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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggataattttagcttgtggattctgttgataataactatgacatatactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG

Basic information

species Vitis vinifera
transcript Vv08s0007g07570.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 2
---ggataattttagcttgtggattctgttgataataactatgacatatactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG-----
   | || || | |  |||  | | |   |||   |     | |||| ||||   || |||||   || ||    |||| |  |   |||| |||||||||||||||||||||||||||||||||||||  ||||||| || ||||  || || || || |||||| |||||||| | ||||| || |||||||| || || |     
tttgtatgatat-attttgccgttgcaaatgacttttttgttaacat-tacttactg-ttctgggtttaac--ccatttataat---atatgtgttgacataggttagTGCCTCTTATGAGCAGGCTCTTATGGATGCCCGAAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTT

upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g44900.1 (Oryza sativa), 3'ss of exon 2
ggataattttagcttgtggattctgttgataataactatgacatatactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG---------------------
              ||  | | |   |||   |     | |||| ||||   || |||||   || ||    |||| |  |   |||| |||||||||||||||||||||||||||||||||||||  ||||||| || ||||  || || || || |||||| |||||||| | ||||| || |||||||| || || |                     
--------------tgccgttgcaaatgacttttttgttaacat-tacttactg-ttctgggtttaac--ccatttataat---atatgtgttgacataggttagtgcctcttatgagcagGCTCTTATGGATGCCCGAAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAG

upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
---------ggataattttagcttgtggattctgttgataataactatgacatatactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG
           |||||  | | ||| | | |  |  ||||| |  | |    || |  || |  |  |   |||     ||| ||| || | |||||||||||||||||||||||||||||||||||||||||||| |||||||||| ||||  || || || || |||||| |||||||  ||||||| || ||||| || || || |
cttcatgtgatataatactcgtttgcgaaat--gcagataa-atttttagtttacataccctactgttctggtt-----ttaattgattgt-gatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG

upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 2
ggataattttagct--tgtggattctgttgataataactatgacatatactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG
   | || || | |  | || | | |  |  || |||   |   || |    |||| || |||| |||||| |  ||| | |||| | | ||  ||||||||||||||||||| ||||||||||||||| ||||||| || |||||||| |||||||||||||||||||| ||||| ||||| || || || ||||||||||
--gtgatattgggtggtatgaaatattcttgtactaaaatttggatttttgacttggttttgaatttgacaatgttttctcttttaacacatcgtgacatagGTTAGTGCCTCATATGAGCAGGCTCTGGTGGATGCACGCAAGCTTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAGACAAAAG

upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 2
ggataattttagcttgtggattctgttgataata----actatgacatata-ctccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG
   |  | | |   |||| ||  ||||   ||||    |  |||| ||||| |||||||    |||  ||||||    ||| | || ||| || |  ||||| ||||||||||||| |||||||||||| || ||||||| || ||||| || ||||| |||||||||||||||||||||||||| || ||||||||||| ||||
---ttgtgtgatggtgtgtataatgttttaaatattgaatgatgaaatataactccttggcattgagtttgacaacactttctcttgtgacatct--tgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG

upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 2
ggataattttagcttgtggattctgttgataataactatgacatatactccttgattctgaagttgacagt-tatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG
 |||| |    | |  || |   |  | ||| | | | |   || |    |||| || |||| |||||| | | ||   ||||| | | ||  ||||||||||||||||||| ||||||||||||||| ||||||| || ||| |||| |||||||||||||||||||| ||||| ||||| || || || || |||||||
tgatagtgagtggt-atgaaacgttcttatactgaattttggatttttaacttggttttgaatttgacattgttttctctttttaacacattgtgacatagGTTAGTGCCTCATATGAGCAGGCTCTGGTGGATGCACGCAAGATTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAAACAAAAG

upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 2
ggataattttagct----tgtggattctgttgataataactatgacata-tactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG
   ||  || | ||    |     |||||||     ||| | || | || ||  | ||  || |     ||| | | ||  | || |   | |   ||||| ||||| ||||| |||||||||||  | ||| ||||||||||||||||||| |||   || ||||| || |||||||||||||||||||| || ||||||||||
--gtagcttcatctctgatacatgttctgtttcacgtaattctgtcttaatatccgtttgttttttgactga-actgatcagattgtc--tgtcaattgacttagGTCAGTGCATCTTATGAGCAATCCCTGGTGGATGCTCGGAAGCTTATTGAGAAAGAGATGGAGAGGTTTAAGATATGTGAAAAAGAGACCAAGACAAAAG

upper sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S101_120V6.1 (Physcomitrella patens), 3'ss of exon 3
ggataattttagcttgtggattctgttgataataactatgacatatactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG---------------------
                ||||||   |   | |||| |   | |        | ||| ||| | | |   | | |    || || |||  | ||    |   ||     || |   | | ||||| | || || ||||||||||  || ||| | |||||||||||||||||  ||||||| || ||||| ||||||||||                     
----------gaaggatggattgattctctcataattgaaaaag-----tttagatactggaatagtggggtgtaatgttgttaata-gtattcctgtgtttt-----ctttgtggtgtagGCTTTACTTGAGGCTCGGAAGCAGATAGAGAGAGAAATGGAAAGATTTAAAGTATGTGAGAAGGAAACCAAGACAAAAGCATTTTCCAAAGAAGGCCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG
                                            tgttgac  putative branch site (score: 3)
                         ttatttgttttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggataattttagcttgtggattctgttgataataactatgacatatactccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - -gcttgtg
- - - - - - - - - - - ctgttga
- - - - - - - - - - - - - - - - - - - - - - - -ctccttg