCTACAACAGCAACACCAAACATGTTCAGCTG

upper sequence: Vv04s0008g03120.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ08472 (Selaginella moellendorffii), 3'ss of exon 18
ttatttgcttgcttttttttatttttttatttttatacataccattgctggaaaaactttcatcat--aataatcactgtatattttacatctgatttctagGATTTGCTGGCTATTTTGATGCAACTCTTTACAAAGATGTACATCTTGGTATTGAACCATCGACGGCAACTCCAAACATGTTCAGCTG
                                       |||  |||      |   |||  |||      ||||| ||| ||  || || ||  |    |||||| |  ||||| ||||| ||   | | ||||| ||| | || || || ||||||||||| || ||||| |||||||||||||||||
--------------------------------------gtactgttgtcttcgactgtttattcacccgcaaatcaatgtttacgtttca-ctcttacgcagGATTCGGAGGCTACTTTGACGCTGTTTTGTACAAGGATATTCACCTCGGCATTGAACCATCTACAGCAACACCAAACATGTTCAGCTG

upper sequence: Vv04s0008g03120.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ11093 (Selaginella moellendorffii), 3'ss of exon 20
ttatttgcttgcttttttttatttttttatttttatacataccattgc--tggaaaa-actttcatcataataatcactgtatattttacatctgatttctagGATTTGCTGGCTATTTTGATGCAACTCTTTACAAAGATGTACATCTTGGTATTGAACCATCGACGGCAACTCCAAACATGTTCAGCTG
                                       |||  |||   ||||    |  |||| |     ||||| ||  ||  || || ||  |    |||||| |  ||||| ||||| ||   | | ||||| ||| | || || || ||||||||||| || ||||| |||||||||||||||||
--------------------------------------gtactgttgtattggactgtagattcacc-cgcaaatcaatgcttacgtttca-ctcttacgcagGATTCGGAGGCTACTTTGACGCTGTTTTGTACAAGGATATTCACCTCGGCATTGAACCATCTACAGCAACACCAAACATGTTCAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctggaaaaactttcatcataataatcactgtatattttacatctgatttctagGATTTGCTGGCTATTTTGATGCAACTCTTTACAAAGATGTACATCTTGGTATTGAACCATCGACGGCAACTCCAAACATGTTCAGCTG
                                          atctgat  putative branch site (score: 4)
                                                tttct  CT-rich tract
                   ataataatcactgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttgcttgcttttttttatttttttatttttatacataccattgctggaaaaactttcatcataataatcactgtatattttacatctgatttctagGATTTGCTGGCTATTTTGATGCAACTCTTTACAAAGATGTACATCTTGGTATTGAACCATCGACGGCAACTCCAAACATGTTCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - gcttgct
- - - - - - - - - - - - - - - - - - -catacca
- - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgta