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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

Basic information

species Vitis vinifera
transcript Vv08s0040g00600.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttatta---ttcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                                        | |  ||  | ||  | | | ||    ||| | |    |  |  || ||      || ||||     |||| ||||   ||||       ||||||| || ||||||||||| || || ||||| ||||||||||| || || ||||| ||||| || ||||||||||| ||||| |||||  |||| || || |
---------------------------------------gtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgat----gtttgctatttcttttgccccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                     ||    | |||  |   | | |||      | |||||  | | |    |  |||  || ||  |||   |     | |||       || ||| |    |  | ||  |||||||| || |||||||| || |||||||| |||||||||||||  |||||||| || || || || || ||||| ||||| |||||| |||| || || |
---------------------gtgagctgcttaatcactgttatg------ccattgtttcttgtaggctcacagaattgtta-tataccattgcattttgc------ttaacttttccctgcactac-cagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                                                      |  |   |  |||| |   |     |   ||   |||   | |||||    | |  ||  ||| | |    | | ||||| |||||||||||||| || |||||||||||||||||||| | ||| ||||| ||||| ||||| |||||||| ||||| |||||  | || || || |
-----------------------------------------------------gtaattcaccatttactcagatcacacaaactggcttatc-tttattgttgcctggctaacatgatatgctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctt-tctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                     ||   | ||     |   |      |     ||||||   ||   ||| ||    | | || ||| | ||    |||    ||     |  |      | ||| |    ||||| || ||||||||||||||||||||||||||||||||||| |  |||||||| || || ||||| |||||||| ||||| |||||  | || || || |
---------------------gtaattcaccacgcaaact--ggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttc--ccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttac-aatctattgaaagca-gtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                        | ||   |||| | ||| || ||  | | ||  | |  ||||| || |||    ||   || |  ||   |||| ||    | |  ||| || |||        |  |||||  | |||||||| || ||||| |||||||||||||| ||| | |||||||| ||||| || ||||| ||||| ||||| ||||||||||| || ||  
------------------------gtttgtgttttctctttaatattcagtcaatcttaatttcttttat-tcacacatcaggctttaatattgatctgttttggggacatttgctttgga-------acacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggt-ttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                                    ||| |  | ||  |   |||   | |||| |  | | |  | ||   | | |||   |||  ||||| || |      | ||| ||  |   | |||||  | ||||| || || || || |||||||||||||| ||| ||||||| || ||||| || ||||| ||||| ||||| ||||||||||| || || |
-----------------------------------gtttgtgctcttcagaaaattaa-atctctcttgtgttaattgtttcctatgtttccaaattcattgatagaa------tgtggattgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattt-tacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                                  ||| |   |  |      |   ||   ||  |   | || ||| |||    |    |  | ||| |||      |   |  ||| | |  | | | ||||| ||||| || |||||    || |||||||||||||||||  | |||||||| ||  | || |||||||| || ||||||||||| |||||||| ||||
-------------------------------aaatatctccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggcttacgacca--atgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                           ||| ||  || |||   |  |   |||   |   || |   ||    |   | |    ||||  ||||   ||| ||| |  ||   || ||    |   | ||||| |||||||| ||||||||||| |||||||||||||||||  | ||||||||||| ||||| || ||||||||||||||||||||||||||||| ||| 
-------------------------tataccttcaatctttatcgcagattctac-atattctttcagatccttgagatgtcagaattt--caatagcttgcaagtaactt--catcgtgc--aacttgcagATCCTCTTTGTGATCTCGAAGCCTGATGTGTTCAAGAGCCCTGCATCAGACACTTACGTAATCTTCGGCGAGGCAAAGATTGAGGATTTGAGTTCTCAAT

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctatt--ttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                                 |||  ||  ||  ||     |||||  |     || | | || | ||   | ||   ||   | || | |       |||  | || |||  | |   |||||||| ||||| ||||| ||||| ||||| |||||||||||  | || |||||  || | || ||||| ||||| ||||| |||||||||||||| || |
---------------------------------ttaacttcaattctgcttgaattgt-gcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S122_100V6.1 (Physcomitrella patens), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttattat-tcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                            | | |  | || |  | ||   ||  |||  |      | || ||    ||  ||   || | |   || |  || | |   | || ||| |  || | | ||||||| | || || ||||||||||| || ||||||||||||||| | || ||  || |  | || ||||| ||||| ||||||||||||||||| |||||||
-------------------------gcgattctccaattgttttattttcccc-ttg--aatctggtgatttcgaagttagtttcgttattctgcctct--aatgta---tgctctggctgctaatgtatcagATTTTGTTCGTAATCTCGAAGCCTGACGTGTTCAAGAGCCCAGCATCTGATGCTCACATCATCTTTGGAGAGGCGAAGATTGAGGATTTGAGCTCACAAC

upper sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttc-tattttacaatctattgaaagcagttta--ctatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                                                                       | || || | ||  ||  |   |    || || |  |  ||    | ||||| ||    | ||||| || ||||| ||||| ||||| || ||||||||||||||  | || |||||| |  | || ||||||||||| ||||| ||||| |||||||| || |
----------------------------------------------------------------------gtaagcttgcgttggtagatcgaagagaatagagactaacttcgcttctggttctt----tccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC
                                         tttttatt  CT-rich tract
                               tttactatggttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT